Citrus Sinensis ID: 043110

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310------
Protein Sequence
LFAQPLNSQTISKKKKRNDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKLVQRYVKGIS
Secondary Structure (PSIPRED)
cccccccccHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHcccccccHHHHHHHHcccccccEEEEcccccHHHHHHHHHHHHHHHccccccccccccEEEEEcccHHHHHHHHHHHHHHHHccccccEEEEEEccccHHHHHHHHccccEEEEcccHHHHHHccccccccccEEEEEEEccccccccccHHHHHHHHHHHccccccccccccccccccccEEEEEEcccHHHHHHHHHHcccccEEEccccccccccccEEEEEccccHHHHHccccccccccccccccccccEEEEEEEcc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHHHcccccccccccccccccccHHHccccHHHHHHHHHHcccccccccHHHHHHHHHccHcEEEEccccccHHHHHHHHHHHHHHHcccccccccccEEEEEccHHHHHHHHHHHHHHHHHHcccccEEEEEccccccHHHHHHHccccEEEEcccHHHHHHHcccccHHHcEEEEEEcHHHHHHHccccHHHHHHHHHcccccccccccccccccccccEEEEEccccHHHHHHHHHHHcccEEEEEEEcccccccEEEEEEEEcHHHHHHHHHHHHHHHcccccEEEEEEEccccccccc
Coil and Loop (DISEMBL)
lfaqplnsqtiskkkkrndkmsKKKETVKEIFASCcfsslgldsTLCDQLRerlgfeaptkvqaQAIPVILSGRDVLVNaatgtgktVAYLAPIINHlqsyspridrssgtFALVLVPTSELCLLVYEILQKLLHRFrwivpgyvmgggnrskeKARLRKGISILvatpghlldhLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGsrniasigegnevsnvkRQNLLLSATLNEKVNHLTKIsletpvligldekkfpedksnvhfgslesdvkeevehpnttlssstedfmlPAKLVQRYVKGIS
Flexible Loop (DISEMBL)
lfaqplnsqtiskkkkrndkmskkKETVKEIFASCCFSSLGLDSTLCDQLRERLGfeaptkvqaqaipvilsGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPgyvmgggnrskEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIgegnevsnvKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNVHFgslesdvkeeVEHPNttlssstedfmlpaKLVQRYVKGIS
Low Complexity Region (SEG)
LFAQPLNSQTISkkkkrndkmskkkETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKLVQRYVKGIS
Disordered region (IsUnstruct)
***************************VKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD*****************************************************
Disordered Region (DISOPRED)
***********************************CFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSY*****RSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSK***RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNVHFGSLESD*****************DFMLPAKLVQRYVKGI*
Disordered Region (DISEMBL)
**************************TVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNVHFGSLES****************TEDFMLPAKLVQRYVKGIS
Disordered Region (DISPRO)
*****LNSQTISKKKKRNDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKLVQR******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiHHHHHHHHHHHHHHHHHHHHooooooooooooooooHHHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
LFAQPLNSQTISKKKKRNDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKLVQRYVKGIS
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	316	2.2.26 [Sep-21-2011]
Q7XJN0	609	DEAD-box ATP-dependent RN	yes	no	0.958	0.497	0.616	1e-107
Q0DLB9	591	DEAD-box ATP-dependent RN	yes	no	0.914	0.489	0.631	1e-104
Q869P0	908	Probable ATP-dependent RN	yes	no	0.715	0.248	0.487	1e-58
Q9H8H2	851	Probable ATP-dependent RN	yes	no	0.746	0.277	0.476	2e-58
Q86B47	975	Probable ATP-dependent RN	yes	no	0.724	0.234	0.452	2e-53
Q6BKH3	798	ATP-dependent RNA helicas	yes	no	0.851	0.337	0.410	4e-48
Q5BGX6	778	ATP-dependent RNA helicas	yes	no	0.914	0.371	0.356	2e-44
A1CB55	755	ATP-dependent RNA helicas	N/A	no	0.797	0.333	0.388	3e-44
Q59S50	727	ATP-dependent RNA helicas	N/A	no	0.718	0.312	0.430	3e-44
A7F8V8	877	ATP-dependent RNA helicas	N/A	no	0.879	0.316	0.375	4e-44

>sp|Q7XJN0|RH17_ARATH DEAD-box ATP-dependent RNA helicase 17 OS=Arabidopsis thaliana GN=RH17 PE=2 SV=1

 Score =  386 bits (992), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 190/308 (61%), Positives = 246/308 (79%), Gaps = 5/308 (1%)

Query: 8   SQTISKKKKRNDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAI 67
           +Q  +++ K+  K + K ++   +FASC FSSLGLD+ L DQL+ER+GFEAPT VQAQAI
Sbjct: 4   AQQSARETKQEAKDASKAKS--GLFASCSFSSLGLDTKLSDQLKERMGFEAPTLVQAQAI 61

Query: 68  PVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY 127
           PVILSGRDVLVNA TGTGKT+AYLAP+I+HLQ +SP++DRS GTFALV+VPT ELCL VY
Sbjct: 62  PVILSGRDVLVNAPTGTGKTIAYLAPLIHHLQGHSPKVDRSHGTFALVIVPTRELCLQVY 121

Query: 128 EILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNL 187
           E L+KLLHRF WIVPGYVMGG  ++KEKARLRKGISIL+ATPG LLDHLK+T+SF+H NL
Sbjct: 122 ETLEKLLHRFHWIVPGYVMGGEKKAKEKARLRKGISILIATPGRLLDHLKNTASFVHKNL 181

Query: 188 RWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEV--SNVKRQNLLLSATLNEK 245
           RW+IFDEAD ILELG+GKEIE+I+ +LGS      GE +++    +++QNLLLSATLN+K
Sbjct: 182 RWVIFDEADSILELGYGKEIEQIIKLLGSGQNEQ-GEEDDIVPKGIQKQNLLLSATLNDK 240

Query: 246 VNHLTKISLETPVLIGLDEKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPA 305
           VN L K+SL+ PV+IGLD  K  ++ S     + +SD ++ V H N + +  +ED+ +P+
Sbjct: 241 VNDLAKLSLDDPVMIGLDNTKLQQNLSIESPAAPDSDAEDMVIHVNKSANPLSEDYGIPS 300

Query: 306 KLVQRYVK 313
           +LVQRY++
Sbjct: 301 QLVQRYLR 308

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

>sp|Q0DLB9|RH17_ORYSJ DEAD-box ATP-dependent RNA helicase 17 OS=Oryza sativa subsp. japonica GN=Os05g0110500 PE=2 SV=2

 Score =  379 bits (973), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 183/290 (63%), Positives = 229/290 (78%), Gaps = 1/290 (0%)

Query: 24  KKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATG 83
           K+E  + +FASC F+ LGL  TLC  L++++GF+APT++QAQAIPV +SG+ +LV AATG
Sbjct: 12  KEEDKEGLFASCSFTDLGLHPTLCAHLQDKMGFQAPTRIQAQAIPVAMSGQHMLVKAATG 71

Query: 84  TGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPG 143
           TGKT+AYLAPI++ LQ   PR++R+ GTFALVLVPT ELCL VY I Q+L+HRF W+VPG
Sbjct: 72  TGKTLAYLAPIVHLLQMREPRVERTDGTFALVLVPTRELCLQVYGIAQQLVHRFHWLVPG 131

Query: 144 YVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGF 203
           Y+MGG NR+KEKARLRKGISIL+ATPG LLDHL+HTSSF++ N+RWI+FDEAD ILELGF
Sbjct: 132 YIMGGENRAKEKARLRKGISILIATPGRLLDHLQHTSSFVYPNMRWIVFDEADSILELGF 191

Query: 204 GKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD 263
           GK +E+IL+ LGSRN  S    N++  +KRQNLLLSATLNEKVN L KISL+ PV+IGLD
Sbjct: 192 GKALEDILEHLGSRNDTSNQNKNKMEPMKRQNLLLSATLNEKVNRLAKISLKNPVMIGLD 251

Query: 264 EKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKLVQRYVK 313
           E+       N H   L  D +E +E  N T+  + +DF LPA+LVQRYVK
Sbjct: 252 EQNSSAHGKN-HTSLLSDDEEEILEKHNVTVEQAVDDFKLPAQLVQRYVK 300

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q869P0|DDX31_DICDI Probable ATP-dependent RNA helicase ddx31 OS=Dictyostelium discoideum GN=ddx31 PE=3 SV=2

 Score =  226 bits (577), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 115/236 (48%), Positives = 154/236 (65%), Gaps = 10/236 (4%)

Query: 30  EIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVA 89
           E F+S  + SL L  TL   L   +  E PT +Q  +I  IL G D LV A TG+GKT++
Sbjct: 202 ETFSSMNWGSLQLSETLVRNLVGHMKHEKPTHIQEASITPILKGNDALVKAQTGSGKTLS 261

Query: 90  YLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGG 149
           YL P++  L     R+ RS G + +++ PT EL   +YE LQKLL  F WIVPG +MGG 
Sbjct: 262 YLIPVVQKLTE--QRVTRSDGCYCVIITPTRELSSQIYEELQKLLKPFYWIVPGIIMGGE 319

Query: 150 NRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEE 209
           NRS EKAR+RKGI+ILVATPG LLDHL++T SF   N++W I DEAD++L+LGF K++  
Sbjct: 320 NRSAEKARIRKGINILVATPGRLLDHLQNTQSFPTDNIKWCILDEADKLLDLGFEKDVTT 379

Query: 210 ILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK 265
           I+++L S+              KRQN+L+SATL+E ++ L  +SL +PV IGLD K
Sbjct: 380 IINLLDSK--------KRTMKFKRQNILVSATLSEGISRLASLSLTSPVYIGLDSK 427

Probable ATP-dependent RNA helicase.

Dictyostelium discoideum (taxid: 44689)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9H8H2|DDX31_HUMAN Probable ATP-dependent RNA helicase DDX31 OS=Homo sapiens GN=DDX31 PE=1 SV=2

 Score =  226 bits (576), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 120/252 (47%), Positives = 159/252 (63%), Gaps = 16/252 (6%)

Query: 25  KETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGT 84
           K+  +++F S  F  LGL   L   +   L   + T VQ Q+IPV+L GRD LV + TG+
Sbjct: 220 KQVQEKVFTSAAFHELGLHPHLISTINTVLKMSSMTSVQKQSIPVLLEGRDALVRSQTGS 279

Query: 85  GKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGY 144
           GKT+AY  P++  LQ+   +I RS G +ALVLVPT EL L  ++ +QKLL  F WIVPG 
Sbjct: 280 GKTLAYCIPVVQSLQAMESKIQRSDGPYALVLVPTRELALQSFDTVQKLLKPFTWIVPGV 339

Query: 145 VMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFG 204
           +MGG  R  EKARLRKGI+IL++TPG L+DH+K T +   + LRW++FDEADRIL+LGF 
Sbjct: 340 LMGGEKRKSEKARLRKGINILISTPGRLVDHIKSTKNIHFSRLRWLVFDEADRILDLGFE 399

Query: 205 KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDE 264
           K+I  IL+ + +               KRQN+LLSATL E V  L  ISL  PV I + +
Sbjct: 400 KDITVILNAVNA------------ECQKRQNVLLSATLTEGVTRLADISLHDPVSISVLD 447

Query: 265 KKF----PEDKS 272
           K      P+DK+
Sbjct: 448 KSHDQLNPKDKA 459

Probable ATP-dependent RNA helicase.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q86B47|Y8611_DROME Probable ATP-dependent RNA helicase CG8611 OS=Drosophila melanogaster GN=CG8611 PE=1 SV=1

 Score =  209 bits (533), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 106/234 (45%), Positives = 153/234 (65%), Gaps = 5/234 (2%)

Query: 28  VKE-IFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGK 86
           VKE IF     S+LGL       L + L     T VQ + IP +L G+DVLV + TG+GK
Sbjct: 319 VKETIFTGSKISTLGLHPHAVKNLEDLLSIRELTSVQQKTIPEVLQGKDVLVRSQTGSGK 378

Query: 87  TVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVM 146
           T+AY  P++  LQ   PRI R  G  ALV+VPT EL +  YE++QKL+  + WIVPG ++
Sbjct: 379 TLAYALPLVELLQKQQPRIQRKDGVLALVIVPTRELVMQTYELIQKLVKPYTWIVPGSLL 438

Query: 147 GGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKE 206
           GG +R  EKARLRKGI+IL+ TPG L+DHL HT+SF  T L+++I DEADR+LELG+ ++
Sbjct: 439 GGESRKSEKARLRKGINILIGTPGRLVDHLLHTASFKLTKLQFLILDEADRLLELGYERD 498

Query: 207 IEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
           ++++++ +  +      E  E+  ++R  +LLSATL  +V  L  ++L+ P+ I
Sbjct: 499 VKQLVEAIDKQRAEC--EDKELPQLQR--MLLSATLTSQVQQLAGLTLKNPLYI 548

Probable ATP-dependent RNA helicase.

Drosophila melanogaster (taxid: 7227)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6BKH3|DBP7_DEBHA ATP-dependent RNA helicase DBP7 OS=Debaryomyces hansenii (strain ATCC 36239 / CBS 767 / JCM 1990 / NBRC 0083 / IGC 2968) GN=DBP7 PE=3 SV=1

 Score =  191 bits (486), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 115/280 (41%), Positives = 165/280 (58%), Gaps = 11/280 (3%)

Query: 34  SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIP-VILSGRDVLVNAATGTGKTVAYLA 92
           +  F  LGL+  L   L E L F+APTKVQ   IP +I + RD+ V A TG+GKT+++L 
Sbjct: 160 ATTFDGLGLNDKLATHLTESLRFKAPTKVQRSVIPSLIATQRDLFVKAQTGSGKTLSFLL 219

Query: 93  PIINHLQSYSP-RIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR 151
           PI + L S    +I R SG FA++LVPT ELC  +Y +L+ L+     IVPG V+GG  +
Sbjct: 220 PIFHKLMSEEKYKITRESGLFAIILVPTRELCTQIYGVLETLVRCHHHIVPGIVIGGEKK 279

Query: 152 SKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEIL 211
             EKARLRKG++ILVATPG L DH+++T+S   + LRW+I DE DR+ ELGF + I +I 
Sbjct: 280 KSEKARLRKGVNILVATPGRLADHMENTTSLDVSQLRWLILDEGDRLTELGFEETITKIT 339

Query: 212 D-ILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPED 270
           D I  +  I+      +    +R N+L SAT+ + V  L  + L  P  I +D  K  E 
Sbjct: 340 DNISKNSKISETIHKYQGLPTERVNVLCSATIQDNVKKLGNMILNNPETISVDSNKQIE- 398

Query: 271 KSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKLVQR 310
                 G+L  D +EE  + ++  +S  +    P +L+Q+
Sbjct: 399 ------GTLNFDDEEEQNNFDSN-NSEGKRMSAPDQLIQK 431

ATP-binding RNA helicase involved in the biogenesis of 60S ribosomal subunits and is required for the normal formation of 25S and 5.8S rRNAs.

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|Q5BGX6|DBP7_EMENI ATP-dependent RNA helicase dbp7 OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) GN=dbp7 PE=3 SV=1

 Score =  180 bits (456), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 116/325 (35%), Positives = 169/325 (52%), Gaps = 36/325 (11%)

Query: 1   LFAQPLNSQTISKKKKRNDKMSKKKETVKEIFASC-CFSSLGLDSTLCDQLRERLGFEAP 59
           LF++    +   ++ K ++ M   K T   +      F++LGL  TL   L  +L  +AP
Sbjct: 116 LFSKNPRPRNAVEEDKNDEPMEDAKPTNAPLIDGLDTFTNLGLSPTLAAHLLTKLELKAP 175

Query: 60  TKVQAQAIPVILSGR-DVLVNAATGTGKTVAYLAPIINHLQSYS-----------PRIDR 107
           T +Q  +I  +L    D  + A TG+GKT+AYL P++  + + S             + R
Sbjct: 176 TAIQKASITQLLKEETDAFIQAETGSGKTLAYLLPLVQRIMALSRAKNEGDAKGDTSVHR 235

Query: 108 SSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVA 167
            SG FA++L PT ELC  +  +L+ LL    WIV G V+GG  +  EKARLRKG++ILVA
Sbjct: 236 DSGLFAIILAPTRELCKQISVVLEGLLRCAHWIVAGTVIGGEKKKSEKARLRKGLNILVA 295

Query: 168 TPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNE 227
           TPG L DHL++T +   +N+RW++ DE DR++ELGF KE++EI+  L +R   S   G  
Sbjct: 296 TPGRLADHLENTQALDVSNVRWLVLDEGDRLMELGFEKELQEIISKLDARQRPSRIPG-- 353

Query: 228 VSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNVHFGSLESDVKEEV 287
               KR  +L SATL   V  L +ISL+  V I  D    P D+                
Sbjct: 354 -VPAKRATILCSATLKMNVQKLGEISLKDAVHIKAD----PADE---------------- 392

Query: 288 EHPNTTLSSSTEDFMLPAKLVQRYV 312
           +   T      + F +PA+L Q Y 
Sbjct: 393 DGEKTAEDKDGDAFRVPAQLKQSYA 417

ATP-binding RNA helicase involved in the biogenesis of 60S ribosomal subunits and is required for the normal formation of 25S and 5.8S rRNAs.

Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (taxid: 227321)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A1CB55|DBP7_ASPCL ATP-dependent RNA helicase dbp7 OS=Aspergillus clavatus (strain ATCC 1007 / CBS 513.65 / DSM 816 / NCTC 3887 / NRRL 1) GN=dbp7 PE=3 SV=1

 Score =  179 bits (453), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 112/288 (38%), Positives = 157/288 (54%), Gaps = 36/288 (12%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVIL-SGRDVLVNAATGTGKTVAYLAPII 95
           F++LGL  +L   L  +L  +APT +Q  +I  +L    D  + A TG+GKT+AYL P++
Sbjct: 138 FTNLGLSPSLAAHLLTKLELKAPTAIQKASISQLLKEDGDAFIQAETGSGKTLAYLLPLV 197

Query: 96  NHLQSYS---------PRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVM 146
             + + S         P + R SG FA+VL PT ELC  +  +L+ LL    WIV G V+
Sbjct: 198 QRIMTLSKPTTDATGQPIVHRDSGLFAIVLAPTRELCKQISVVLESLLRCAHWIVAGTVI 257

Query: 147 GGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKE 206
           GG  +  EKARLRKG++ILVATPG L DHL++T     +N+RW++ DE DR++ELGF +E
Sbjct: 258 GGEKKKSEKARLRKGLNILVATPGRLADHLENTKVLDVSNVRWLVLDEGDRLMELGFEEE 317

Query: 207 IEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK 266
           I+ I+  L +R   S   G      KR  +L SAT+   V  L +ISL+  V I  D   
Sbjct: 318 IQGIVKKLDARQRPSRIPG---IPTKRTTVLCSATMKMNVQKLGEISLKDAVHIKAD--- 371

Query: 267 FPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTED--FMLPAKLVQRYV 312
            PED                 E     L++  ED  + +PA+L Q Y 
Sbjct: 372 -PED-----------------EDEKARLANKEEDSAYRVPAQLKQSYA 401

ATP-binding RNA helicase involved in the biogenesis of 60S ribosomal subunits and is required for the normal formation of 25S and 5.8S rRNAs.

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

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q59S50|DBP7_CANAL ATP-dependent RNA helicase DBP7 OS=Candida albicans (strain SC5314 / ATCC MYA-2876) GN=DBP7 PE=3 SV=1

 Score =  179 bits (453), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 99/230 (43%), Positives = 141/230 (61%), Gaps = 3/230 (1%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGR-DVLVNAATGTGKTVAYLAPII 95
           FS LGL+  L   L + L F  PTK+Q   IP ++S   D+ V A TG+GKT+A++ PI 
Sbjct: 137 FSGLGLNEKLSIHLTDHLRFMHPTKIQQLVIPSLISTENDLFVKAQTGSGKTLAFVLPIF 196

Query: 96  NHLQSYSP-RIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE 154
           + L   +  +I+R SG FA++L PT EL   +Y +L+ L     WIVPG V+GG  +  E
Sbjct: 197 HKLMRENKFKINRESGLFAIILTPTRELATQIYGVLETLTRCHHWIVPGIVIGGEKKKSE 256

Query: 155 KARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDIL 214
           KARLRKG +ILVATPG L DHL++T +   + LRW++ DE D+++ELGF   I +I   +
Sbjct: 257 KARLRKGCNILVATPGRLADHLENTKTLDISQLRWLVLDEGDKLMELGFEDTIAQITAKI 316

Query: 215 GSRN-IASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD 263
            S + IA   E  +    +R N+L SATL+  V  L  I L+ P +I ++
Sbjct: 317 DSNSKIADTAEKWQGLPSRRINMLCSATLHSNVKKLGSIVLKDPEMISVE 366

ATP-binding RNA helicase involved in the biogenesis of 60S ribosomal subunits and is required for the normal formation of 25S and 5.8S rRNAs.

Candida albicans (strain SC5314 / ATCC MYA-2876) (taxid: 237561)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|A7F8V8|DBP7_SCLS1 ATP-dependent RNA helicase dbp7 OS=Sclerotinia sclerotiorum (strain ATCC 18683 / 1980 / Ss-1) GN=dbp7 PE=3 SV=1

 Score =  178 bits (452), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 116/309 (37%), Positives = 172/309 (55%), Gaps = 31/309 (10%)

Query: 15  KKRNDKMSKKKETVKEIFAS-----CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPV 69
           KK+ D+  ++ E  K   A        F++LGL   L   L  +L  +APT +Q  ++  
Sbjct: 230 KKKFDEPEEESEPAKPSNAPLTEEMATFTNLGLSRRLAAHLSTKLDMKAPTAIQKASVTQ 289

Query: 70  ILSG-RDVLVNAATGTGKTVAYLAPIINHLQSYSP---RIDRSSGTFALVLVPTSELCLL 125
           ++S   D  + A TG+GKT+AYL PI+  + + S    +I R SG FA++L PT ELC  
Sbjct: 290 LISDDSDAFIQAETGSGKTLAYLLPIVERILALSDNGIQIHRDSGLFAIILSPTRELCKQ 349

Query: 126 VYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHT 185
           +  +L+K+L    WIV   V GG ++  EKARLRKG++ILVATPG L DHL +T      
Sbjct: 350 IAAVLEKVLRCAPWIVGTTVNGGESKQSEKARLRKGVNILVATPGRLADHLDNTEVLNVA 409

Query: 186 NLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQ-NLLLSATLNE 244
            +RW++ DE DR++ELGF +EI+ I++ +G R++AS G    +S  KR+  +L SAT+  
Sbjct: 410 TVRWLVLDEGDRLMELGFEEEIKGIVEKIGRRSVAS-GSSEMMSLPKRRVTILCSATMKM 468

Query: 245 KVNHLTKISLETPVLIGLD-EKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFML 303
            V  L +ISL+  V I  D  ++  +DK+N     +E+D K                F  
Sbjct: 469 NVQRLGEISLKDAVHIQADPSEQEKQDKAN----GIEADDKA---------------FSA 509

Query: 304 PAKLVQRYV 312
           P +L Q Y 
Sbjct: 510 PTQLKQSYA 518

ATP-binding RNA helicase involved in the biogenesis of 60S ribosomal subunits and is required for the normal formation of 25S and 5.8S rRNAs.

Sclerotinia sclerotiorum (strain ATCC 18683 / 1980 / Ss-1) (taxid: 665079)

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	316
255571988	603	dead box ATP-dependent RNA helicase, put	0.898	0.470	0.756	1e-122
225444645	600	PREDICTED: DEAD-box ATP-dependent RNA he	0.952	0.501	0.728	1e-121
224145000	594	predicted protein [Populus trichocarpa]	0.895	0.476	0.766	1e-120
297738524	584	unnamed protein product [Vitis vinifera]	0.905	0.489	0.708	1e-116
297824007	609	hypothetical protein ARALYDRAFT_483128 [	0.958	0.497	0.633	1e-108
357472211	613	DEAD-box ATP-dependent RNA helicase [Med	0.927	0.477	0.665	1e-108
356558435	591	PREDICTED: LOW QUALITY PROTEIN: DEAD-box	0.898	0.480	0.683	1e-107
356530461	596	PREDICTED: LOW QUALITY PROTEIN: DEAD-box	0.892	0.473	0.693	1e-105
15226735	609	DEAD-box ATP-dependent RNA helicase 17 [	0.958	0.497	0.616	1e-105
218195957	591	hypothetical protein OsI_18162 [Oryza sa	0.914	0.489	0.634	1e-103

>gi|255571988|ref|XP_002526935.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223533687|gb|EEF35422.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score =  443 bits (1140), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 217/287 (75%), Positives = 244/287 (85%), Gaps = 3/287 (1%)

Query: 30  EIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVA 89
           E+FASC F +LGL  TLCDQLRER+GFEAPT VQAQAIPV+LSGR VLVNAATGTGKTVA
Sbjct: 26  EMFASCSFLNLGLHPTLCDQLRERMGFEAPTTVQAQAIPVVLSGRHVLVNAATGTGKTVA 85

Query: 90  YLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGG 149
           YLAPII+HLQSYSPRI+R+ GTFALVLVPT ELCL VYEILQ LLHRF WIVPGY+MGG 
Sbjct: 86  YLAPIIHHLQSYSPRIERAHGTFALVLVPTRELCLQVYEILQGLLHRFHWIVPGYIMGGE 145

Query: 150 NRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEE 209
           +RSKEKARLRKGISILVATPG LLDHLK+TSSF HTNLRWIIFDEADRILELGFGKEIE+
Sbjct: 146 SRSKEKARLRKGISILVATPGRLLDHLKNTSSFSHTNLRWIIFDEADRILELGFGKEIED 205

Query: 210 ILDILGSRNIASIGEGNE---VSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK 266
           ILD+LGSR   S+G+GN    +SN +RQNLLLSATLNEKVNHL  ISLE PV+IGLD++K
Sbjct: 206 ILDLLGSRLTRSVGKGNRDSSISNYQRQNLLLSATLNEKVNHLANISLENPVMIGLDDEK 265

Query: 267 FPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKLVQRYVK 313
              +    H  SL+SD  +E+EHP+  L  ST DF +P +LVQ+YVK
Sbjct: 266 MQPEPLLEHTKSLKSDADDELEHPSKVLKPSTGDFKVPVQLVQKYVK 312

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225444645|ref|XP_002277600.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 17-like [Vitis vinifera]

 Score =  441 bits (1133), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 223/306 (72%), Positives = 247/306 (80%), Gaps = 5/306 (1%)

Query: 13  KKKKRNDKMSKKKETV----KEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIP 68
           +K+   ++M K K+       EIFASC FSSLGL  TLCDQLRER+GFE PT VQA+AIP
Sbjct: 4   RKRTTEEEMKKTKQNSYNGESEIFASCSFSSLGLHPTLCDQLRERMGFEVPTIVQAEAIP 63

Query: 69  VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE 128
           VIL+GR VLVNAATGTGKT+AYLAP+INHL  Y PRI+RS+GTFALVLVPT ELC+ VYE
Sbjct: 64  VILAGRHVLVNAATGTGKTIAYLAPVINHLHKYDPRIERSAGTFALVLVPTRELCMQVYE 123

Query: 129 ILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLR 188
           ILQKLLHRF WIVPGYVMGG NRSKEKARLRKGISILVATPG LLDHLK+TSSFLHTNLR
Sbjct: 124 ILQKLLHRFHWIVPGYVMGGENRSKEKARLRKGISILVATPGRLLDHLKNTSSFLHTNLR 183

Query: 189 WIIFDEADRILELGFGKEIEEILDILGSR-NIASIGEGNEVSNVKRQNLLLSATLNEKVN 247
           WIIFDEADRILELGFGKEIEEILD+LGSR N  +I E    S  +RQNLLLSATLNEKVN
Sbjct: 184 WIIFDEADRILELGFGKEIEEILDLLGSRTNGPTIREDAVTSEFQRQNLLLSATLNEKVN 243

Query: 248 HLTKISLETPVLIGLDEKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKL 307
           HL +ISLE PV IGLD KK        HFGS+E DV E+ E  +  +S S  D+ LPA+L
Sbjct: 244 HLAQISLENPVTIGLDGKKMQPKPPLEHFGSVEFDVDEDSEKLHKIISPSNGDYKLPAQL 303

Query: 308 VQRYVK 313
           VQRYVK
Sbjct: 304 VQRYVK 309

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224145000|ref|XP_002325490.1| predicted protein [Populus trichocarpa] gi|222862365|gb|EEE99871.1| predicted protein [Populus trichocarpa]

 Score =  437 bits (1124), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 220/287 (76%), Positives = 243/287 (84%), Gaps = 4/287 (1%)

Query: 30  EIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVA 89
           EIFASC FS+LGL  +LC+QL+ERLGFE PT VQAQAIPVILSGR VLVNAATGTGKTVA
Sbjct: 16  EIFASCSFSALGLHPSLCNQLQERLGFEGPTLVQAQAIPVILSGRHVLVNAATGTGKTVA 75

Query: 90  YLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGG 149
           YLAPII+HL SY  RIDR +GTFALVLVPT ELCL VYEILQKLLHRF WIVPGYVMGG 
Sbjct: 76  YLAPIIHHLHSYPSRIDRENGTFALVLVPTRELCLQVYEILQKLLHRFHWIVPGYVMGGE 135

Query: 150 NRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEE 209
           NRSKEKARLRKGISILVATPG LLDHLK+T+SF+HTNLRWIIFDEADRILELGFGKEIEE
Sbjct: 136 NRSKEKARLRKGISILVATPGRLLDHLKNTASFVHTNLRWIIFDEADRILELGFGKEIEE 195

Query: 210 ILDILGSRNIASIGEGNEV---SNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK 266
           ILD+LGSR I S+G GN+V   SN + QNLLLSATLNEKVNHL KISLE PV+IGLD+KK
Sbjct: 196 ILDLLGSRQIGSVGNGNQVSSLSNFQGQNLLLSATLNEKVNHLAKISLENPVMIGLDDKK 255

Query: 267 FPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKLVQRYVK 313
              D+S  H  + ESD  + + +     +SST D+ LPA+LVQRYVK
Sbjct: 256 IQPDQSVDHIETAESDEDDGLGYSKVK-NSSTGDYKLPAQLVQRYVK 301

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297738524|emb|CBI27769.3| unnamed protein product [Vitis vinifera]

 Score =  425 bits (1093), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 216/305 (70%), Positives = 239/305 (78%), Gaps = 19/305 (6%)

Query: 13  KKKKRNDKMSKKKETV----KEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIP 68
           +K+   ++M K K+       EIFASC FSSLGL  TLCDQLRER+GFE PT VQA+AIP
Sbjct: 4   RKRTTEEEMKKTKQNSYNGESEIFASCSFSSLGLHPTLCDQLRERMGFEVPTIVQAEAIP 63

Query: 69  VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE 128
           VIL+GR VLVNAATGTGKT+AYLAP+INHL  Y PRI+RS+GTFALVLVPT ELC+ VYE
Sbjct: 64  VILAGRHVLVNAATGTGKTIAYLAPVINHLHKYDPRIERSAGTFALVLVPTRELCMQVYE 123

Query: 129 ILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLR 188
           ILQKLLHRF WIVPGYVMGG NRSKEKARLRKGISILVATPG LLDHLK+TSSFLHTNLR
Sbjct: 124 ILQKLLHRFHWIVPGYVMGGENRSKEKARLRKGISILVATPGRLLDHLKNTSSFLHTNLR 183

Query: 189 WIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNH 248
           WIIFDEADRILELGFGKEIEEILD+L                 +RQNLLLSATLNEKVNH
Sbjct: 184 WIIFDEADRILELGFGKEIEEILDLL---------------EFQRQNLLLSATLNEKVNH 228

Query: 249 LTKISLETPVLIGLDEKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKLV 308
           L +ISLE PV IGLD KK        HFGS+E DV E+ E  +  +S S  D+ LPA+LV
Sbjct: 229 LAQISLENPVTIGLDGKKMQPKPPLEHFGSVEFDVDEDSEKLHKIISPSNGDYKLPAQLV 288

Query: 309 QRYVK 313
           QRYVK
Sbjct: 289 QRYVK 293

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297824007|ref|XP_002879886.1| hypothetical protein ARALYDRAFT_483128 [Arabidopsis lyrata subsp. lyrata] gi|297325725|gb|EFH56145.1| hypothetical protein ARALYDRAFT_483128 [Arabidopsis lyrata subsp. lyrata]

 Score =  396 bits (1018), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 195/308 (63%), Positives = 247/308 (80%), Gaps = 5/308 (1%)

Query: 8   SQTISKKKKRNDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAI 67
           +Q  +++ K+  K + K ++   +FASC FSSLGLD  L DQL+ER+GFEAPT VQAQAI
Sbjct: 4   TQQSARETKQEAKDASKAKS--GLFASCSFSSLGLDPKLSDQLQERMGFEAPTLVQAQAI 61

Query: 68  PVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY 127
           PVILSGRDVLVNAATGTGKT+AYLAP+I+HLQ YSP++DRS GTFALV+VPT ELCL VY
Sbjct: 62  PVILSGRDVLVNAATGTGKTIAYLAPLIHHLQGYSPKVDRSHGTFALVIVPTRELCLQVY 121

Query: 128 EILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNL 187
           E L+KLLHRF WIVPGYVMGG  ++KEKARLRKGISIL+ATPG LLDHLK+T+SF+H NL
Sbjct: 122 ETLEKLLHRFHWIVPGYVMGGEKKAKEKARLRKGISILIATPGRLLDHLKNTASFVHKNL 181

Query: 188 RWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEV--SNVKRQNLLLSATLNEK 245
           RW+IFDEAD ILELG+GKEIE+I+ +LGS      GE +++    +++QNLLLSATLNEK
Sbjct: 182 RWVIFDEADSILELGYGKEIEQIIKLLGSGQYEE-GETDDIVPKGIQKQNLLLSATLNEK 240

Query: 246 VNHLTKISLETPVLIGLDEKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPA 305
           VN L K+SL+ PV+IGLD  K  ++ S     S +SD  + V H N +++ S+ED+ +P+
Sbjct: 241 VNDLAKLSLDDPVMIGLDNSKLQQNLSIESPASPDSDADDMVIHVNKSVNPSSEDYGIPS 300

Query: 306 KLVQRYVK 313
           +LVQ+YV+
Sbjct: 301 QLVQKYVR 308

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357472211|ref|XP_003606390.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula] gi|355507445|gb|AES88587.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula]

 Score =  396 bits (1017), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 199/299 (66%), Positives = 237/299 (79%), Gaps = 6/299 (2%)

Query: 18  NDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVL 77
           +D  + K +    +FASC FSSLGL  TLCDQLRER+GFEAPT +QAQAIPV+LSGR  L
Sbjct: 26  HDDGTNKGDNNNNVFASCSFSSLGLHQTLCDQLRERMGFEAPTLIQAQAIPVVLSGRHAL 85

Query: 78  VNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF 137
           VNAATGTGKT+AYLAPII+HLQSY  R+ RS GTFALVLVPT ELCL V+EILQKLLHRF
Sbjct: 86  VNAATGTGKTIAYLAPIIHHLQSYDKRVQRSDGTFALVLVPTRELCLQVHEILQKLLHRF 145

Query: 138 RWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADR 197
            WIVPGY+MGG +RSKEKARLRKGISIL+ATPG LLDHLK+TSSF++TNLRWIIFDEADR
Sbjct: 146 HWIVPGYIMGGESRSKEKARLRKGISILIATPGRLLDHLKNTSSFVYTNLRWIIFDEADR 205

Query: 198 ILELGFGKEIEEILDILGSRNIASIGEGNEV---SNVKRQNLLLSATLNEKVNHLTKISL 254
           ILELGFGKEI+EIL++LGS       + + V   S  +RQNLLLSATLNEKVNHL KISL
Sbjct: 206 ILELGFGKEIQEILNLLGSMKTGHDDQESGVPRPSKFQRQNLLLSATLNEKVNHLAKISL 265

Query: 255 ETPVLIGLDEKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKLVQRYVK 313
           E PV+IG+D+ K  E  S + F +  SD  E+ E  +++   +   + +P +L+QRY+K
Sbjct: 266 EDPVMIGIDD-KIMEPTSRIRFDN--SDCDEDNEDTHSSKIPAIGAYKVPEQLIQRYMK 321

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356558435|ref|XP_003547512.1| PREDICTED: LOW QUALITY PROTEIN: DEAD-box ATP-dependent RNA helicase 17-like [Glycine max]

 Score =  392 bits (1008), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 199/291 (68%), Positives = 232/291 (79%), Gaps = 7/291 (2%)

Query: 27  TVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGK 86
           T  ++FASC FSSLGL+S LC+QLRERLGFE PT VQAQAIPVILSGR  LVNAATGTGK
Sbjct: 17  TNSDVFASCSFSSLGLESNLCEQLRERLGFEVPTLVQAQAIPVILSGRHALVNAATGTGK 76

Query: 87  TVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVM 146
           TVAYLAPII+HLQ Y  RI RS GTFALVLVPT ELCL VYEILQKLLH F WIVPGY+M
Sbjct: 77  TVAYLAPIIHHLQGYENRIQRSDGTFALVLVPTRELCLQVYEILQKLLHWFHWIVPGYIM 136

Query: 147 GGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKE 206
           GG NRSKEKARLRKGISIL+ATPG LLDHLK+T+SFL++NLRWIIFDEADRIL+LGFGK 
Sbjct: 137 GGENRSKEKARLRKGISILIATPGSLLDHLKNTTSFLYSNLRWIIFDEADRILKLGFGKN 196

Query: 207 IEEILDILGSRNIASIGEGNEV---SNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD 263
           IEEILD+LGSR      + N V   S ++RQNLLLS TLNE+VNHL K+SL+ PV+IGLD
Sbjct: 197 IEEILDLLGSRKTGHDDKKNTVPTHSKMQRQNLLLSTTLNERVNHLAKMSLDNPVMIGLD 256

Query: 264 EKKFPEDKSNVHFGSLE-SDVKEEVEHPNTTLSSSTEDFMLPAKLVQRYVK 313
            KK   + +N +   L+ S+  E+ E    +   +  D+ +P +L+QRY+K
Sbjct: 257 GKK---NGTNFNIKRLDPSESDEDSEDKYYSKVPTVGDYKVPLQLIQRYMK 304

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356530461|ref|XP_003533799.1| PREDICTED: LOW QUALITY PROTEIN: DEAD-box ATP-dependent RNA helicase 17-like [Glycine max]

 Score =  388 bits (997), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 199/287 (69%), Positives = 230/287 (80%), Gaps = 5/287 (1%)

Query: 30  EIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVA 89
           ++FASC FSSLGLDS LC+QLR+RLGFE PT VQAQAIPVILSGR  LVNAATGTGKTVA
Sbjct: 20  DVFASCSFSSLGLDSNLCEQLRDRLGFEVPTLVQAQAIPVILSGRHALVNAATGTGKTVA 79

Query: 90  YLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGG 149
           YLAPII+HLQ Y  RI RS GTFALVLVPT ELCL VYEILQKLLHRF WIVPGY+MGG 
Sbjct: 80  YLAPIIHHLQGYENRIQRSDGTFALVLVPTRELCLQVYEILQKLLHRFHWIVPGYIMGGE 139

Query: 150 NRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEE 209
            RSKEK+RLRKGISIL+ATPG LLDHLK+T++FL++NLRWIIFDEADRILELGFGK+IEE
Sbjct: 140 KRSKEKSRLRKGISILIATPGRLLDHLKNTTAFLYSNLRWIIFDEADRILELGFGKDIEE 199

Query: 210 ILDILGSRNIASIGEGNEV---SNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK 266
           ILD+LGSR      + N V   S ++RQNLLLSATLNEKVNHL K+SL+ PV+IGLD KK
Sbjct: 200 ILDLLGSRKKGHGDQENTVLTHSKIQRQNLLLSATLNEKVNHLAKMSLDNPVMIGLDGKK 259

Query: 267 FPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKLVQRYVK 313
                +     S ESD   E ++ +     +  D+ +P +L+QRY+K
Sbjct: 260 MEPISTIKRLDSSESDEDSEDKYSSKV--PTVGDYKVPIQLIQRYMK 304

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15226735|ref|NP_181602.1| DEAD-box ATP-dependent RNA helicase 17 [Arabidopsis thaliana] gi|75327220|sp|Q7XJN0.1|RH17_ARATH RecName: Full=DEAD-box ATP-dependent RNA helicase 17 gi|330254771|gb|AEC09865.1| DEAD-box ATP-dependent RNA helicase 17 [Arabidopsis thaliana]

 Score =  386 bits (992), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 190/308 (61%), Positives = 246/308 (79%), Gaps = 5/308 (1%)

Query: 8   SQTISKKKKRNDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAI 67
           +Q  +++ K+  K + K ++   +FASC FSSLGLD+ L DQL+ER+GFEAPT VQAQAI
Sbjct: 4   AQQSARETKQEAKDASKAKS--GLFASCSFSSLGLDTKLSDQLKERMGFEAPTLVQAQAI 61

Query: 68  PVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY 127
           PVILSGRDVLVNA TGTGKT+AYLAP+I+HLQ +SP++DRS GTFALV+VPT ELCL VY
Sbjct: 62  PVILSGRDVLVNAPTGTGKTIAYLAPLIHHLQGHSPKVDRSHGTFALVIVPTRELCLQVY 121

Query: 128 EILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNL 187
           E L+KLLHRF WIVPGYVMGG  ++KEKARLRKGISIL+ATPG LLDHLK+T+SF+H NL
Sbjct: 122 ETLEKLLHRFHWIVPGYVMGGEKKAKEKARLRKGISILIATPGRLLDHLKNTASFVHKNL 181

Query: 188 RWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEV--SNVKRQNLLLSATLNEK 245
           RW+IFDEAD ILELG+GKEIE+I+ +LGS      GE +++    +++QNLLLSATLN+K
Sbjct: 182 RWVIFDEADSILELGYGKEIEQIIKLLGSGQNEQ-GEEDDIVPKGIQKQNLLLSATLNDK 240

Query: 246 VNHLTKISLETPVLIGLDEKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPA 305
           VN L K+SL+ PV+IGLD  K  ++ S     + +SD ++ V H N + +  +ED+ +P+
Sbjct: 241 VNDLAKLSLDDPVMIGLDNTKLQQNLSIESPAAPDSDAEDMVIHVNKSANPLSEDYGIPS 300

Query: 306 KLVQRYVK 313
           +LVQRY++
Sbjct: 301 QLVQRYLR 308

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|218195957|gb|EEC78384.1| hypothetical protein OsI_18162 [Oryza sativa Indica Group]

 Score =  380 bits (977), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 184/290 (63%), Positives = 230/290 (79%), Gaps = 1/290 (0%)

Query: 24  KKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATG 83
           K+E  + +FASC F+ LGL  TLC  L++++GF+APT++QAQAIPV +SG+ +LV AATG
Sbjct: 12  KEEDKEGLFASCSFTDLGLHPTLCAHLQDKMGFQAPTRIQAQAIPVAMSGQHMLVKAATG 71

Query: 84  TGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPG 143
           TGKT+AYLAPI++ LQ   PR++R+ GTFALVLVPT ELCL VY I Q+L+HRF W+VPG
Sbjct: 72  TGKTLAYLAPIVHLLQMREPRVERTDGTFALVLVPTRELCLQVYGIAQQLVHRFHWLVPG 131

Query: 144 YVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGF 203
           Y+MGG NR+KEKARLRKGISIL+ATPG LLDHL+HTSSF++ N+RWI+FDEAD ILELGF
Sbjct: 132 YIMGGENRAKEKARLRKGISILIATPGRLLDHLQHTSSFVYPNMRWIVFDEADSILELGF 191

Query: 204 GKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD 263
           GK +E+IL+ LGSRN AS    N++  +KRQNLLLSATLNEKVN L KISL+ PV+IGLD
Sbjct: 192 GKALEDILEHLGSRNDASNQNKNKMEPMKRQNLLLSATLNEKVNRLAKISLKNPVMIGLD 251

Query: 264 EKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKLVQRYVK 313
           E+       N H   L  D +E +E  N T+  + +DF LPA+LVQRYVK
Sbjct: 252 EQNSSAHGKN-HTSLLSDDEEEILEKHNVTVEQAVDDFKLPAQLVQRYVK 300

Source: Oryza sativa Indica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

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	316
TAIR|locus:2064844	609	AT2G40700 [Arabidopsis thalian	0.892	0.463	0.652	1.8e-96
DICTYBASE|DDB_G0271708	908	ddx31 "DEAD/DEAH box helicase"	0.765	0.266	0.464	3.6e-54
UNIPROTKB|F8WAJ0	722	DDX31 "Probable ATP-dependent	0.734	0.321	0.483	3.8e-53
UNIPROTKB|Q9H8H2	851	DDX31 "Probable ATP-dependent	0.734	0.272	0.483	1.2e-52
RGD|1304895	682	Ddx31 "DEAD (Asp-Glu-Ala-Asp)	0.724	0.335	0.464	1.7e-50
UNIPROTKB|F1N5H8	736	DDX31 "Uncharacterized protein	0.708	0.304	0.481	5.8e-50
ZFIN|ZDB-GENE-030131-3973	739	ddx31 "DEAD (Asp-Glu-Ala-Asp)	0.712	0.304	0.466	1.4e-49
FB|FBgn0027602	975	CG8611 [Drosophila melanogaste	0.724	0.234	0.452	6e-49
UNIPROTKB|F1S0U0	784	DDX31 "Uncharacterized protein	0.844	0.340	0.414	8.5e-49
UNIPROTKB|F1NM06	690	DDX31 "Uncharacterized protein	0.854	0.391	0.414	1.8e-48

TAIR|locus:2064844 AT2G40700 [Arabidopsis thaliana (taxid:3702)]

 Score = 959 (342.6 bits), Expect = 1.8e-96, P = 1.8e-96
 Identities = 186/285 (65%), Positives = 234/285 (82%)

Query:    31 IFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY 90
             +FASC FSSLGLD+ L DQL+ER+GFEAPT VQAQAIPVILSGRDVLVNA TGTGKT+AY
Sbjct:    25 LFASCSFSSLGLDTKLSDQLKERMGFEAPTLVQAQAIPVILSGRDVLVNAPTGTGKTIAY 84

Query:    91 LAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGN 150
             LAP+I+HLQ +SP++DRS GTFALV+VPT ELCL VYE L+KLLHRF WIVPGYVMGG  
Sbjct:    85 LAPLIHHLQGHSPKVDRSHGTFALVIVPTRELCLQVYETLEKLLHRFHWIVPGYVMGGEK 144

Query:   151 RSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEI 210
             ++KEKARLRKGISIL+ATPG LLDHLK+T+SF+H NLRW+IFDEAD ILELG+GKEIE+I
Sbjct:   145 KAKEKARLRKGISILIATPGRLLDHLKNTASFVHKNLRWVIFDEADSILELGYGKEIEQI 204

Query:   211 LDILGSRNIASIGEGNEV--SNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFP 268
             + +LGS      GE +++    +++QNLLLSATLN+KVN L K+SL+ PV+IGLD  K  
Sbjct:   205 IKLLGSGQNEQ-GEEDDIVPKGIQKQNLLLSATLNDKVNDLAKLSLDDPVMIGLDNTKLQ 263

Query:   269 EDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKLVQRYVK 313
             ++ S     + +SD ++ V H N + +  +ED+ +P++LVQRY++
Sbjct:   264 QNLSIESPAAPDSDAEDMVIHVNKSANPLSEDYGIPSQLVQRYLR 308

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:0006312 "mitotic recombination" evidence=RCA

GO:0006406 "mRNA export from nucleus" evidence=RCA

GO:0006606 "protein import into nucleus" evidence=RCA

GO:0006626 "protein targeting to mitochondrion" evidence=RCA

GO:0009560 "embryo sac egg cell differentiation" evidence=RCA

GO:0009561 "megagametogenesis" evidence=RCA

GO:0009640 "photomorphogenesis" evidence=RCA

GO:0010388 "cullin deneddylation" evidence=RCA

GO:0042991 "transcription factor import into nucleus" evidence=RCA

GO:0051604 "protein maturation" evidence=RCA

DICTYBASE|DDB_G0271708 ddx31 "DEAD/DEAH box helicase" [Dictyostelium discoideum (taxid:44689)]

 Score = 552 (199.4 bits), Expect = 3.6e-54, Sum P(2) = 3.6e-54
 Identities = 118/254 (46%), Positives = 161/254 (63%)

Query:    30 EIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVA 89
             E F+S  + SL L  TL   L   +  E PT +Q  +I  IL G D LV A TG+GKT++
Sbjct:   202 ETFSSMNWGSLQLSETLVRNLVGHMKHEKPTHIQEASITPILKGNDALVKAQTGSGKTLS 261

Query:    90 YLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGG 149
             YL P++  L     R+ RS G + +++ PT EL   +YE LQKLL  F WIVPG +MGG 
Sbjct:   262 YLIPVVQKLTEQ--RVTRSDGCYCVIITPTRELSSQIYEELQKLLKPFYWIVPGIIMGGE 319

Query:   150 NRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEE 209
             NRS EKAR+RKGI+ILVATPG LLDHL++T SF   N++W I DEAD++L+LGF K++  
Sbjct:   320 NRSAEKARIRKGINILVATPGRLLDHLQNTQSFPTDNIKWCILDEADKLLDLGFEKDVTT 379

Query:   210 ILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPE 269
             I+++L S+              KRQN+L+SATL+E ++ L  +SL +PV IGLD K    
Sbjct:   380 IINLLDSKK--------RTMKFKRQNILVSATLSEGISRLASLSLTSPVYIGLDSKVL-- 429

Query:   270 DKSNVHFGSLESDV 283
             +K    F + E ++
Sbjct:   430 EKGENPFQAAEKEM 443

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:0016787 "hydrolase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|F8WAJ0 DDX31 "Probable ATP-dependent RNA helicase DDX31" [Homo sapiens (taxid:9606)]

 Score = 550 (198.7 bits), Expect = 3.8e-53, P = 3.8e-53
 Identities = 120/248 (48%), Positives = 158/248 (63%)

Query:    29 KEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTV 88
             +++F S  F  LGL   L   +   L   + T VQ Q+IPV+L GRD LV + TG+GKT+
Sbjct:    95 EKVFTSAAFHELGLHPHLISTINTVLKMSSMTSVQKQSIPVLLEGRDALVRSQTGSGKTL 154

Query:    89 AYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGG 148
             AY  P++  LQ+   +I RS G +ALVLVPT EL L  ++ +QKLL  F WIVPG +MGG
Sbjct:   155 AYCIPVVQSLQAMESKIQRSDGPYALVLVPTRELALQSFDTVQKLLKPFTWIVPGVLMGG 214

Query:   149 GNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIE 208
               R  EKARLRKGI+IL++TPG L+DH+K T +   + LRW++FDEADRIL+LGF K+I 
Sbjct:   215 EKRKSEKARLRKGINILISTPGRLVDHIKSTKNIHFSRLRWLVFDEADRILDLGFEKDIT 274

Query:   209 EILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKF- 267
              IL+ + +          E    KRQN+LLSATL E V  L  ISL  PV I + +K   
Sbjct:   275 VILNAVNA----------ECQ--KRQNVLLSATLTEGVTRLADISLHDPVSISVLDKSHD 322

Query:   268 ---PEDKS 272
                P+DK+
Sbjct:   323 QLNPKDKA 330

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q9H8H2 DDX31 "Probable ATP-dependent RNA helicase DDX31" [Homo sapiens (taxid:9606)]

 Score = 550 (198.7 bits), Expect = 1.2e-52, P = 1.2e-52
 Identities = 120/248 (48%), Positives = 158/248 (63%)

Query:    29 KEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTV 88
             +++F S  F  LGL   L   +   L   + T VQ Q+IPV+L GRD LV + TG+GKT+
Sbjct:   224 EKVFTSAAFHELGLHPHLISTINTVLKMSSMTSVQKQSIPVLLEGRDALVRSQTGSGKTL 283

Query:    89 AYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGG 148
             AY  P++  LQ+   +I RS G +ALVLVPT EL L  ++ +QKLL  F WIVPG +MGG
Sbjct:   284 AYCIPVVQSLQAMESKIQRSDGPYALVLVPTRELALQSFDTVQKLLKPFTWIVPGVLMGG 343

Query:   149 GNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIE 208
               R  EKARLRKGI+IL++TPG L+DH+K T +   + LRW++FDEADRIL+LGF K+I 
Sbjct:   344 EKRKSEKARLRKGINILISTPGRLVDHIKSTKNIHFSRLRWLVFDEADRILDLGFEKDIT 403

Query:   209 EILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKF- 267
              IL+ + +          E    KRQN+LLSATL E V  L  ISL  PV I + +K   
Sbjct:   404 VILNAVNA----------ECQ--KRQNVLLSATLTEGVTRLADISLHDPVSISVLDKSHD 451

Query:   268 ---PEDKS 272
                P+DK+
Sbjct:   452 QLNPKDKA 459

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0005730 "nucleolus" evidence=IEA

RGD|1304895 Ddx31 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 31" [Rattus norvegicus (taxid:10116)]

 Score = 525 (189.9 bits), Expect = 1.7e-50, P = 1.7e-50
 Identities = 112/241 (46%), Positives = 153/241 (63%)

Query:    29 KEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTV 88
             +++F+   F  L L   L   +   L   + T VQ Q+IPV+L GRD LV + TG+GKT+
Sbjct:    97 EQVFSPEAFQELDLHPHLISTINTVLKMSSMTSVQKQSIPVLLEGRDALVRSQTGSGKTL 156

Query:    89 AYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGG 148
             AY  P++  LQ+ + +I RS G +ALVLVPT EL L  ++ +QKLL  F WIVPG +MGG
Sbjct:   157 AYCIPVVQSLQALTSKIQRSDGPYALVLVPTRELALQSFDTVQKLLKPFTWIVPGVLMGG 216

Query:   149 GNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIE 208
               R  EKARLRKGI+IL++TPG L+DH+K T +     +RW++ DEADRIL+LGF K++ 
Sbjct:   217 EKRKSEKARLRKGINILISTPGRLVDHIKSTKNIHFNRVRWLVVDEADRILDLGFEKDVT 276

Query:   209 EILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFP 268
              IL+ + +          E    KRQN+LLSATL E V  L  ISL  PV I + +K + 
Sbjct:   277 VILNAVNA----------ECQ--KRQNVLLSATLTEGVTRLADISLHNPVSISVLDKSWD 324

Query:   269 E 269
             +
Sbjct:   325 Q 325

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

UNIPROTKB|F1N5H8 DDX31 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 520 (188.1 bits), Expect = 5.8e-50, P = 5.8e-50
 Identities = 114/237 (48%), Positives = 150/237 (63%)

Query:    29 KEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTV 88
             +++F S  F +L L   L   +   L   + T VQ Q+IPV+L GRD LV + TG+GKT+
Sbjct:   126 EKVFTSDAFQALDLHPHLISTINTVLKMSSMTSVQKQSIPVLLEGRDALVRSQTGSGKTL 185

Query:    89 AYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGG 148
             AY  P++  LQ+   +I R  G +AL+LVPT EL L  ++ +QKLL  F WIVPG +MGG
Sbjct:   186 AYCIPVVQSLQAMQSKIQRGDGPYALILVPTRELALQSFDTVQKLLKPFTWIVPGVLMGG 245

Query:   149 GNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIE 208
               R  EKARLRKGI+IL++TPG L+DH+K T +     +RW+I DEADRIL+LGF K++ 
Sbjct:   246 EKRKSEKARLRKGINILISTPGRLVDHIKSTKNIHFRQIRWLILDEADRILDLGFEKDLT 305

Query:   209 EILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIG-LDE 264
              IL+ + +       E  E     RQN+LLSATL E V  L  ISL  PV I  LDE
Sbjct:   306 VILNAVNA-------ECQE-----RQNVLLSATLTEGVARLADISLHDPVSISVLDE 350

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

ZFIN|ZDB-GENE-030131-3973 ddx31 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 31" [Danio rerio (taxid:7955)]

 Score = 517 (187.1 bits), Expect = 1.4e-49, P = 1.4e-49
 Identities = 111/238 (46%), Positives = 156/238 (65%)

Query:    28 VKE-IFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGK 86
             VKE +F S  F  L L   L   L + L   + T VQ Q IPV++SG+D +V + TG+GK
Sbjct:   146 VKEKVFTSNTFEELNLHPHLVATLHKVLNVSSMTSVQKQTIPVLMSGKDAVVRSQTGSGK 205

Query:    87 TVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVM 146
             T+AY  P++  LQ+  P++ RS G  A+V+VPT EL L  +++ QKLL  F WIVPG +M
Sbjct:   206 TLAYGIPMVQFLQAIQPKVKRSDGPLAVVIVPTRELALQSFQMFQKLLRPFTWIVPGVLM 265

Query:   147 GGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKE 206
             GG  +  EKARLRKGI++L++TPG L+DH+K+T S   + +RW+I DEADRIL+LGF K+
Sbjct:   266 GGEKKKAEKARLRKGINVLISTPGRLVDHIKNTLSIAFSAVRWLILDEADRILDLGFEKD 325

Query:   207 IEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDE 264
             +  IL+ L   N A    G +     RQN+LLSAT+ E ++ L  IS++ PV + + E
Sbjct:   326 LTVILNAL---NAA----GPD-----RQNVLLSATITEGLSRLASISMKDPVSVHVSE 371

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0004386 "helicase activity" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0003723 "RNA binding" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

FB|FBgn0027602 CG8611 [Drosophila melanogaster (taxid:7227)]

 Score = 519 (187.8 bits), Expect = 6.0e-49, P = 6.0e-49
 Identities = 106/234 (45%), Positives = 153/234 (65%)

Query:    28 VKE-IFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGK 86
             VKE IF     S+LGL       L + L     T VQ + IP +L G+DVLV + TG+GK
Sbjct:   319 VKETIFTGSKISTLGLHPHAVKNLEDLLSIRELTSVQQKTIPEVLQGKDVLVRSQTGSGK 378

Query:    87 TVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVM 146
             T+AY  P++  LQ   PRI R  G  ALV+VPT EL +  YE++QKL+  + WIVPG ++
Sbjct:   379 TLAYALPLVELLQKQQPRIQRKDGVLALVIVPTRELVMQTYELIQKLVKPYTWIVPGSLL 438

Query:   147 GGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKE 206
             GG +R  EKARLRKGI+IL+ TPG L+DHL HT+SF  T L+++I DEADR+LELG+ ++
Sbjct:   439 GGESRKSEKARLRKGINILIGTPGRLVDHLLHTASFKLTKLQFLILDEADRLLELGYERD 498

Query:   207 IEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
             ++++++ +  +      E  E+  ++R  +LLSATL  +V  L  ++L+ P+ I
Sbjct:   499 VKQLVEAIDKQRAEC--EDKELPQLQR--MLLSATLTSQVQQLAGLTLKNPLYI 548

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

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1S0U0 DDX31 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 513 (185.6 bits), Expect = 8.5e-49, P = 8.5e-49
 Identities = 117/282 (41%), Positives = 163/282 (57%)

Query:    29 KEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGT-GKT 87
             + +F S  F +L L   L   +   L   + T +Q Q+IPV+L GRD LV + TG+ GKT
Sbjct:   180 ESVFTSDAFQALDLHPHLISTINTVLKMSSLTSIQKQSIPVLLEGRDALVRSQTGSEGKT 239

Query:    88 VAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMG 147
             +AY  P++  LQ+  P+I R  G +AL+LVPT EL L  ++ +QKLL  F WIVPG +MG
Sbjct:   240 LAYCIPMVQSLQAVKPKIQRGDGPYALILVPTRELALQSFDTVQKLLKPFTWIVPGVLMG 299

Query:   148 GGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEI 207
             G  R  EKARLRKGI+IL++TPG L+DH+K T +     +RW+I DEADR+L+LGF K+I
Sbjct:   300 GEKRKSEKARLRKGINILISTPGRLVDHIKSTKNMRFCRIRWLILDEADRLLDLGFEKDI 359

Query:   208 EEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKF 267
               IL+ + +               +RQN+LLSATL E V  L  ISL  PV I + E   
Sbjct:   360 ALILNAVNAER------------PERQNVLLSATLTEGVTRLADISLHEPVRISVLEGSQ 407

Query:   268 PE--DKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFMLPAKL 307
              +   KS    G+       E++     +       ++P+KL
Sbjct:   408 DQMHPKSRAILGASPPAASSELDGFAIPVGLEQHVALVPSKL 449

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|F1NM06 DDX31 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 506 (183.2 bits), Expect = 1.8e-48, P = 1.8e-48
 Identities = 118/285 (41%), Positives = 163/285 (57%)

Query:    26 ETVKE-IFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGT 84
             + V+E +F +  FS L L   L   +   L   + T VQ Q IPV+L G+D LV + TG+
Sbjct:    86 QQVQENVFTTDSFSQLDLHPHLIATITTVLKICSMTSVQKQTIPVLLQGKDALVRSQTGS 145

Query:    85 GKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGY 144
             GKT+AY  P++  LQ    +I RS G +ALVLVPT EL L  ++ +QKLL  F WIVPG 
Sbjct:   146 GKTLAYGIPLVQSLQGMQSKIQRSDGPYALVLVPTRELALQTFDTIQKLLKPFTWIVPGV 205

Query:   145 VMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFG 204
             +MGG  R  EKARLRKGI+IL++TPG L+DH+K T        +W+I DEADRIL+LGF 
Sbjct:   206 LMGGEKRKSEKARLRKGINILISTPGRLVDHIKSTECIHFRRTQWLIIDEADRILDLGFE 265

Query:   205 KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDE 264
             K++  IL+ L +          E     RQN+LLSATL E V  L  ISL  P+ I + +
Sbjct:   266 KDVTVILNALNAER--------ET----RQNVLLSATLTEGVTRLADISLNDPIRISIAD 313

Query:   265 KKFPEDKSNVHFGSLESDVKEEVEHPNTTLSSSTEDF--MLPAKL 307
             +     K  +      +     ++  N  +    + +  M+P+KL
Sbjct:   314 EIRESLKPALQTEKEANSSSNRMDQENFAVPEKLKQYFMMVPSKL 358

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

GO:0003723 "RNA binding" 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

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

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	316
cd00268	203	cd00268, DEADc, DEAD-box helicases	5e-65
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	2e-57
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	5e-47
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	5e-40
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	1e-38
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	4e-37
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	2e-31
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-30
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	1e-30
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	7e-30
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	8e-30
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	5e-28
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	2e-27
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	3e-24
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	1e-17
COG1205	851	COG1205, COG1205, Distinct helicase family with a	1e-12
COG1201	814	COG1201, Lhr, Lhr-like helicases [General function	6e-12
PRK13767	876	PRK13767, PRK13767, ATP-dependent helicase; Provis	1e-05
COG1199	654	COG1199, DinG, Rad3-related DNA helicases [Transcr	2e-05
TIGR03817	742	TIGR03817, DECH_helic, helicase/secretion neighbor	3e-05
COG1204	766	COG1204, COG1204, Superfamily II helicase [General	4e-05
pfam04851	100	pfam04851, ResIII, Type III restriction enzyme, re	2e-04
TIGR04121	803	TIGR04121, DEXH_lig_assoc, DEXH box helicase, DNA	3e-04

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

 Score =  203 bits (518), Expect = 5e-65
 Identities = 87/224 (38%), Positives = 124/224 (55%), Gaps = 22/224 (9%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F  LGL   L   +   LGFE PT +QA+AIP +LSGRDV+  A TG+GKT A+L PI+ 
Sbjct: 1   FEELGLSPELLRGIYA-LGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILE 59

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            L        +  G  AL+L PT EL L + E+ +K L +   +    + GG +  K+  
Sbjct: 60  KLDPS----PKKDGPQALILAPTRELALQIAEVARK-LGKHTNLKVVVIYGGTSIDKQIR 114

Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS 216
           +L++G  I+VATPG LLD L+     L   +++++ DEADR+L++GF  +I EIL +L  
Sbjct: 115 KLKRGPHIVVATPGRLLDLLERGKLDLS-KVKYLVLDEADRMLDMGFEDQIREILKLL-- 171

Query: 217 RNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                           RQ LL SAT+ ++V  L +  L  PV I
Sbjct: 172 -------------PKDRQTLLFSATMPKEVRDLARKFLRNPVRI 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|223587 COG0513, SrmB, Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]

 Score =  192 bits (490), Expect = 2e-57
 Identities = 91/260 (35%), Positives = 131/260 (50%), Gaps = 23/260 (8%)

Query: 7   NSQTISKKKKRNDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQA 66
                   K ++          ++      F+SLGL   L   L++ LGFE PT +Q  A
Sbjct: 3   REDYDRFVKLKSAHNVALSRGEEKTPPE--FASLGLSPELLQALKD-LGFEEPTPIQLAA 59

Query: 67  IPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV 126
           IP+IL+GRDVL  A TGTGKT A+L P++  +     R   S    AL+L PT EL + +
Sbjct: 60  IPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVERKYVS----ALILAPTRELAVQI 115

Query: 127 YEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTN 186
            E L+KL      +    V GG +  K+   L++G+ I+VATPG LLD +K     L   
Sbjct: 116 AEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRGKLDLS-G 174

Query: 187 LRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKV 246
           +  ++ DEADR+L++GF  +IE+IL  L                  RQ LL SAT+ + +
Sbjct: 175 VETLVLDEADRMLDMGFIDDIEKILKAL---------------PPDRQTLLFSATMPDDI 219

Query: 247 NHLTKISLETPVLIGLDEKK 266
             L +  L  PV I +  +K
Sbjct: 220 RELARRYLNDPVEIEVSVEK 239

Length = 513

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

 Score =  155 bits (395), Expect = 5e-47
 Identities = 80/188 (42%), Positives = 107/188 (56%), Gaps = 23/188 (12%)

Query: 60  TKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPT 119
           T +QAQAIP ILSG+DVLV A TG+GKT+A+L PI+  L      + +  G  ALVL PT
Sbjct: 1   TPIQAQAIPAILSGKDVLVQAPTGSGKTLAFLLPILQAL------LPKKGGPQALVLAPT 54

Query: 120 SELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKG-ISILVATPGHLLDHLKH 178
            EL   +YE L+KL      +    + GG +  ++  +L+KG   ILV TPG LLD L+ 
Sbjct: 55  RELAEQIYEELKKLFK-ILGLRVALLTGGTSLKEQARKLKKGKADILVGTPGRLLDLLRR 113

Query: 179 TSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLL 238
               L  NL+ ++ DEA R+L++GFG ++EEIL  L                  RQ LLL
Sbjct: 114 GKLKLLKNLKLLVLDEAHRLLDMGFGDDLEEILSRLPPD---------------RQILLL 158

Query: 239 SATLNEKV 246
           SATL   +
Sbjct: 159 SATLPRNL 166

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

 Score =  144 bits (366), Expect = 5e-40
 Identities = 82/226 (36%), Positives = 118/226 (52%), Gaps = 23/226 (10%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           FS L LD +L + L++  G+  PT +QA+AIP  L GRDVL +A TGTGKT A+L P + 
Sbjct: 3   FSELELDESLLEALQD-KGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQ 61

Query: 97  HLQSYSPRIDRSSG-TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK 155
           HL  + PR  R SG    L+L PT EL + V +   + L +   +    + GG       
Sbjct: 62  HLLDF-PR--RKSGPPRILILTPTRELAMQVAD-QARELAKHTHLDIATITGGVAYMNHA 117

Query: 156 ARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILG 215
               +   I+VATPG LL ++K   +F    +  +I DEADR+L++GF ++IE I     
Sbjct: 118 EVFSENQDIVVATPGRLLQYIK-EENFDCRAVETLILDEADRMLDMGFAQDIETI----- 171

Query: 216 SRNIASIGEGNEVSNVKRQNLLLSATLN-EKVNHLTKISLETPVLI 260
                   E    +  ++Q LL SATL  + V    +  L  PV +
Sbjct: 172 ------AAE----TRWRKQTLLFSATLEGDAVQDFAERLLNDPVEV 207

Length = 434

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

 Score =  135 bits (341), Expect = 1e-38
 Identities = 78/211 (36%), Positives = 111/211 (52%), Gaps = 26/211 (12%)

Query: 52  ERLGFEAPTKVQAQAIPVILSG-RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSG 110
           E+ GFE     Q +AI  +LSG RDV++ A TG+GKT+A L P +  L+       R  G
Sbjct: 2   EKFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALK-------RGKG 54

Query: 111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKG-ISILVATP 169
              LVLVPT EL     E L+KL      +    + GG ++ ++  +L  G   ILV TP
Sbjct: 55  GRVLVLVPTRELAEQWAEELKKLGPSLG-LKVVGLYGGDSKREQLRKLESGKTDILVTTP 113

Query: 170 GHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVS 229
           G LLD L++    L  N+  +I DEA R+L+ GFG ++E++L +L               
Sbjct: 114 GRLLDLLENDKLSLS-NVDLVILDEAHRLLDGGFGDQLEKLLKLLPK------------- 159

Query: 230 NVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
               Q LLLSAT  E++ +L ++ L  PV I
Sbjct: 160 --NVQLLLLSATPPEEIENLLELFLNDPVFI 188

Length = 201

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

 Score =  137 bits (347), Expect = 4e-37
 Identities = 85/245 (34%), Positives = 131/245 (53%), Gaps = 26/245 (10%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F SLGL   +   + E+ G+  PT +Q QAIP +L GRD++ +A TGTGKT  +  P++ 
Sbjct: 3   FDSLGLSPDILRAVAEQ-GYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQ 61

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ---KLLHRFRWIVPGYVMGGGNRSK 153
           HL +  P         AL+L PT EL   + E ++   K L   R +V   V GG + + 
Sbjct: 62  HLITRQPHAKGRRPVRALILTPTRELAAQIGENVRDYSKYL-NIRSLV---VFGGVSINP 117

Query: 154 EKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDI 213
           +  +LR G+ +LVATPG LLD L+H ++     +  ++ DEADR+L++GF  +I  +L  
Sbjct: 118 QMMKLRGGVDVLVATPGRLLD-LEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAK 176

Query: 214 LGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDK-- 271
           L +               KRQNLL SAT ++ +  L +  L  P+ I +  +    ++  
Sbjct: 177 LPA---------------KRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVT 221

Query: 272 SNVHF 276
            +VHF
Sbjct: 222 QHVHF 226

Length = 456

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

 Score =  123 bits (309), Expect = 2e-31
 Identities = 83/226 (36%), Positives = 125/226 (55%), Gaps = 33/226 (14%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F+ LGL + + + L + LG+E P+ +QA+ IP +L+GRDVL  A TG+GKT A+  P+++
Sbjct: 8   FADLGLKAPILEALND-LGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLH 66

Query: 97  HLQS--YSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWI--VPGYVMGGGNRS 152
           +L     +P+I        LVL PT EL + V E +       R +  V  Y   GG R 
Sbjct: 67  NLDPELKAPQI--------LVLAPTRELAVQVAEAMTDFSKHMRGVNVVALY---GGQRY 115

Query: 153 KEKAR-LRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEIL 211
             + R LR+G  I+V TPG LLDHLK  +  L + L  ++ DEAD +L +GF +++E I+
Sbjct: 116 DVQLRALRQGPQIVVGTPGRLLDHLKRGTLDL-SKLSGLVLDEADEMLRMGFIEDVETIM 174

Query: 212 DILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETP 257
                   A I EG+       Q  L SAT+ E +  +T+  ++ P
Sbjct: 175 --------AQIPEGH-------QTALFSATMPEAIRRITRRFMKEP 205

Length = 629

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

 Score =  120 bits (302), Expect = 1e-30
 Identities = 78/227 (34%), Positives = 114/227 (50%), Gaps = 22/227 (9%)

Query: 36  CFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPII 95
            FSS GL   L   L E  G+E PT +Q QAIP  LSGR +LV+A TG+GKT ++L PII
Sbjct: 122 SFSSCGLPPKLLLNL-ETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPII 180

Query: 96  NHLQSYSPR-IDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE 154
           +   +             A+VL PT ELC+ V E   K+L +        V+GG    ++
Sbjct: 181 SRCCTIRSGHPSEQRNPLAMVLTPTRELCVQV-EDQAKVLGKGLPFKTALVVGGDAMPQQ 239

Query: 155 KARLRKGISILVATPGHLLDHL-KHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDI 213
             R+++G+ ++V TPG L+D L KH       N+  ++ DE D +LE GF  ++ +I   
Sbjct: 240 LYRIQQGVELIVGTPGRLIDLLSKHDIEL--DNVSVLVLDEVDCMLERGFRDQVMQIFQA 297

Query: 214 LGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
           L                 + Q LL SAT++ +V        +  +LI
Sbjct: 298 LS----------------QPQVLLFSATVSPEVEKFASSLAKDIILI 328

Length = 518

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

 Score =  119 bits (301), Expect = 1e-30
 Identities = 74/231 (32%), Positives = 115/231 (49%), Gaps = 29/231 (12%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           FS+L L   L   L E LG+   T +QAQ++P IL+G+DV+  A TG+GKT A+   ++ 
Sbjct: 6   FSTLPLPPALLANLNE-LGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQ 64

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL---LHRFRWIVPGYVMGGGNRSK 153
            L     R+       ALVL PT EL   V + +++L   +   + +    + GG     
Sbjct: 65  KLDVKRFRVQ------ALVLCPTRELADQVAKEIRRLARFIPNIKVLT---LCGGVPMGP 115

Query: 154 EKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDI 213
           +   L  G  I+V TPG +LDHL+  +  L   L  ++ DEADR+L++GF   I+ I+  
Sbjct: 116 QIDSLEHGAHIIVGTPGRILDHLRKGTLDL-DALNTLVLDEADRMLDMGFQDAIDAIIRQ 174

Query: 214 LGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDE 264
             +R               RQ LL SAT  E +  +++     PV + ++ 
Sbjct: 175 APAR---------------RQTLLFSATYPEGIAAISQRFQRDPVEVKVES 210

Length = 460

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

 Score =  118 bits (297), Expect = 7e-30
 Identities = 81/219 (36%), Positives = 112/219 (51%), Gaps = 26/219 (11%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           FSS  L   L   L E  GF   T +QA  +PV L G DV   A TGTGKT+A+L  ++N
Sbjct: 11  FSSFDLHPALLAGL-ESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMN 69

Query: 97  HLQSYSPRIDRS-SGTFALVLVPTSELCLLVYEILQK----LLHRFRWIVPGYVMGGGNR 151
            L S     DR      AL+L PT EL + +++   K    L  RF       V GG + 
Sbjct: 70  RLLSRPALADRKPEDPRALILAPTRELAIQIHKDAVKFGADLGLRF-----ALVYGGVDY 124

Query: 152 SKEKARLRKGISILVATPGHLLDHLK-HTSSFLHTNLRWIIFDEADRILELGFGKEIEEI 210
            K++  L++G+ +++ATPG L+D++K H    LH      + DEADR+ +LGF K+I  +
Sbjct: 125 DKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHA-CEICVLDEADRMFDLGFIKDIRFL 183

Query: 211 LDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHL 249
           L  +  R               RQ LL SATL+ +V  L
Sbjct: 184 LRRMPERG-------------TRQTLLFSATLSHRVLEL 209

Length = 572

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

 Score =  110 bits (276), Expect = 8e-30
 Identities = 65/169 (38%), Positives = 82/169 (48%), Gaps = 25/169 (14%)

Query: 74  RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL 133
           RDVL+ A TG+GKT+A L PI+  L       D   G   LVL PT EL   V E L++L
Sbjct: 1   RDVLLAAPTGSGKTLAALLPILELL-------DSLKGGQVLVLAPTRELANQVAERLKEL 53

Query: 134 LHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD 193
                 I  GY++GG +  +++  L     I+V TPG LLD L+     L   L  +I D
Sbjct: 54  F--GEGIKVGYLIGGTSIKQQEKLLSGKTDIVVGTPGRLLDELERLKLSLK-KLDLLILD 110

Query: 194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATL 242
           EA R+L  GFG    +IL  L                  RQ LLLSAT 
Sbjct: 111 EAHRLLNQGFGLLGLKILLKLPK---------------DRQVLLLSATP 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|240273 PTZ00110, PTZ00110, helicase; Provisional

 Score =  113 bits (284), Expect = 5e-28
 Identities = 75/215 (34%), Positives = 111/215 (51%), Gaps = 29/215 (13%)

Query: 52  ERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT 111
           +  GF  PT +Q Q  P+ LSGRD++  A TG+GKT+A+L P I H+ +  P +    G 
Sbjct: 146 KNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINA-QPLLRYGDGP 204

Query: 112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGH 171
             LVL PT EL   + E   K     + I      GG  +  +   LR+G+ IL+A PG 
Sbjct: 205 IVLVLAPTRELAEQIREQCNKFGASSK-IRNTVAYGGVPKRGQIYALRRGVEILIACPGR 263

Query: 172 LLDHLKHTSSFLHTNLR---WIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEV 228
           L+D L+       TNLR   +++ DEADR+L++GF  +I +I                 V
Sbjct: 264 LIDFLESNV----TNLRRVTYLVLDEADRMLDMGFEPQIRKI-----------------V 302

Query: 229 SNVK--RQNLLLSATLNEKVNHLTK-ISLETPVLI 260
           S ++  RQ L+ SAT  ++V  L + +  E PV +
Sbjct: 303 SQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHV 337

Length = 545

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

 Score =  110 bits (277), Expect = 2e-27
 Identities = 85/274 (31%), Positives = 130/274 (47%), Gaps = 46/274 (16%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           FS   L   + + L ++ GF   T +QA A+P+ L+GRDV   A TGTGKT+A+L    +
Sbjct: 10  FSDFALHPQVVEALEKK-GFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFH 68

Query: 97  HLQSYSPRIDR-SSGTFALVLVPTSELCLLVY---EILQKLLHRFRWIVPGYVMGGGNRS 152
           +L S+    DR  +   AL++ PT EL + ++   E L +       +  G   GG    
Sbjct: 69  YLLSHPAPEDRKVNQPRALIMAPTRELAVQIHADAEPLAQATG----LKLGLAYGGDGYD 124

Query: 153 KEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWI---IFDEADRILELGFGKEIEE 209
           K+   L  G+ IL+ T G L+D+ K      H NL  I   + DEADR+ +LGF K+I  
Sbjct: 125 KQLKVLESGVDILIGTTGRLIDYAKQN----HINLGAIQVVVLDEADRMFDLGFIKDIRW 180

Query: 210 ILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPE 269
           +      R +    +        R N+L SATL+ +V  L    +  P  + ++    PE
Sbjct: 181 LF-----RRMPPANQ--------RLNMLFSATLSYRVRELAFEHMNNPEYVEVE----PE 223

Query: 270 DKSNVHFGSLESDVKEEVEHPNTTLSSSTEDFML 303
            K+          +KEE+ +P      S E+ M 
Sbjct: 224 QKTGHR-------IKEELFYP------SNEEKMR 244

Length = 423

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

 Score =  102 bits (255), Expect = 3e-24
 Identities = 72/222 (32%), Positives = 110/222 (49%), Gaps = 21/222 (9%)

Query: 54  LGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT-F 112
           LGF   T +QAQ +   L+G D +  A TGTGKT A+L  IIN L    P  +R  G   
Sbjct: 105 LGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGEPR 164

Query: 113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLR-KGISILVATPGH 171
           AL++ PT EL + +       L ++  +     +GG +  K+  +L  +   ILVATPG 
Sbjct: 165 ALIIAPTRELVVQI-AKDAAALTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGR 223

Query: 172 LLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNV 231
           LLD  +     L   +  ++ DEADR+L++GF  ++ +I+     R      E       
Sbjct: 224 LLDFNQRGEVHLDM-VEVMVLDEADRMLDMGFIPQVRQII-----RQTPRKEE------- 270

Query: 232 KRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSN 273
            RQ LL SAT  + V +L K     P ++ ++    PE+ ++
Sbjct: 271 -RQTLLFSATFTDDVMNLAKQWTTDPAIVEIE----PENVAS 307

Length = 475

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

 Score = 82.2 bits (203), Expect = 1e-17
 Identities = 65/228 (28%), Positives = 102/228 (44%), Gaps = 30/228 (13%)

Query: 36  CFSSLGLDSTLCDQLRE--RLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAP 93
            F +L L+  L   LR     GFE P+ +Q + I  IL G D +  A +GTGKT  +   
Sbjct: 29  SFDALKLNEDL---LRGIYSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATF--- 82

Query: 94  IINHLQSYSPRIDRS-SGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS 152
           +I  LQ     ID   +   AL+L PT EL   + +++   L  +  +     +GG    
Sbjct: 83  VIAALQ----LIDYDLNACQALILAPTRELAQQIQKVV-LALGDYLKVRCHACVGGTVVR 137

Query: 153 KEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILD 212
            +  +L+ G+ ++V TPG + D +         +L+  I DEAD +L  GF  +I ++  
Sbjct: 138 DDINKLKAGVHMVVGTPGRVYDMID-KRHLRVDDLKLFILDEADEMLSRGFKGQIYDVFK 196

Query: 213 ILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
            L               +V  Q  L SAT+  ++  LT   +  P  I
Sbjct: 197 KL-------------PPDV--QVALFSATMPNEILELTTKFMRDPKRI 229

Length = 401

>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 = 68.2 bits (167), Expect = 1e-12
 Identities = 44/164 (26%), Positives = 74/164 (45%), Gaps = 16/164 (9%)

Query: 38  SSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINH 97
                D +L   L +       +  Q  A+ +I  GR+V+V   TG+GKT ++L PI++H
Sbjct: 51  FPELRDESLKSALVKAGIERLYSH-QVDALRLIREGRNVVVTTGTGSGKTESFLLPILDH 109

Query: 98  LQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF--RWIVPGYVMGGGNRSKEK 155
           L      +   S   AL+L PT+ L     E L++L+     +     Y  G     + +
Sbjct: 110 L------LRDPSAR-ALLLYPTNALANDQAERLRELISDLPGKVTFGRYT-GDTPPEERR 161

Query: 156 ARLRKGISILVATPGHLLDHL----KHTSSFLHTNLRWIIFDEA 195
           A +R    IL+  P  +L +L         +L  NL++++ DE 
Sbjct: 162 AIIRNPPDILLTNP-DMLHYLLLRNHDAWLWLLRNLKYLVVDEL 204

Length = 851

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

 Score = 65.7 bits (161), Expect = 6e-12
 Identities = 47/163 (28%), Positives = 71/163 (43%), Gaps = 23/163 (14%)

Query: 44  STLCDQLRE--RLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSY 101
           + L  ++RE  +  F + T  Q  AIP I SG +VL+ A TG+GKT A   P+IN L S 
Sbjct: 6   NILDPRVREWFKRKFTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSL 65

Query: 102 SPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKG 161
                   G +AL + P   L   +   L++ L      +   V  G     EK ++ K 
Sbjct: 66  GKGKLE-DGIYALYISPLKALNNDIRRRLEEPLRELG--IEVAVRHGDTPQSEKQKMLKN 122

Query: 162 IS-ILVATP---------GHLLDHLKHTSSFLHTNLRWIIFDE 194
              IL+ TP             + L+        ++R++I DE
Sbjct: 123 PPHILITTPESLAILLNSPKFRELLR--------DVRYVIVDE 157

Length = 814

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

 Score = 46.4 bits (111), Expect = 1e-05
 Identities = 19/43 (44%), Positives = 28/43 (65%)

Query: 56 FEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHL 98
          F   T  Q  AIP+I  G++VL+++ TG+GKT+A    II+ L
Sbjct: 30 FGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDEL 72

Length = 876

>gnl|CDD|224120 COG1199, DinG, Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

 Score = 46.0 bits (109), Expect = 2e-05
 Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 5/69 (7%)

Query: 50  LRERLGFEAPTKVQAQAI----PVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRI 105
                GFE P   Q +        +  G  +L+ A TGTGKT+AYL P + + +    ++
Sbjct: 8   AVAFPGFE-PRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEGKKV 66

Query: 106 DRSSGTFAL 114
             S+ T AL
Sbjct: 67  IISTRTKAL 75

Length = 654

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

 Score = 45.1 bits (107), Expect = 3e-05
 Identities = 23/71 (32%), Positives = 34/71 (47%), Gaps = 7/71 (9%)

Query: 52  ERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT 111
           E  G   P + QA+A  +  +GR V+V   T +GK++AY  P+++ L             
Sbjct: 30  EAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALAD-------DPRA 82

Query: 112 FALVLVPTSEL 122
            AL L PT  L
Sbjct: 83  TALYLAPTKAL 93

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

>gnl|CDD|224125 COG1204, COG1204, Superfamily II helicase [General function prediction only]

 Score = 44.7 bits (106), Expect = 4e-05
 Identities = 44/187 (23%), Positives = 77/187 (41%), Gaps = 39/187 (20%)

Query: 63  QAQAI-PVILSGRDVLVNAATGTGKT-VAYLAPIINHLQSYSPRIDRSSGTFALVLVPTS 120
           Q +A+   +LS  +VL++A TG+GKT +A LA I++ L     +         + +VP  
Sbjct: 36  QQEAVEKGLLSDENVLISAPTGSGKTLIALLA-ILSTLLEGGGK--------VVYIVPLK 86

Query: 121 ELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTS 180
               L  E  ++   R   +     +  G+   +  RL     ++V TP  L    +   
Sbjct: 87  A---LAEEKYEE-FSRLEELGIRVGISTGDYDLDDERL-ARYDVIVTTPEKLDSLTRKRP 141

Query: 181 SFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLL--- 237
           S++   +  ++ DE   + +   G  +E I                 V+ ++R N L   
Sbjct: 142 SWI-EEVDLVVIDEIHLLGDRTRGPVLESI-----------------VARMRRLNELIRI 183

Query: 238 --LSATL 242
             LSATL
Sbjct: 184 VGLSATL 190

Length = 766

>gnl|CDD|218292 pfam04851, ResIII, Type III restriction enzyme, res subunit

 Score = 39.9 bits (94), Expect = 2e-04
 Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 9/65 (13%)

Query: 59  PTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVP 118
               Q +AI  +L  +  L+  ATG+GKT+   A +I  L     ++        L +VP
Sbjct: 4   LRPYQEEAIERLLEKKRGLIVMATGSGKTLTAAA-LIARLAKGKKKV--------LFVVP 54

Query: 119 TSELC 123
             +L 
Sbjct: 55  RKDLL 59

Length = 100

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

 Score = 42.1 bits (100), Expect = 3e-04
 Identities = 39/139 (28%), Positives = 58/139 (41%), Gaps = 15/139 (10%)

Query: 63  QAQAIPVILSGRDVLVNAATGTGKTVA-YLAPIINHLQSYSPRIDRSSGTFALVLVPTSE 121
           Q +     L GR  L+ A TG+GKT+A +L  +I+      P+     G   L + P   
Sbjct: 18  QLEMWAAALEGRSGLLIAPTGSGKTLAGFLPSLIDLAGPEKPK----KGLHTLYITP--- 70

Query: 122 LCLLVYEILQKLLHRFRWIVPGYVMG---GGNRSKEKARLRKGI-SILVATPG--HLLDH 175
           L  L  +I + L      +     +    G   S E+AR RK    IL+ TP    LL  
Sbjct: 71  LRALAVDIARNLQAPIEELGLPIRVETRTGDTSSSERARQRKKPPDILLTTPESLALLLS 130

Query: 176 LKHTSSFLHTNLRWIIFDE 194
               +     +LR ++ DE
Sbjct: 131 YPDAARLF-KDLRCVVVDE 148

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	316
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
PTZ00110	545	helicase; Provisional	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	100.0
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0334	997	consensus RNA helicase [RNA processing and modific	100.0
PTZ00424	401	helicase 45; Provisional	100.0
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	100.0
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	100.0
KOG0327	397	consensus Translation initiation factor 4F, helica	100.0
KOG4284	980	consensus DEAD box protein [Transcription]	100.0
KOG0347	731	consensus RNA helicase [RNA processing and modific	100.0
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	100.0
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.98
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.97
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.97
PRK02362	737	ski2-like helicase; Provisional	99.96
PRK00254	720	ski2-like helicase; Provisional	99.96
PRK13767	876	ATP-dependent helicase; Provisional	99.96
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.95
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.95
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.95
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.95
PRK09401	1176	reverse gyrase; Reviewed	99.95
PRK01172	674	ski2-like helicase; Provisional	99.95
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.94
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.94
PRK14701	1638	reverse gyrase; Provisional	99.94
PRK10689	1147	transcription-repair coupling factor; Provisional	99.93
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.93
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.93
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.93
COG1205	851	Distinct helicase family with a unique C-terminal	99.92
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.91
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.91
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.9
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.89
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.89
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.89
COG1204	766	Superfamily II helicase [General function predicti	99.89
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.89
PHA02653	675	RNA helicase NPH-II; Provisional	99.87
PHA02558	501	uvsW UvsW helicase; Provisional	99.85
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.84
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.83
COG1202	830	Superfamily II helicase, archaea-specific [General	99.83
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.82
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.82
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.81
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.79
PRK13766	773	Hef nuclease; Provisional	99.78
KOG0354	746	consensus DEAD-box like helicase [General function	99.78
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.78
PRK05580	679	primosome assembly protein PriA; Validated	99.78
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.77
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.77
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.77
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.76
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.76
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.74
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.74
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.74
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.72
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	99.7
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.7
PRK09694	878	helicase Cas3; Provisional	99.69
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.69
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.63
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.62
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	99.61
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.6
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.6
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	99.59
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.57
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.56
PRK13107	908	preprotein translocase subunit SecA; Reviewed	99.55
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	99.53
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.48
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	99.45
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	99.43
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	99.43
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.42
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	99.39
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	99.38
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	99.35
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	99.33
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	99.33
COG4096	875	HsdR Type I site-specific restriction-modification	99.29
COG1198	730	PriA Primosomal protein N' (replication factor Y)	99.27
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	99.27
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	99.26
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	99.26
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	99.24
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	99.22
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	99.2
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	99.2
PRK12326	764	preprotein translocase subunit SecA; Reviewed	99.19
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	99.08
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	99.06
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	99.06
CHL00122	870	secA preprotein translocase subunit SecA; Validate	99.06
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	99.03
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	98.99
PRK04914	956	ATP-dependent helicase HepA; Validated	98.98
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	98.97
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	98.91
COG1199	654	DinG Rad3-related DNA helicases [Transcription / D	98.91
TIGR00604	705	rad3 DNA repair helicase (rad3). All proteins in t	98.82
PRK15483	986	type III restriction-modification system StyLTI en	98.78
PRK14873	665	primosome assembly protein PriA; Provisional	98.77
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	98.76
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	98.75
KOG1123	776	consensus RNA polymerase II transcription initiati	98.68
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	98.66
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	98.59
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	98.5
COG0610	962	Type I site-specific restriction-modification syst	98.47
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	98.45
PF02562	205	PhoH: PhoH-like protein; InterPro: IPR003714 PhoH	98.45
KOG2340	698	consensus Uncharacterized conserved protein [Funct	98.42
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	98.42
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	98.4
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	98.4
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	98.33
KOG0387	923	consensus Transcription-coupled repair protein CSB	98.32
KOG4439	901	consensus RNA polymerase II transcription terminat	98.31
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	98.3
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	98.29
COG4889	1518	Predicted helicase [General function prediction on	98.26
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	98.22
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	98.22
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	98.14
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	98.12
PRK10536	262	hypothetical protein; Provisional	98.12
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	98.1
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	98.08
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	98.08
PRK10875	615	recD exonuclease V subunit alpha; Provisional	98.06
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	98.05
KOG1803	649	consensus DNA helicase [Replication, recombination	98.05
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	97.99
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	97.98
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	97.97
KOG1002	791	consensus Nucleotide excision repair protein RAD16	97.95
COG3587	985	Restriction endonuclease [Defense mechanisms]	97.92
KOG1132	945	consensus Helicase of the DEAD superfamily [Replic	97.92
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	97.9
KOG1802	935	consensus RNA helicase nonsense mRNA reducing fact	97.89
TIGR01448	720	recD_rel helicase, putative, RecD/TraA family. Thi	97.84
PF13245	76	AAA_19: Part of AAA domain	97.79
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	97.75
PF00580	315	UvrD-helicase: UvrD/REP helicase N-terminal domain	97.71
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	97.67
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	97.65
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	97.64
COG1875	436	NYN ribonuclease and ATPase of PhoH family domains	97.59
PRK13889	988	conjugal transfer relaxase TraA; Provisional	97.55
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	97.5
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	97.48
KOG1805	1100	consensus DNA replication helicase [Replication, r	97.34
TIGR00376	637	DNA helicase, putative. The gene product may repre	97.3
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	97.29
PF05970	364	PIF1: PIF1-like helicase; InterPro: IPR010285 This	97.28
PRK04296	190	thymidine kinase; Provisional	97.25
TIGR02768	744	TraA_Ti Ti-type conjugative transfer relaxase TraA	97.23
PRK06526	254	transposase; Provisional	97.21
PRK13826	1102	Dtr system oriT relaxase; Provisional	97.18
PRK08181	269	transposase; Validated	97.17
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	97.15
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	97.15
PHA02533	534	17 large terminase protein; Provisional	97.14
PRK12723	388	flagellar biosynthesis regulator FlhF; Provisional	97.08
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	97.06
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	97.0
KOG0953	700	consensus Mitochondrial RNA helicase SUV3, DEAD-bo	96.82
smart00382	148	AAA ATPases associated with a variety of cellular	96.78
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	96.77
cd01124	187	KaiC KaiC is a circadian clock protein primarily f	96.76
KOG1131	755	consensus RNA polymerase II transcription initiati	96.76
PRK14974	336	cell division protein FtsY; Provisional	96.72
PRK11889	436	flhF flagellar biosynthesis regulator FlhF; Provis	96.72
PRK14722	374	flhF flagellar biosynthesis regulator FlhF; Provis	96.71
PRK06921	266	hypothetical protein; Provisional	96.68
PRK08116	268	hypothetical protein; Validated	96.67
PHA03368	738	DNA packaging terminase subunit 1; Provisional	96.57
PRK08727	233	hypothetical protein; Validated	96.54
PF00448	196	SRP54: SRP54-type protein, GTPase domain; InterPro	96.54
PRK07952	244	DNA replication protein DnaC; Validated	96.5
TIGR02785	1232	addA_Gpos recombination helicase AddA, Firmicutes	96.5
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	96.48
PRK05642	234	DNA replication initiation factor; Validated	96.48
PRK14712	1623	conjugal transfer nickase/helicase TraI; Provision	96.47
PRK00149	450	dnaA chromosomal replication initiation protein; R	96.44
PRK14087	450	dnaA chromosomal replication initiation protein; P	96.44
PRK06893	229	DNA replication initiation factor; Validated	96.44
PRK10919	672	ATP-dependent DNA helicase Rep; Provisional	96.43
COG3421	812	Uncharacterized protein conserved in bacteria [Fun	96.35
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	96.32
PRK06835	329	DNA replication protein DnaC; Validated	96.31
PRK12377	248	putative replication protein; Provisional	96.31
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	96.28
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	96.24
PRK11331	459	5-methylcytosine-specific restriction enzyme subun	96.24
PRK05298	652	excinuclease ABC subunit B; Provisional	96.21
TIGR01075	715	uvrD DNA helicase II. Designed to identify uvrD me	96.18
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	96.18
PRK11054	684	helD DNA helicase IV; Provisional	96.17
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	96.17
PRK13709	1747	conjugal transfer nickase/helicase TraI; Provision	96.15
PHA03333	752	putative ATPase subunit of terminase; Provisional	96.15
PHA02544	316	44 clamp loader, small subunit; Provisional	96.12
COG3973	747	Superfamily I DNA and RNA helicases [General funct	96.11
PRK11773	721	uvrD DNA-dependent helicase II; Provisional	96.11
PRK05703	424	flhF flagellar biosynthesis regulator FlhF; Valida	96.1
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	96.1
PRK05707	328	DNA polymerase III subunit delta'; Validated	96.09
PHA03372	668	DNA packaging terminase subunit 1; Provisional	96.03
PRK14088	440	dnaA chromosomal replication initiation protein; P	96.03
PTZ00112	1164	origin recognition complex 1 protein; Provisional	96.01
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	95.99
TIGR02760	1960	TraI_TIGR conjugative transfer relaxase protein Tr	95.97
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	95.94
COG1474	366	CDC6 Cdc6-related protein, AAA superfamily ATPase	95.93
PRK08084	235	DNA replication initiation factor; Provisional	95.9
cd01122	271	GP4d_helicase GP4d_helicase is a homohexameric 5'-	95.9
TIGR01074	664	rep ATP-dependent DNA helicase Rep. Designed to id	95.88
PRK08769	319	DNA polymerase III subunit delta'; Validated	95.88
COG1444	758	Predicted P-loop ATPase fused to an acetyltransfer	95.86
PF00004	132	AAA: ATPase family associated with various cellula	95.78
PRK12726	407	flagellar biosynthesis regulator FlhF; Provisional	95.77
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	95.76
PLN03025	319	replication factor C subunit; Provisional	95.75
PRK13342	413	recombination factor protein RarA; Reviewed	95.75
PRK12422	445	chromosomal replication initiation protein; Provis	95.73
COG2805	353	PilT Tfp pilus assembly protein, pilus retraction	95.72
PRK08903	227	DnaA regulatory inactivator Hda; Validated	95.69
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	95.66
CHL00181	287	cbbX CbbX; Provisional	95.65
PRK12727	559	flagellar biosynthesis regulator FlhF; Provisional	95.65
KOG1133	821	consensus Helicase of the DEAD superfamily [Replic	95.6
TIGR01547	396	phage_term_2 phage terminase, large subunit, PBSX	95.59
PRK00411	394	cdc6 cell division control protein 6; Reviewed	95.58
PRK04195	482	replication factor C large subunit; Provisional	95.5
PRK09183	259	transposase/IS protein; Provisional	95.5
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	95.46
PF06745	226	KaiC: KaiC; InterPro: IPR014774 This entry represe	95.45
PRK08533	230	flagellar accessory protein FlaH; Reviewed	95.41
TIGR01073	726	pcrA ATP-dependent DNA helicase PcrA. Designed to	95.39
PRK11823	446	DNA repair protein RadA; Provisional	95.28
PF13177	162	DNA_pol3_delta2: DNA polymerase III, delta subunit	95.25
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	95.25
PRK13341	725	recombination factor protein RarA/unknown domain f	95.23
PRK12402	337	replication factor C small subunit 2; Reviewed	95.22
COG0470	325	HolB ATPase involved in DNA replication [DNA repli	95.2
PRK14086	617	dnaA chromosomal replication initiation protein; P	95.18
PRK13833	323	conjugal transfer protein TrbB; Provisional	95.18
PRK13894	319	conjugal transfer ATPase TrbB; Provisional	95.14
COG1419	407	FlhF Flagellar GTP-binding protein [Cell motility	95.13
COG4962	355	CpaF Flp pilus assembly protein, ATPase CpaF [Intr	95.12
TIGR02880	284	cbbX_cfxQ probable Rubsico expression protein CbbX	95.11
PRK08939	306	primosomal protein DnaI; Reviewed	95.03
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	95.01
KOG1001	674	consensus Helicase-like transcription factor HLTF/	94.96
PF13173	128	AAA_14: AAA domain	94.95
TIGR00064	272	ftsY signal recognition particle-docking protein F	94.92
PF05876	557	Terminase_GpA: Phage terminase large subunit (GpA)	94.9
PRK06731	270	flhF flagellar biosynthesis regulator FlhF; Valida	94.89
cd01121	372	Sms Sms (bacterial radA) DNA repair protein. This	94.87
PF01695	178	IstB_IS21: IstB-like ATP binding protein; InterPro	94.86
TIGR03499	282	FlhF flagellar biosynthetic protein FlhF.	94.85
KOG0921	1282	consensus Dosage compensation complex, subunit MLE	94.83
TIGR02688	449	conserved hypothetical protein TIGR02688. Members	94.81
TIGR03015	269	pepcterm_ATPase putative secretion ATPase, PEP-CTE	94.78
PRK06645	507	DNA polymerase III subunits gamma and tau; Validat	94.75
TIGR03881	229	KaiC_arch_4 KaiC domain protein, PAE1156 family. M	94.71
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	94.67
PRK14956	484	DNA polymerase III subunits gamma and tau; Provisi	94.63
PRK05563	559	DNA polymerase III subunits gamma and tau; Validat	94.61
PRK00771	437	signal recognition particle protein Srp54; Provisi	94.6
COG2256	436	MGS1 ATPase related to the helicase subunit of the	94.56
TIGR02928	365	orc1/cdc6 family replication initiation protein. M	94.52
KOG0737	386	consensus AAA+-type ATPase [Posttranslational modi	94.51
PRK06995	484	flhF flagellar biosynthesis regulator FlhF; Valida	94.51
PRK14958	509	DNA polymerase III subunits gamma and tau; Provisi	94.5
PF05729	166	NACHT: NACHT domain	94.47
PRK07003	830	DNA polymerase III subunits gamma and tau; Validat	94.44
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	94.35
PRK07764	824	DNA polymerase III subunits gamma and tau; Validat	94.33
TIGR02782	299	TrbB_P P-type conjugative transfer ATPase TrbB. Th	94.3
PRK08699	325	DNA polymerase III subunit delta'; Validated	94.3
TIGR03878	259	thermo_KaiC_2 KaiC domain protein, AF_0795 family.	94.28
PF14516	331	AAA_35: AAA-like domain	94.26
PRK13851	344	type IV secretion system protein VirB11; Provision	94.24
PRK14960	702	DNA polymerase III subunits gamma and tau; Provisi	94.23
PRK06964	342	DNA polymerase III subunit delta'; Validated	94.14
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	94.13
KOG0738	491	consensus AAA+-type ATPase [Posttranslational modi	94.13
PRK06067	234	flagellar accessory protein FlaH; Validated	94.13
cd00984	242	DnaB_C DnaB helicase C terminal domain. The hexame	94.09
COG2804	500	PulE Type II secretory pathway, ATPase PulE/Tfp pi	94.06
PRK14723	767	flhF flagellar biosynthesis regulator FlhF; Provis	94.04
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	94.02
PRK09111	598	DNA polymerase III subunits gamma and tau; Validat	94.01
PRK10867	433	signal recognition particle protein; Provisional	94.01
PRK08691	709	DNA polymerase III subunits gamma and tau; Validat	94.0
KOG0742	630	consensus AAA+-type ATPase [Posttranslational modi	93.99
PRK05973	237	replicative DNA helicase; Provisional	93.89
PRK07994	647	DNA polymerase III subunits gamma and tau; Validat	93.89
TIGR01425	429	SRP54_euk signal recognition particle protein SRP5	93.81
TIGR00959	428	ffh signal recognition particle protein. This mode	93.76
PRK14964	491	DNA polymerase III subunits gamma and tau; Provisi	93.74
COG0630	312	VirB11 Type IV secretory pathway, VirB11 component	93.71
PRK14961	363	DNA polymerase III subunits gamma and tau; Provisi	93.71
KOG0298	1394	consensus DEAD box-containing helicase-like transc	93.7
PRK12724	432	flagellar biosynthesis regulator FlhF; Provisional	93.69
PRK00440	319	rfc replication factor C small subunit; Reviewed	93.66
KOG0739	439	consensus AAA+-type ATPase [Posttranslational modi	93.64
PRK14949	944	DNA polymerase III subunits gamma and tau; Provisi	93.62
COG0593	408	DnaA ATPase involved in DNA replication initiation	93.55
PRK14962	472	DNA polymerase III subunits gamma and tau; Provisi	93.51
TIGR03877	237	thermo_KaiC_1 KaiC domain protein, Ph0284 family.	93.5
COG1484	254	DnaC DNA replication protein [DNA replication, rec	93.5
TIGR02237	209	recomb_radB DNA repair and recombination protein R	93.47
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	93.45
PRK13900	332	type IV secretion system ATPase VirB11; Provisiona	93.37
PRK06871	325	DNA polymerase III subunit delta'; Validated	93.33
PRK07993	334	DNA polymerase III subunit delta'; Validated	93.29
PRK14969	527	DNA polymerase III subunits gamma and tau; Provisi	93.25
PF03969	362	AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654	93.21
PRK12323	700	DNA polymerase III subunits gamma and tau; Provisi	93.19
PRK07940	394	DNA polymerase III subunit delta'; Validated	93.17
PRK06904	472	replicative DNA helicase; Validated	93.13
PRK14963	504	DNA polymerase III subunits gamma and tau; Provisi	93.07
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	93.07
PF03796	259	DnaB_C: DnaB-like helicase C terminal domain; Inte	93.06
COG2909	894	MalT ATP-dependent transcriptional regulator [Tran	92.99
PRK14965	576	DNA polymerase III subunits gamma and tau; Provisi	92.93
PRK03992	389	proteasome-activating nucleotidase; Provisional	92.89
PHA00012	361	I assembly protein	92.88
PRK14952	584	DNA polymerase III subunits gamma and tau; Provisi	92.87
PRK14721	420	flhF flagellar biosynthesis regulator FlhF; Provis	92.76
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	92.75
PRK10865	857	protein disaggregation chaperone; Provisional	92.75
PF01637	234	Arch_ATPase: Archaeal ATPase; InterPro: IPR011579	92.7
KOG0732	1080	consensus AAA+-type ATPase containing the bromodom	92.69
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	92.67
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	92.66
TIGR00416	454	sms DNA repair protein RadA. The gene protuct code	92.63
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	92.59
PRK14957	546	DNA polymerase III subunits gamma and tau; Provisi	92.59
PRK09354	349	recA recombinase A; Provisional	92.51
PRK09087	226	hypothetical protein; Validated	92.45
TIGR01243	733	CDC48 AAA family ATPase, CDC48 subfamily. This sub	92.38
TIGR00678	188	holB DNA polymerase III, delta' subunit. At positi	92.37
PF02534	469	T4SS-DNA_transf: Type IV secretory system Conjugat	92.36
TIGR02655	484	circ_KaiC circadian clock protein KaiC. Members of	92.33
PRK07471	365	DNA polymerase III subunit delta'; Validated	92.32
KOG0060	659	consensus Long-chain acyl-CoA transporter, ABC sup	92.29
PRK05896	605	DNA polymerase III subunits gamma and tau; Validat	92.27
COG2874	235	FlaH Predicted ATPases involved in biogenesis of a	92.26
PRK14948	620	DNA polymerase III subunits gamma and tau; Provisi	92.22
TIGR03880	224	KaiC_arch_3 KaiC domain protein, AF_0351 family. T	92.22
TIGR03600	421	phage_DnaB phage replicative helicase, DnaB family	92.2
PRK09376	416	rho transcription termination factor Rho; Provisio	92.13
PRK14970	367	DNA polymerase III subunits gamma and tau; Provisi	92.12
PF12846	304	AAA_10: AAA-like domain	92.12
PRK06090	319	DNA polymerase III subunit delta'; Validated	92.03
TIGR00763	775	lon ATP-dependent protease La. This protein is ind	91.97
cd01126	384	TraG_VirD4 The TraG/TraD/VirD4 family are bacteria	91.96
PF00437	270	T2SE: Type II/IV secretion system protein; InterPr	91.89
COG3972	660	Superfamily I DNA and RNA helicases [General funct	91.79
TIGR00602	637	rad24 checkpoint protein rad24. This family is bas	91.76
cd01127	410	TrwB Bacterial conjugation protein TrwB, ATP bindi	91.76
KOG0058	716	consensus Peptide exporter, ABC superfamily [Intra	91.74
PRK14950	585	DNA polymerase III subunits gamma and tau; Provisi	91.72
TIGR02525	372	plasmid_TraJ plasmid transfer ATPase TraJ. Members	91.72
PRK13764	602	ATPase; Provisional	91.69
PRK14959	624	DNA polymerase III subunits gamma and tau; Provisi	91.69
PRK10416	318	signal recognition particle-docking protein FtsY;	91.59
COG4626	546	Phage terminase-like protein, large subunit [Gener	91.57
PTZ00293	211	thymidine kinase; Provisional	91.57
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	91.54
PRK13897	606	type IV secretion system component VirD4; Provisio	91.52
PF03237	384	Terminase_6: Terminase-like family; InterPro: IPR0	91.5
KOG2004	906	consensus Mitochondrial ATP-dependent protease PIM	91.49
COG1219	408	ClpX ATP-dependent protease Clp, ATPase subunit [P	91.48
PRK14955	397	DNA polymerase III subunits gamma and tau; Provisi	91.44
PRK14951	618	DNA polymerase III subunits gamma and tau; Provisi	91.35
TIGR03346	852	chaperone_ClpB ATP-dependent chaperone ClpB. Membe	91.32
PRK04841	903	transcriptional regulator MalT; Provisional	91.24
KOG0729	435	consensus 26S proteasome regulatory complex, ATPas	91.2
KOG2228	408	consensus Origin recognition complex, subunit 4 [R	91.01
cd01129	264	PulE-GspE PulE/GspE The type II secretory pathway	90.98
PHA00729	226	NTP-binding motif containing protein	90.98
cd01130	186	VirB11-like_ATPase Type IV secretory pathway compo	90.97
PF10412	386	TrwB_AAD_bind: Type IV secretion-system coupling p	90.83
PRK04328	249	hypothetical protein; Provisional	90.81
TIGR02012	321	tigrfam_recA protein RecA. This model describes or	90.78
cd01394	218	radB RadB. The archaeal protein radB shares simila	90.71
cd03115	173	SRP The signal recognition particle (SRP) mediates	90.71
PRK07133	725	DNA polymerase III subunits gamma and tau; Validat	90.67
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	90.66
PRK08840	464	replicative DNA helicase; Provisional	90.65
COG0466	782	Lon ATP-dependent Lon protease, bacterial type [Po	90.62
TIGR00665	434	DnaB replicative DNA helicase. This model describe	90.57
TIGR02640	262	gas_vesic_GvpN gas vesicle protein GvpN. Members o	90.55
COG0210	655	UvrD Superfamily I DNA and RNA helicases [DNA repl	90.51
PRK08006	471	replicative DNA helicase; Provisional	90.51
CHL00176	638	ftsH cell division protein; Validated	90.5
PRK05748	448	replicative DNA helicase; Provisional	90.39
CHL00095	821	clpC Clp protease ATP binding subunit	90.37
TIGR03743	634	SXT_TraD conjugative coupling factor TraD, SXT/TOL	90.33
TIGR02524	358	dot_icm_DotB Dot/Icm secretion system ATPase DotB.	90.24
PRK14953	486	DNA polymerase III subunits gamma and tau; Provisi	90.24
COG1074	1139	RecB ATP-dependent exoDNAse (exonuclease V) beta s	90.21
COG0467	260	RAD55 RecA-superfamily ATPases implicated in signa	90.06
KOG2543	438	consensus Origin recognition complex, subunit 5 [R	90.02
PRK09112	351	DNA polymerase III subunit delta'; Validated	89.96
PF01443	234	Viral_helicase1: Viral (Superfamily 1) RNA helicas	89.96
PRK08506	472	replicative DNA helicase; Provisional	89.95
KOG0652	424	consensus 26S proteasome regulatory complex, ATPas	89.95
cd01393	226	recA_like RecA is a bacterial enzyme which has rol	89.84
PRK14954	620	DNA polymerase III subunits gamma and tau; Provisi	89.83
PRK08451	535	DNA polymerase III subunits gamma and tau; Validat	89.77
PRK10436	462	hypothetical protein; Provisional	89.63
PRK13850	670	type IV secretion system protein VirD4; Provisiona	89.52
KOG0740	428	consensus AAA+-type ATPase [Posttranslational modi	89.37
KOG2036	1011	consensus Predicted P-loop ATPase fused to an acet	89.33
PRK06305	451	DNA polymerase III subunits gamma and tau; Validat	89.17
PRK08760	476	replicative DNA helicase; Provisional	89.17
TIGR03754	643	conj_TOL_TraD conjugative coupling factor TraD, TO	89.08
PRK07004	460	replicative DNA helicase; Provisional	88.94
COG2401	593	ABC-type ATPase fused to a predicted acetyltransfe	88.79
PRK14971	614	DNA polymerase III subunits gamma and tau; Provisi	88.79
TIGR02538	564	type_IV_pilB type IV-A pilus assembly ATPase PilB.	88.75
TIGR02788	308	VirB11 P-type DNA transfer ATPase VirB11. The VirB	88.65
KOG0744	423	consensus AAA+-type ATPase [Posttranslational modi	88.62
PRK11034	758	clpA ATP-dependent Clp protease ATP-binding subuni	88.51
PF12775	272	AAA_7: P-loop containing dynein motor region D3; P	88.14
PF13555	62	AAA_29: P-loop containing region of AAA domain	88.06
KOG0741	744	consensus AAA+-type ATPase [Posttranslational modi	88.06
PRK10689	1147	transcription-repair coupling factor; Provisional	87.81
TIGR00767	415	rho transcription termination factor Rho. Members	87.79
COG1132	567	MdlB ABC-type multidrug transport system, ATPase a	87.78
PRK05636	505	replicative DNA helicase; Provisional	87.69
PRK13876	663	conjugal transfer coupling protein TraG; Provision	87.54
TIGR02639	731	ClpA ATP-dependent Clp protease ATP-binding subuni	87.49
PF13481	193	AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C.	87.47
PF04665	241	Pox_A32: Poxvirus A32 protein; InterPro: IPR006758	87.39
PRK09165	497	replicative DNA helicase; Provisional	87.38
cd01128	249	rho_factor Transcription termination factor rho is	87.38
TIGR01420	343	pilT_fam pilus retraction protein PilT. This model	87.33
PRK13695	174	putative NTPase; Provisional	87.23
PRK05595	444	replicative DNA helicase; Provisional	87.23
TIGR02784	1141	addA_alphas double-strand break repair helicase Ad	87.19
PF08423	256	Rad51: Rad51; InterPro: IPR013632 This domain is f	87.12
cd01131	198	PilT Pilus retraction ATPase PilT. PilT is a nucle	87.11
PRK06321	472	replicative DNA helicase; Provisional	87.03
TIGR03819	340	heli_sec_ATPase helicase/secretion neighborhood AT	86.89
TIGR02397	355	dnaX_nterm DNA polymerase III, subunit gamma and t	86.87
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	86.84
COG1674	858	FtsK DNA segregation ATPase FtsK/SpoIIIE and relat	86.84
TIGR02868	529	CydC thiol reductant ABC exporter, CydC subunit. T	86.82
PRK10787	784	DNA-binding ATP-dependent protease La; Provisional	86.75
TIGR02533	486	type_II_gspE general secretory pathway protein E.	86.74
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	86.73
PF01078	206	Mg_chelatase: Magnesium chelatase, subunit ChlI; I	86.71
COG2842	297	Uncharacterized ATPase, putative transposase [Gene	86.55
PF01580	205	FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR00	86.51
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	86.28
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	86.27
) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor" target="_blank" href="http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=PF06309">PF06309	127	Torsin: Torsin; InterPro: IPR010448 This family co	86.25
TIGR02767	623	TraG-Ti Ti-type conjugative transfer system protie	86.24
TIGR03575	340	selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryoti	86.06
PRK05917	290	DNA polymerase III subunit delta'; Validated	85.79
TIGR03345	852	VI_ClpV1 type VI secretion ATPase, ClpV1 family. M	85.76
PRK13531	498	regulatory ATPase RavA; Provisional	85.74
PRK06647	563	DNA polymerase III subunits gamma and tau; Validat	85.65

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

Probab=100.00  E-value=9.6e-52  Score=373.58  Aligned_cols=273  Identities=48%  Similarity=0.784  Sum_probs=235.3

Q ss_pred             ccccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCC
Q 043110           29 KEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRS  108 (316)
Q Consensus        29 ~~~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~  108 (316)
                      +.++..+.|..+||++.+...|..+|++..||.+|+++||.+++|+|+++.++||||||++|++|+++.+....++..+.
T Consensus       130 e~~fts~~f~~LGL~~~lv~~L~~~m~i~~pTsVQkq~IP~lL~grD~lV~aQTGSGKTLAYllPiVq~Lq~m~~ki~Rs  209 (708)
T KOG0348|consen  130 EAPFTSAAFASLGLHPHLVSHLNTKMKISAPTSVQKQAIPVLLEGRDALVRAQTGSGKTLAYLLPIVQSLQAMEPKIQRS  209 (708)
T ss_pred             ccccccccchhcCCCHHHHHHHHHHhccCccchHhhcchhhhhcCcceEEEcCCCCcccHHHHHHHHHHHHhcCcccccc
Confidence            34588899999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCcee
Q 043110          109 SGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLR  188 (316)
Q Consensus       109 ~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~  188 (316)
                      .|+.|||++||||||.|+|+.++++...+.|++.++++||.....+..++++|++|+|+|||||++++.+...+.++.++
T Consensus       210 ~G~~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLRKGiNILIgTPGRLvDHLknT~~i~~s~LR  289 (708)
T KOG0348|consen  210 DGPYALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLRKGINILIGTPGRLVDHLKNTKSIKFSRLR  289 (708)
T ss_pred             CCceEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHhcCceEEEcCchHHHHHHhccchheeeeee
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCC
Q 043110          189 WIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFP  268 (316)
Q Consensus       189 ~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~  268 (316)
                      |||+||||++++.||..++..|++.+.+..  +..-.....+...|.+++|||+++.|.+++...|+||++|..+.....
T Consensus       290 wlVlDEaDrlleLGfekdit~Il~~v~~~~--~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~  367 (708)
T KOG0348|consen  290 WLVLDEADRLLELGFEKDITQILKAVHSIQ--NAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQ  367 (708)
T ss_pred             EEEecchhHHHhccchhhHHHHHHHHhhcc--chhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhh
Confidence            999999999999999999999999996421  111112223446899999999999999999999999999996554311


Q ss_pred             CCCCCcccccccchhhhhhcCCCCC-CCCCCCccccCcceeeeEEee
Q 043110          269 EDKSNVHFGSLESDVKEEVEHPNTT-LSSSTEDFMLPAKLVQRYVKG  314 (316)
Q Consensus       269 ~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~q~~~~~  314 (316)
                      .         .+. .+ .+++.+.. -....+.|.+|..|.|+|+.+
T Consensus       368 ~---------~p~-~~-a~~ev~~~~~~~~l~~~~iPeqL~qry~vV  403 (708)
T KOG0348|consen  368 L---------NPK-DK-AVQEVDDGPAGDKLDSFAIPEQLLQRYTVV  403 (708)
T ss_pred             c---------Ccc-hh-hhhhcCCcccccccccccCcHHhhhceEec
Confidence            1         111 11 11111222 112235689999999999875

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

Probab=100.00  E-value=7.2e-50  Score=349.57  Aligned_cols=238  Identities=37%  Similarity=0.562  Sum_probs=218.2

Q ss_pred             ccCchhhhhhhhccccccccccccc----cccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEc
Q 043110            5 PLNSQTISKKKKRNDKMSKKKETVK----EIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNA   80 (316)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a   80 (316)
                      +++|..|++...+.+..+.+.....    ......+|.++++++++.+++ +..||..||++|+++||.++.|+|+|+.|
T Consensus        27 ~las~~~~~~~~~~~~~~~s~~~~~~~~~~~e~~~sf~dLgv~~~L~~ac-~~l~~~~PT~IQ~~aiP~~L~g~dvIglA  105 (476)
T KOG0330|consen   27 SLASEGWKKNEESGDKFILSAANRNEEMQTDESFKSFADLGVHPELLEAC-QELGWKKPTKIQSEAIPVALGGRDVIGLA  105 (476)
T ss_pred             cccchhhhhhhhhccchhhhhhhhcchhhhhhhhcchhhcCcCHHHHHHH-HHhCcCCCchhhhhhcchhhCCCcEEEEe
Confidence            7889999999998888877654332    345667899999999999999 66799999999999999999999999999


Q ss_pred             CCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhc
Q 043110           81 ATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRK  160 (316)
Q Consensus        81 ~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~  160 (316)
                      .||||||.+|++|+++.+....      ..++++|++||||||.||.++++.++...+ +.+.++.||.+...+...+.+
T Consensus       106 eTGSGKT~afaLPIl~~LL~~p------~~~~~lVLtPtRELA~QI~e~fe~Lg~~ig-lr~~~lvGG~~m~~q~~~L~k  178 (476)
T KOG0330|consen  106 ETGSGKTGAFALPILQRLLQEP------KLFFALVLTPTRELAQQIAEQFEALGSGIG-LRVAVLVGGMDMMLQANQLSK  178 (476)
T ss_pred             ccCCCchhhhHHHHHHHHHcCC------CCceEEEecCcHHHHHHHHHHHHHhccccC-eEEEEEecCchHHHHHHHhhc
Confidence            9999999999999999998732      248899999999999999999999988765 778889999999999999999


Q ss_pred             CCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEee
Q 043110          161 GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSA  240 (316)
Q Consensus       161 ~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SA  240 (316)
                      .|||+|+|||+|++++.+.+.+.+..++++|+||||+++++.|.+.++.|++.+|.               ++|+++|||
T Consensus       179 kPhilVaTPGrL~dhl~~Tkgf~le~lk~LVlDEADrlLd~dF~~~ld~ILk~ip~---------------erqt~LfsA  243 (476)
T KOG0330|consen  179 KPHILVATPGRLWDHLENTKGFSLEQLKFLVLDEADRLLDMDFEEELDYILKVIPR---------------ERQTFLFSA  243 (476)
T ss_pred             CCCEEEeCcHHHHHHHHhccCccHHHhHHHhhchHHhhhhhhhHHHHHHHHHhcCc---------------cceEEEEEe
Confidence            99999999999999999989999999999999999999999999999999999997               999999999


Q ss_pred             ecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          241 TLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       241 T~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                      |||+.+.++.+..+++|+.|.+...
T Consensus       244 TMt~kv~kL~rasl~~p~~v~~s~k  268 (476)
T KOG0330|consen  244 TMTKKVRKLQRASLDNPVKVAVSSK  268 (476)
T ss_pred             ecchhhHHHHhhccCCCeEEeccch
Confidence            9999999999999999999987754

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

Probab=100.00  E-value=2e-46  Score=337.43  Aligned_cols=226  Identities=38%  Similarity=0.580  Sum_probs=208.4

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      .+|.+++|+..+++++ ..+||..|||||..+||..+.|+|++.+|.||||||.+|++|+++++......   ....++|
T Consensus       181 ~sF~~mNLSRPlLka~-~~lGy~~PTpIQ~a~IPvallgkDIca~A~TGsGKTAAF~lPiLERLlYrPk~---~~~TRVL  256 (691)
T KOG0338|consen  181 ESFQSMNLSRPLLKAC-STLGYKKPTPIQVATIPVALLGKDICACAATGSGKTAAFALPILERLLYRPKK---VAATRVL  256 (691)
T ss_pred             hhHHhcccchHHHHHH-HhcCCCCCCchhhhcccHHhhcchhhheecccCCchhhhHHHHHHHHhcCccc---CcceeEE
Confidence            3899999999999999 88999999999999999999999999999999999999999999999874432   3467899


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      ||+|||||+.|++.+.++++.... +.+++..||.+...+...|+..|||+|+|||||.+|+.+...+.+.++..+|+||
T Consensus       257 VL~PTRELaiQv~sV~~qlaqFt~-I~~~L~vGGL~lk~QE~~LRs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLvlDE  335 (691)
T KOG0338|consen  257 VLVPTRELAIQVHSVTKQLAQFTD-ITVGLAVGGLDLKAQEAVLRSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLVLDE  335 (691)
T ss_pred             EEeccHHHHHHHHHHHHHHHhhcc-ceeeeeecCccHHHHHHHHhhCCCEEEecchhHHHHhccCCCccccceeEEEech
Confidence            999999999999999999998765 8889999999999999999999999999999999999999999999999999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCCCCc
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNV  274 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~~~~  274 (316)
                      ||+|++.||.++++.|++.+++               ++|+++|||||+..|+.|++.-|+.|+.|.++.+........+
T Consensus       336 ADRMLeegFademnEii~lcpk---------------~RQTmLFSATMteeVkdL~slSL~kPvrifvd~~~~~a~~LtQ  400 (691)
T KOG0338|consen  336 ADRMLEEGFADEMNEIIRLCPK---------------NRQTMLFSATMTEEVKDLASLSLNKPVRIFVDPNKDTAPKLTQ  400 (691)
T ss_pred             HHHHHHHHHHHHHHHHHHhccc---------------cccceeehhhhHHHHHHHHHhhcCCCeEEEeCCccccchhhhH
Confidence            9999999999999999999999               9999999999999999999999999999999988755555555


Q ss_pred             cccccc
Q 043110          275 HFGSLE  280 (316)
Q Consensus       275 ~~~~~~  280 (316)
                      .|+...
T Consensus       401 EFiRIR  406 (691)
T KOG0338|consen  401 EFIRIR  406 (691)
T ss_pred             HHheec
Confidence            555443

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

Probab=100.00  E-value=1.1e-44  Score=335.01  Aligned_cols=214  Identities=37%  Similarity=0.640  Sum_probs=199.6

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      ..|++++|++++.+.| +..||..|||||.+.||.++.|+|++..|.||||||++|++|++.++........+..++++|
T Consensus        91 ~~f~~~~ls~~~~~~l-k~~g~~~PtpIQaq~wp~~l~GrD~v~iA~TGSGKTLay~lP~i~~l~~~~~~~~~~~~P~vL  169 (519)
T KOG0331|consen   91 AAFQELGLSEELMKAL-KEQGFEKPTPIQAQGWPIALSGRDLVGIARTGSGKTLAYLLPAIVHLNNEQGKLSRGDGPIVL  169 (519)
T ss_pred             hhhhcccccHHHHHHH-HhcCCCCCchhhhcccceeccCCceEEEeccCCcchhhhhhHHHHHHHhccccccCCCCCeEE
Confidence            4799999999999999 567999999999999999999999999999999999999999999998866666777899999


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      ||+||||||.|+.+.+..++.... +.+.|++||.....|...+.++++|+|+|||||.+++.. ....++++.++|+||
T Consensus       170 VL~PTRELA~QV~~~~~~~~~~~~-~~~~cvyGG~~~~~Q~~~l~~gvdiviaTPGRl~d~le~-g~~~l~~v~ylVLDE  247 (519)
T KOG0331|consen  170 VLAPTRELAVQVQAEAREFGKSLR-LRSTCVYGGAPKGPQLRDLERGVDVVIATPGRLIDLLEE-GSLNLSRVTYLVLDE  247 (519)
T ss_pred             EEcCcHHHHHHHHHHHHHHcCCCC-ccEEEEeCCCCccHHHHHHhcCCcEEEeCChHHHHHHHc-CCccccceeEEEecc
Confidence            999999999999999999998765 678899999999999999999999999999999999998 677889999999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                      ||+|+|+||+++++.|++.++..              .+|++++|||+|+.+..++..+|.+|+.|.+...
T Consensus       248 ADrMldmGFe~qI~~Il~~i~~~--------------~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~  304 (519)
T KOG0331|consen  248 ADRMLDMGFEPQIRKILSQIPRP--------------DRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNK  304 (519)
T ss_pred             HHhhhccccHHHHHHHHHhcCCC--------------cccEEEEeeeccHHHHHHHHHHhcCceEEEecch
Confidence            99999999999999999999542              5699999999999999999999999999988765

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

Probab=100.00  E-value=5.6e-44  Score=319.12  Aligned_cols=233  Identities=33%  Similarity=0.531  Sum_probs=203.2

Q ss_pred             cCCcccCC--CCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCe
Q 043110           34 SCCFSSLG--LDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT  111 (316)
Q Consensus        34 ~~~f~~~~--l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~  111 (316)
                      ...|++++  |++++++++ +.+||..+||+|..+||.++.++|+++.|+||||||+||++|++..+.++..+.... .+
T Consensus         3 ~~~~~~l~~~L~~~l~~~l-~~~GF~~mTpVQa~tIPlll~~KDVvveavTGSGKTlAFllP~le~i~rr~~~~~~~-~v   80 (567)
T KOG0345|consen    3 PKSFSSLAPPLSPWLLEAL-DESGFEKMTPVQAATIPLLLKNKDVVVEAVTGSGKTLAFLLPMLEIIYRREAKTPPG-QV   80 (567)
T ss_pred             CcchhhcCCCccHHHHHHH-HhcCCcccCHHHHhhhHHHhcCCceEEEcCCCCCchhhHHHHHHHHHHhhccCCCcc-ce
Confidence            34677775  669999999 778999999999999999999999999999999999999999999997655543332 46


Q ss_pred             eEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHh-cCCcEEEeCcHHHHHHHhcC-CccccCceeE
Q 043110          112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLR-KGISILVATPGHLLDHLKHT-SSFLHTNLRW  189 (316)
Q Consensus       112 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~IlV~Tp~~l~~~l~~~-~~~~~~~l~~  189 (316)
                      -+|||+||||||.||.+++..+...+..+.+.++.||.+.......+. ++++|+|||||||.+++.+. ..+.+.++.+
T Consensus        81 galIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~  160 (567)
T KOG0345|consen   81 GALIISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEI  160 (567)
T ss_pred             eEEEecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccce
Confidence            799999999999999999999999988888999999988877766654 56899999999999999873 3345669999


Q ss_pred             EEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCC--
Q 043110          190 IIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKF--  267 (316)
Q Consensus       190 lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~--  267 (316)
                      ||+||||+++|+||...++.|++.||+               ++++-+||||....+.++++..|+||+.|.+..++.  
T Consensus       161 LVLDEADrLldmgFe~~~n~ILs~LPK---------------QRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~~~  225 (567)
T KOG0345|consen  161 LVLDEADRLLDMGFEASVNTILSFLPK---------------QRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSKSA  225 (567)
T ss_pred             EEecchHhHhcccHHHHHHHHHHhccc---------------ccccccccchhhHHHHHHHHhhccCceeeeeccccccc
Confidence            999999999999999999999999999               999999999999999999999999999999988775  


Q ss_pred             CCCCCCcccccccchh
Q 043110          268 PEDKSNVHFGSLESDV  283 (316)
Q Consensus       268 ~~~~~~~~~~~~~~~~  283 (316)
                      .|++....|...++++
T Consensus       226 tPS~L~~~Y~v~~a~e  241 (567)
T KOG0345|consen  226 TPSSLALEYLVCEADE  241 (567)
T ss_pred             CchhhcceeeEecHHH
Confidence            5555666666655544

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1.9e-44  Score=319.79  Aligned_cols=230  Identities=33%  Similarity=0.518  Sum_probs=200.6

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      .+|+++||++.+++++ .++||+.||-+|+.+||.+++|+|+++.|.||||||++|++|+++.+...+.......++.++
T Consensus        19 ktFe~~gLD~RllkAi-~~lG~ekpTlIQs~aIplaLEgKDvvarArTGSGKT~AYliPllqkll~~k~t~~~e~~~sa~   97 (569)
T KOG0346|consen   19 KTFEEFGLDSRLLKAI-TKLGWEKPTLIQSSAIPLALEGKDVVARARTGSGKTAAYLIPLLQKLLAEKKTNDGEQGPSAV   97 (569)
T ss_pred             ccHHHhCCCHHHHHHH-HHhCcCCcchhhhcccchhhcCcceeeeeccCCCchHHHHHHHHHHHHHhhhcccccccceeE
Confidence            6899999999999999 678999999999999999999999999999999999999999999998877665667899999


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcC-CceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFR-WIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      |++||+|||.|++.++.++..++. .+....+....+.......+...++|+|+||++++.++.......+..+++||+|
T Consensus        98 iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L~d~pdIvV~TP~~ll~~~~~~~~~~~~~l~~LVvD  177 (569)
T KOG0346|consen   98 ILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVALMDLPDIVVATPAKLLRHLAAGVLEYLDSLSFLVVD  177 (569)
T ss_pred             EEechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHHccCCCeEEeChHHHHHHHhhccchhhhheeeEEec
Confidence            999999999999999999988775 3333334434444455567788899999999999999987555677899999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCCCC
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSN  273 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~~~  273 (316)
                      |||.++..||.+++..+.+.+|.               .+|.++||||+++++..+.+++|++|+.+.+.+++.++...-
T Consensus       178 EADLllsfGYeedlk~l~~~LPr---------------~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~el~~~dqL  242 (569)
T KOG0346|consen  178 EADLLLSFGYEEDLKKLRSHLPR---------------IYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGELPNPDQL  242 (569)
T ss_pred             hhhhhhhcccHHHHHHHHHhCCc---------------hhhheeehhhhhhHHHHHHHHhccCCeEEEeccccCCCcccc
Confidence            99999999999999999999998               899999999999999999999999999999988875544444


Q ss_pred             ccccccc
Q 043110          274 VHFGSLE  280 (316)
Q Consensus       274 ~~~~~~~  280 (316)
                      ++|....
T Consensus       243 ~Qy~v~c  249 (569)
T KOG0346|consen  243 TQYQVKC  249 (569)
T ss_pred             eEEEEEe
Confidence            4444443

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=6.1e-45  Score=330.53  Aligned_cols=213  Identities=37%  Similarity=0.606  Sum_probs=196.2

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ....|++++|+....++| +..+|..||.+|+.+||..+.|+|++..|.||||||++|++|+++.+.+...  ....|.-
T Consensus        67 ~~~kF~dlpls~~t~kgL-ke~~fv~~teiQ~~~Ip~aL~G~DvlGAAkTGSGKTLAFlvPvlE~L~r~kW--s~~DGlG  143 (758)
T KOG0343|consen   67 TIKKFADLPLSQKTLKGL-KEAKFVKMTEIQRDTIPMALQGHDVLGAAKTGSGKTLAFLVPVLEALYRLKW--SPTDGLG  143 (758)
T ss_pred             hhhhHHhCCCchHHHHhH-hhcCCccHHHHHHhhcchhccCcccccccccCCCceeeehHHHHHHHHHcCC--CCCCCce
Confidence            345899999999999999 5569999999999999999999999999999999999999999999987543  2346788


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      ||||+||||||.|+++++.+.+.. .....++++||.+...+..++. +++|+|||||||++|+.....+..+++.+||+
T Consensus       144 alIISPTRELA~QtFevL~kvgk~-h~fSaGLiiGG~~~k~E~eRi~-~mNILVCTPGRLLQHmde~~~f~t~~lQmLvL  221 (758)
T KOG0343|consen  144 ALIISPTRELALQTFEVLNKVGKH-HDFSAGLIIGGKDVKFELERIS-QMNILVCTPGRLLQHMDENPNFSTSNLQMLVL  221 (758)
T ss_pred             eEEecchHHHHHHHHHHHHHHhhc-cccccceeecCchhHHHHHhhh-cCCeEEechHHHHHHhhhcCCCCCCcceEEEe
Confidence            999999999999999999999976 4578899999999888877765 58999999999999999988888899999999


Q ss_pred             ecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          193 DEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       193 DEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                      ||||+++|+||...++.|++.+|.               .+|+++||||-+..+..++++.+.+|++|.+..+
T Consensus       222 DEADR~LDMGFk~tL~~Ii~~lP~---------------~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~  279 (758)
T KOG0343|consen  222 DEADRMLDMGFKKTLNAIIENLPK---------------KRQTLLFSATQTKSVKDLARLSLKDPVYVSVHEN  279 (758)
T ss_pred             ccHHHHHHHhHHHHHHHHHHhCCh---------------hheeeeeecccchhHHHHHHhhcCCCcEEEEecc
Confidence            999999999999999999999998               9999999999999999999999999999998754

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

Probab=100.00  E-value=5.8e-43  Score=333.96  Aligned_cols=226  Identities=40%  Similarity=0.606  Sum_probs=200.2

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      ..|+++++++++++++ .+.||..|||+|.++||.++.|+|++++|+||||||++|++|+++.+.....   ..... +|
T Consensus        29 ~~F~~l~l~~~ll~~l-~~~gf~~pt~IQ~~~IP~~l~g~Dvi~~A~TGsGKT~Af~lP~l~~l~~~~~---~~~~~-aL  103 (513)
T COG0513          29 PEFASLGLSPELLQAL-KDLGFEEPTPIQLAAIPLILAGRDVLGQAQTGTGKTAAFLLPLLQKILKSVE---RKYVS-AL  103 (513)
T ss_pred             CCHhhcCCCHHHHHHH-HHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhcccc---cCCCc-eE
Confidence            6799999999999999 6689999999999999999999999999999999999999999999764311   01111 99


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      |++||||||.|+++.+..++.......+.+++||.+...+...+..+++|||+||||+++++.+. .+.++.++++|+||
T Consensus       104 il~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~~~~ivVaTPGRllD~i~~~-~l~l~~v~~lVlDE  182 (513)
T COG0513         104 ILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKRGVDIVVATPGRLLDLIKRG-KLDLSGVETLVLDE  182 (513)
T ss_pred             EECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhcCCCEEEECccHHHHHHHcC-CcchhhcCEEEecc
Confidence            99999999999999999999876456788999999999999999989999999999999999984 77889999999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCC--CCCCC
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKF--PEDKS  272 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~--~~~~~  272 (316)
                      ||+|+++||.+++..|+..++.               .+|+++||||+|+.+..+++.++++|+.|.+..+..  .....
T Consensus       183 ADrmLd~Gf~~~i~~I~~~~p~---------------~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~~~~~~~i  247 (513)
T COG0513         183 ADRMLDMGFIDDIEKILKALPP---------------DRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKLERTLKKI  247 (513)
T ss_pred             HhhhhcCCCHHHHHHHHHhCCc---------------ccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccccccccCc
Confidence            9999999999999999999987               899999999999999999999999999998885554  45555


Q ss_pred             Ccccccccc
Q 043110          273 NVHFGSLES  281 (316)
Q Consensus       273 ~~~~~~~~~  281 (316)
                      .+.+..++.
T Consensus       248 ~q~~~~v~~  256 (513)
T COG0513         248 KQFYLEVES  256 (513)
T ss_pred             eEEEEEeCC
Confidence            555555554

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

Probab=100.00  E-value=3.4e-43  Score=315.86  Aligned_cols=218  Identities=42%  Similarity=0.675  Sum_probs=203.7

Q ss_pred             ccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCC
Q 043110           31 IFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSG  110 (316)
Q Consensus        31 ~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~  110 (316)
                      +.....|++..|++...+++ +++||..+|++|+.+||.++.|+|+++.|.||+|||+||++|+++.+.+..+...  ++
T Consensus        78 ~~~~~~f~~~~LS~~t~kAi-~~~GF~~MT~VQ~~ti~pll~gkDvl~~AKTGtGKTlAFLiPaie~l~k~~~~~r--~~  154 (543)
T KOG0342|consen   78 ITTTFRFEEGSLSPLTLKAI-KEMGFETMTPVQQKTIPPLLEGKDVLAAAKTGTGKTLAFLLPAIELLRKLKFKPR--NG  154 (543)
T ss_pred             hhhhhHhhccccCHHHHHHH-HhcCccchhHHHHhhcCccCCCccceeeeccCCCceeeehhHHHHHHHhcccCCC--CC
Confidence            44556789999999999999 8899999999999999999999999999999999999999999999988666533  68


Q ss_pred             eeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEE
Q 043110          111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWI  190 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~l  190 (316)
                      ..+||+|||||||.|++.+++.+..+.....+.+++||.+...+.+++.++++|+|+|||||.+|+.+...+...+++++
T Consensus       155 ~~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k~~niliATPGRLlDHlqNt~~f~~r~~k~l  234 (543)
T KOG0342|consen  155 TGVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVKGCNILIATPGRLLDHLQNTSGFLFRNLKCL  234 (543)
T ss_pred             eeEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhccccEEEeCCchHHhHhhcCCcchhhcccee
Confidence            88999999999999999999999988767888999999999999999999999999999999999999988888889999


Q ss_pred             EEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcC-CCEEEEcCCCC
Q 043110          191 IFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLE-TPVLIGLDEKK  266 (316)
Q Consensus       191 ViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~-~p~~i~~~~~~  266 (316)
                      |+||||++++.||+.+++.|++.+|+               .+|+++||||.|+.|+++++..|. +|++|.+.+..
T Consensus       235 vlDEADrlLd~GF~~di~~Ii~~lpk---------------~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~  296 (543)
T KOG0342|consen  235 VLDEADRLLDIGFEEDVEQIIKILPK---------------QRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGG  296 (543)
T ss_pred             EeecchhhhhcccHHHHHHHHHhccc---------------cceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCC
Confidence            99999999999999999999999998               999999999999999999998887 59999988776

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=2.3e-39  Score=304.66  Aligned_cols=220  Identities=31%  Similarity=0.483  Sum_probs=192.5

Q ss_pred             cccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCC-CCCCC
Q 043110           32 FASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRI-DRSSG  110 (316)
Q Consensus        32 ~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~-~~~~~  110 (316)
                      ....+|++++|+++++++| +++||..|+|+|++|||.+++|+|++++||||||||++|++|+++.+....... ....+
T Consensus         5 ~~~~~f~~~~l~~~l~~~l-~~~g~~~pt~iQ~~aip~il~g~dvi~~ApTGsGKTla~llp~l~~l~~~~~~~~~~~~~   83 (423)
T PRK04837          5 LTEQKFSDFALHPQVVEAL-EKKGFHNCTPIQALALPLTLAGRDVAGQAQTGTGKTMAFLTATFHYLLSHPAPEDRKVNQ   83 (423)
T ss_pred             CCCCCHhhCCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCcEEEECCCCchHHHHHHHHHHHHHHhcccccccccCC
Confidence            3457899999999999999 778999999999999999999999999999999999999999999987643321 12346


Q ss_pred             eeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEE
Q 043110          111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWI  190 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~l  190 (316)
                      +++|||+||+|||.|+++.+..++...+ ..+..++||.....+...+..+++|+|+||++|.+++.. ..+.+++++++
T Consensus        84 ~~~lil~PtreLa~Qi~~~~~~l~~~~~-~~v~~~~gg~~~~~~~~~l~~~~~IlV~TP~~l~~~l~~-~~~~l~~v~~l  161 (423)
T PRK04837         84 PRALIMAPTRELAVQIHADAEPLAQATG-LKLGLAYGGDGYDKQLKVLESGVDILIGTTGRLIDYAKQ-NHINLGAIQVV  161 (423)
T ss_pred             ceEEEECCcHHHHHHHHHHHHHHhccCC-ceEEEEECCCCHHHHHHHhcCCCCEEEECHHHHHHHHHc-CCcccccccEE
Confidence            8899999999999999999999987654 566777888888888888888899999999999999976 55677899999


Q ss_pred             EEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCC
Q 043110          191 IFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKF  267 (316)
Q Consensus       191 ViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~  267 (316)
                      |+||||++++++|..++..+++.++...             .+|.+++|||++..+..++..++.+|..+.+.....
T Consensus       162 ViDEad~l~~~~f~~~i~~i~~~~~~~~-------------~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~~~  225 (423)
T PRK04837        162 VLDEADRMFDLGFIKDIRWLFRRMPPAN-------------QRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPEQK  225 (423)
T ss_pred             EEecHHHHhhcccHHHHHHHHHhCCCcc-------------ceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCCCc
Confidence            9999999999999999999999887521             578899999999999999999999999998776543

>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=6e-41  Score=282.62  Aligned_cols=234  Identities=30%  Similarity=0.479  Sum_probs=210.8

Q ss_pred             cccccccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCC
Q 043110           26 ETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRI  105 (316)
Q Consensus        26 ~~~~~~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~  105 (316)
                      ++.+++.-..+|+++||.+++++++ -..||++|+.+|+.|+|.++.|+|++++|++|+|||.+|.+.+++.+.-.    
T Consensus        18 eTs~~~~v~~~F~~Mgl~edlLrgi-Y~yGfekPS~IQqrAi~~IlkGrdViaQaqSGTGKTa~~si~vlq~~d~~----   92 (400)
T KOG0328|consen   18 ETSEKVKVIPTFDDMGLKEDLLRGI-YAYGFEKPSAIQQRAIPQILKGRDVIAQAQSGTGKTATFSISVLQSLDIS----   92 (400)
T ss_pred             eeccCcccccchhhcCchHHHHHHH-HHhccCCchHHHhhhhhhhhcccceEEEecCCCCceEEEEeeeeeecccc----
Confidence            3445667778999999999999999 66799999999999999999999999999999999999988888776542    


Q ss_pred             CCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccC
Q 043110          106 DRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHT  185 (316)
Q Consensus       106 ~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~  185 (316)
                        ....+++|++|||||+.|+.+.+..++.+++ +.+..+.||.+..+....+.-+.+++.||||+++++++. ..+.-+
T Consensus        93 --~r~tQ~lilsPTRELa~Qi~~vi~alg~~mn-vq~hacigg~n~gedikkld~G~hvVsGtPGrv~dmikr-~~L~tr  168 (400)
T KOG0328|consen   93 --VRETQALILSPTRELAVQIQKVILALGDYMN-VQCHACIGGKNLGEDIKKLDYGQHVVSGTPGRVLDMIKR-RSLRTR  168 (400)
T ss_pred             --cceeeEEEecChHHHHHHHHHHHHHhccccc-ceEEEEecCCccchhhhhhcccceEeeCCCchHHHHHHh-cccccc
Confidence              2357799999999999999999999998765 777788899999999999999999999999999999987 455557


Q ss_pred             ceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          186 NLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                      .++++|+||||.|++.||..++-.+++.+|.               ..|++++|||+|.++.+..+.|+.+|+.|-+..+
T Consensus       169 ~vkmlVLDEaDemL~kgfk~Qiydiyr~lp~---------------~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrd  233 (400)
T KOG0328|consen  169 AVKMLVLDEADEMLNKGFKEQIYDIYRYLPP---------------GAQVVLVSATLPHEILEMTEKFMTDPVRILVKRD  233 (400)
T ss_pred             ceeEEEeccHHHHHHhhHHHHHHHHHHhCCC---------------CceEEEEeccCcHHHHHHHHHhcCCceeEEEecC
Confidence            8999999999999999999999999999998               8999999999999999999999999999999999


Q ss_pred             CCCCCCCCcccccccchh
Q 043110          266 KFPEDKSNVHFGSLESDV  283 (316)
Q Consensus       266 ~~~~~~~~~~~~~~~~~~  283 (316)
                      +.+.....+.|+.++.++
T Consensus       234 eltlEgIKqf~v~ve~Ee  251 (400)
T KOG0328|consen  234 ELTLEGIKQFFVAVEKEE  251 (400)
T ss_pred             CCchhhhhhheeeechhh
Confidence            988888888888877544

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=3e-39  Score=306.08  Aligned_cols=227  Identities=34%  Similarity=0.571  Sum_probs=194.3

Q ss_pred             CcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEE
Q 043110           36 CFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALV  115 (316)
Q Consensus        36 ~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~li  115 (316)
                      +|++++|++++.+.| .++||..||++|+++||.+++|+|++++||||||||++|++|+++.+............+++||
T Consensus         2 ~f~~l~l~~~l~~~l-~~~g~~~pt~iQ~~ai~~il~g~dvlv~apTGsGKTla~~lpil~~l~~~~~~~~~~~~~~aLi   80 (456)
T PRK10590          2 SFDSLGLSPDILRAV-AEQGYREPTPIQQQAIPAVLEGRDLMASAQTGTGKTAGFTLPLLQHLITRQPHAKGRRPVRALI   80 (456)
T ss_pred             CHHHcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHhhhcccccccCCCceEEE
Confidence            699999999999999 6789999999999999999999999999999999999999999999876433222234568999


Q ss_pred             EeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecc
Q 043110          116 LVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEA  195 (316)
Q Consensus       116 l~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEa  195 (316)
                      |+||++||.|+++.++.+..... .....++||.....+...+..+++|+|+||++|++++.. ....++++++||||||
T Consensus        81 l~PtreLa~Qi~~~~~~~~~~~~-~~~~~~~gg~~~~~~~~~l~~~~~IiV~TP~rL~~~~~~-~~~~l~~v~~lViDEa  158 (456)
T PRK10590         81 LTPTRELAAQIGENVRDYSKYLN-IRSLVVFGGVSINPQMMKLRGGVDVLVATPGRLLDLEHQ-NAVKLDQVEILVLDEA  158 (456)
T ss_pred             EeCcHHHHHHHHHHHHHHhccCC-CEEEEEECCcCHHHHHHHHcCCCcEEEEChHHHHHHHHc-CCcccccceEEEeecH
Confidence            99999999999999999887654 566677888888888888888899999999999998876 4556789999999999


Q ss_pred             hhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCCCCcc
Q 043110          196 DRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNVH  275 (316)
Q Consensus       196 d~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~~~~~  275 (316)
                      |++++++|...+..++..++.               .+|++++|||+++.+..++..++.+|..+.+.............
T Consensus       159 h~ll~~~~~~~i~~il~~l~~---------------~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~i~~~  223 (456)
T PRK10590        159 DRMLDMGFIHDIRRVLAKLPA---------------KRQNLLFSATFSDDIKALAEKLLHNPLEIEVARRNTASEQVTQH  223 (456)
T ss_pred             HHHhccccHHHHHHHHHhCCc---------------cCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEecccccccceeEE
Confidence            999999999999999999887               78999999999999999999999999988876554443333334


Q ss_pred             ccccc
Q 043110          276 FGSLE  280 (316)
Q Consensus       276 ~~~~~  280 (316)
                      +...+
T Consensus       224 ~~~~~  228 (456)
T PRK10590        224 VHFVD  228 (456)
T ss_pred             EEEcC
Confidence            43333

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

Probab=100.00  E-value=9.3e-40  Score=294.27  Aligned_cols=228  Identities=32%  Similarity=0.543  Sum_probs=203.7

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ..++|+.+|+++.+..++ .+..|..|||+|.+++|..+.|+|++..|.||||||.+|+.|++.++..+. ....+.|+.
T Consensus       221 pvtsfeh~gfDkqLm~ai-rk~Ey~kptpiq~qalptalsgrdvigIAktgSgktaAfi~pm~~himdq~-eL~~g~gPi  298 (731)
T KOG0339|consen  221 PVTSFEHFGFDKQLMTAI-RKSEYEKPTPIQCQALPTALSGRDVIGIAKTGSGKTAAFIWPMIVHIMDQP-ELKPGEGPI  298 (731)
T ss_pred             CcchhhhcCchHHHHHHH-hhhhcccCCcccccccccccccccchheeeccCcchhHHHHHHHHHhcchh-hhcCCCCCe
Confidence            446899999999999999 556999999999999999999999999999999999999999999997644 345678999


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      +||++||||||.|++..++++++.++ +.+.+++||.....+...|..++.|||||||||.+++.. +...+.++.+||+
T Consensus       299 ~vilvPTrela~Qi~~eaKkf~K~yg-l~~v~~ygGgsk~eQ~k~Lk~g~EivVaTPgRlid~Vkm-Katn~~rvS~LV~  376 (731)
T KOG0339|consen  299 GVILVPTRELASQIFSEAKKFGKAYG-LRVVAVYGGGSKWEQSKELKEGAEIVVATPGRLIDMVKM-KATNLSRVSYLVL  376 (731)
T ss_pred             EEEEeccHHHHHHHHHHHHHhhhhcc-ceEEEeecCCcHHHHHHhhhcCCeEEEechHHHHHHHHh-hcccceeeeEEEE
Confidence            99999999999999999999998776 777888999999999999999999999999999999987 6777789999999


Q ss_pred             ecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCCC
Q 043110          193 DEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKS  272 (316)
Q Consensus       193 DEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~~  272 (316)
                      ||||+|+++||.++++.|...+..               .+|+++||||++..+..+++.+|.+|+.|...+-......+
T Consensus       377 DEadrmfdmGfe~qVrSI~~hirp---------------drQtllFsaTf~~kIe~lard~L~dpVrvVqg~vgean~dI  441 (731)
T KOG0339|consen  377 DEADRMFDMGFEPQVRSIKQHIRP---------------DRQTLLFSATFKKKIEKLARDILSDPVRVVQGEVGEANEDI  441 (731)
T ss_pred             echhhhhccccHHHHHHHHhhcCC---------------cceEEEeeccchHHHHHHHHHHhcCCeeEEEeehhccccch
Confidence            999999999999999999999987               99999999999999999999999999988877554444433


Q ss_pred             Cccccccc
Q 043110          273 NVHFGSLE  280 (316)
Q Consensus       273 ~~~~~~~~  280 (316)
                       .+.+.+.
T Consensus       442 -TQ~V~V~  448 (731)
T KOG0339|consen  442 -TQTVSVC  448 (731)
T ss_pred             -hheeeec
Confidence             3334343

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=6.5e-39  Score=308.72  Aligned_cols=214  Identities=32%  Similarity=0.525  Sum_probs=189.1

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      ..+|+++++++.+++.| .++||.+|||+|.++||.+++|+|++++||||||||++|++|++.++..... .....++++
T Consensus       129 ~~~f~~~~l~~~l~~~l-~~~g~~~pt~iQ~~aip~~l~G~dvI~~ApTGSGKTlaylLP~l~~i~~~~~-~~~~~gp~~  206 (545)
T PTZ00110        129 VVSFEYTSFPDYILKSL-KNAGFTEPTPIQVQGWPIALSGRDMIGIAETGSGKTLAFLLPAIVHINAQPL-LRYGDGPIV  206 (545)
T ss_pred             cCCHhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhcCCCEEEEeCCCChHHHHHHHHHHHHHHhccc-ccCCCCcEE
Confidence            45899999999999999 7789999999999999999999999999999999999999999988865322 223457889


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      |||+||+|||.|+++.++.++.... +...+.+||.....+...+..+++|+|+||++|.+++.. ....+.++++||||
T Consensus       207 LIL~PTreLa~Qi~~~~~~~~~~~~-i~~~~~~gg~~~~~q~~~l~~~~~IlVaTPgrL~d~l~~-~~~~l~~v~~lViD  284 (545)
T PTZ00110        207 LVLAPTRELAEQIREQCNKFGASSK-IRNTVAYGGVPKRGQIYALRRGVEILIACPGRLIDFLES-NVTNLRRVTYLVLD  284 (545)
T ss_pred             EEECChHHHHHHHHHHHHHHhcccC-ccEEEEeCCCCHHHHHHHHHcCCCEEEECHHHHHHHHHc-CCCChhhCcEEEee
Confidence            9999999999999999999987643 566778889888888888889999999999999999986 45567899999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcC-CCEEEEcCCCC
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLE-TPVLIGLDEKK  266 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~-~p~~i~~~~~~  266 (316)
                      |||+|++++|...+..|+..++.               .+|++++|||+|+.+..+++.++. +|+.+.+....
T Consensus       285 EAd~mld~gf~~~i~~il~~~~~---------------~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~  343 (545)
T PTZ00110        285 EADRMLDMGFEPQIRKIVSQIRP---------------DRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLD  343 (545)
T ss_pred             hHHhhhhcchHHHHHHHHHhCCC---------------CCeEEEEEeCCCHHHHHHHHHHhccCCEEEEECCCc
Confidence            99999999999999999998876               889999999999999999998885 68888776543

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=8.2e-39  Score=311.09  Aligned_cols=220  Identities=33%  Similarity=0.536  Sum_probs=194.7

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      .+|++++|++.++++| .++||.+|+|+|.++||.++.|+|++++||||+|||++|++|+++.+...      ..++++|
T Consensus         6 ~~f~~l~L~~~ll~al-~~~G~~~ptpiQ~~ai~~ll~g~dvl~~ApTGsGKT~af~lpll~~l~~~------~~~~~~L   78 (629)
T PRK11634          6 TTFADLGLKAPILEAL-NDLGYEKPSPIQAECIPHLLNGRDVLGMAQTGSGKTAAFSLPLLHNLDPE------LKAPQIL   78 (629)
T ss_pred             CCHhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHHHhhhc------cCCCeEE
Confidence            4699999999999999 77899999999999999999999999999999999999999999987542      2356799


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      ||+||++||.|+++.+..+........+..++||.....+...+..+++|+|+||+++++++.. ..+.++++++|||||
T Consensus        79 IL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l~~~~~IVVgTPgrl~d~l~r-~~l~l~~l~~lVlDE  157 (629)
T PRK11634         79 VLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQGPQIVVGTPGRLLDHLKR-GTLDLSKLSGLVLDE  157 (629)
T ss_pred             EEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHhcCCCCEEEECHHHHHHHHHc-CCcchhhceEEEecc
Confidence            9999999999999999999877666777888899988888888888999999999999999986 556678999999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCCCCc
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNV  274 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~~~~  274 (316)
                      ||.|++++|..++..++..++.               .+|+++||||+|+.+..+.+.++.+|..|.+...........+
T Consensus       158 Ad~ml~~gf~~di~~Il~~lp~---------------~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~~~~~~~i~q  222 (629)
T PRK11634        158 ADEMLRMGFIEDVETIMAQIPE---------------GHQTALFSATMPEAIRRITRRFMKEPQEVRIQSSVTTRPDISQ  222 (629)
T ss_pred             HHHHhhcccHHHHHHHHHhCCC---------------CCeEEEEEccCChhHHHHHHHHcCCCeEEEccCccccCCceEE
Confidence            9999999999999999999987               8899999999999999999999999999887766544333333


Q ss_pred             ccc
Q 043110          275 HFG  277 (316)
Q Consensus       275 ~~~  277 (316)
                      .+.
T Consensus       223 ~~~  225 (629)
T PRK11634        223 SYW  225 (629)
T ss_pred             EEE
Confidence            333

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

Probab=100.00  E-value=1.1e-38  Score=305.96  Aligned_cols=218  Identities=34%  Similarity=0.552  Sum_probs=190.1

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCC-CCCCCCe
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPR-IDRSSGT  111 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~-~~~~~~~  111 (316)
                      ...+|++++|++.+++.| .+.||..|||+|.++||.++.|+|+++.||||||||++|++|++.++...... .....++
T Consensus       119 pi~~f~~~~l~~~l~~~L-~~~g~~~ptpiQ~~aip~il~g~dviv~ApTGSGKTlayllPil~~l~~~~~~~~~~~~~~  197 (518)
T PLN00206        119 PILSFSSCGLPPKLLLNL-ETAGYEFPTPIQMQAIPAALSGRSLLVSADTGSGKTASFLVPIISRCCTIRSGHPSEQRNP  197 (518)
T ss_pred             hhcCHHhCCCCHHHHHHH-HHcCCCCCCHHHHHHHHHHhcCCCEEEEecCCCCccHHHHHHHHHHHHhhccccccccCCc
Confidence            345799999999999999 67899999999999999999999999999999999999999999988653221 1223578


Q ss_pred             eEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEE
Q 043110          112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWII  191 (316)
Q Consensus       112 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lV  191 (316)
                      ++|||+||||||.|+++.++.+....+ .....+.||.....+...+..+++|+|+||++|.+++.. ....++++++||
T Consensus       198 ~aLIL~PTreLa~Qi~~~~~~l~~~~~-~~~~~~~gG~~~~~q~~~l~~~~~IiV~TPgrL~~~l~~-~~~~l~~v~~lV  275 (518)
T PLN00206        198 LAMVLTPTRELCVQVEDQAKVLGKGLP-FKTALVVGGDAMPQQLYRIQQGVELIVGTPGRLIDLLSK-HDIELDNVSVLV  275 (518)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhCCCC-ceEEEEECCcchHHHHHHhcCCCCEEEECHHHHHHHHHc-CCccchheeEEE
Confidence            999999999999999999998876654 556677888888888888888999999999999999987 466778999999


Q ss_pred             EecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCC
Q 043110          192 FDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPE  269 (316)
Q Consensus       192 iDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~  269 (316)
                      +||||+|++++|...+..++..++                .+|++++|||+++.+..+++.++.+|+.|.+.......
T Consensus       276 iDEad~ml~~gf~~~i~~i~~~l~----------------~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~~~~~  337 (518)
T PLN00206        276 LDEVDCMLERGFRDQVMQIFQALS----------------QPQVLLFSATVSPEVEKFASSLAKDIILISIGNPNRPN  337 (518)
T ss_pred             eecHHHHhhcchHHHHHHHHHhCC----------------CCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCCCCCC
Confidence            999999999999999999998875                67999999999999999999999999999887665433

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=1.1e-38  Score=303.10  Aligned_cols=209  Identities=34%  Similarity=0.515  Sum_probs=190.5

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      .+|++++|++.+.++| .++||.+|||+|++|||.+++|+|++++||||||||++|++|+++.+...      ..++++|
T Consensus         4 ~~f~~l~l~~~l~~~l-~~~g~~~~t~iQ~~ai~~~l~g~dvi~~a~TGsGKT~a~~lpil~~l~~~------~~~~~~l   76 (460)
T PRK11776          4 TAFSTLPLPPALLANL-NELGYTEMTPIQAQSLPAILAGKDVIAQAKTGSGKTAAFGLGLLQKLDVK------RFRVQAL   76 (460)
T ss_pred             CChhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHhhhc------cCCceEE
Confidence            5799999999999999 77899999999999999999999999999999999999999999988542      2356799


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      |++||++||.|+.+.++.++.......+..++||.+...+...+..+++|+|+||+++.+++.. ....++++++||+||
T Consensus        77 il~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~~~~~IvV~Tp~rl~~~l~~-~~~~l~~l~~lViDE  155 (460)
T PRK11776         77 VLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLEHGAHIIVGTPGRILDHLRK-GTLDLDALNTLVLDE  155 (460)
T ss_pred             EEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhcCCCCEEEEChHHHHHHHHc-CCccHHHCCEEEEEC
Confidence            9999999999999999999876656777788899999888888888999999999999999986 456678999999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCC
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK  266 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~  266 (316)
                      ||+|++++|...+..++..++.               .+|+++||||+|+.+..++..++.+|..+.+....
T Consensus       156 ad~~l~~g~~~~l~~i~~~~~~---------------~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~~  212 (460)
T PRK11776        156 ADRMLDMGFQDAIDAIIRQAPA---------------RRQTLLFSATYPEGIAAISQRFQRDPVEVKVESTH  212 (460)
T ss_pred             HHHHhCcCcHHHHHHHHHhCCc---------------ccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcCC
Confidence            9999999999999999999987               88999999999999999999999999999887654

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

Probab=100.00  E-value=9.3e-41  Score=285.80  Aligned_cols=224  Identities=30%  Similarity=0.458  Sum_probs=199.7

Q ss_pred             cccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCe
Q 043110           32 FASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT  111 (316)
Q Consensus        32 ~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~  111 (316)
                      .....|++++|..+++..+ -..||++|+|+|.++||.++.|+|+++.|..|+|||.+|++|+++.+...      ....
T Consensus        82 TkG~efEd~~Lkr~LLmgI-fe~G~ekPSPiQeesIPiaLtGrdiLaRaKNGTGKT~a~~IP~Lekid~~------~~~I  154 (459)
T KOG0326|consen   82 TKGNEFEDYCLKRELLMGI-FEKGFEKPSPIQEESIPIALTGRDILARAKNGTGKTAAYCIPVLEKIDPK------KNVI  154 (459)
T ss_pred             ccCccHHHhhhhHHHHHHH-HHhccCCCCCccccccceeecchhhhhhccCCCCCccceechhhhhcCcc------ccce
Confidence            4557899999999999999 55699999999999999999999999999999999999999999988653      3467


Q ss_pred             eEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEE
Q 043110          112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWII  191 (316)
Q Consensus       112 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lV  191 (316)
                      +++|++||||||.|+.+.++.+++.++ +.+....||++..+..-++...++++|+||||++++... +.-.++++.++|
T Consensus       155 Q~~ilVPtrelALQtSqvc~~lskh~~-i~vmvttGGT~lrDDI~Rl~~~VH~~vgTPGRIlDL~~K-gVa~ls~c~~lV  232 (459)
T KOG0326|consen  155 QAIILVPTRELALQTSQVCKELSKHLG-IKVMVTTGGTSLRDDIMRLNQTVHLVVGTPGRILDLAKK-GVADLSDCVILV  232 (459)
T ss_pred             eEEEEeecchhhHHHHHHHHHHhcccC-eEEEEecCCcccccceeeecCceEEEEcCChhHHHHHhc-ccccchhceEEE
Confidence            799999999999999999999999877 777888899999999999999999999999999999986 556778999999


Q ss_pred             EecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCC
Q 043110          192 FDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDK  271 (316)
Q Consensus       192 iDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~  271 (316)
                      +||||.|++..|.+.++.++..+|+               .+|++++|||+|-.|..|...+|++|..|.+-++ .....
T Consensus       233 ~DEADKlLs~~F~~~~e~li~~lP~---------------~rQillySATFP~tVk~Fm~~~l~kPy~INLM~e-Ltl~G  296 (459)
T KOG0326|consen  233 MDEADKLLSVDFQPIVEKLISFLPK---------------ERQILLYSATFPLTVKGFMDRHLKKPYEINLMEE-LTLKG  296 (459)
T ss_pred             echhhhhhchhhhhHHHHHHHhCCc---------------cceeeEEecccchhHHHHHHHhccCcceeehhhh-hhhcc
Confidence            9999999999999999999999999               9999999999999999999999999999987654 33334


Q ss_pred             CCccccccc
Q 043110          272 SNVHFGSLE  280 (316)
Q Consensus       272 ~~~~~~~~~  280 (316)
                      ..++|..++
T Consensus       297 vtQyYafV~  305 (459)
T KOG0326|consen  297 VTQYYAFVE  305 (459)
T ss_pred             hhhheeeec
Confidence            444444443

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

Probab=100.00  E-value=5.8e-40  Score=284.41  Aligned_cols=230  Identities=35%  Similarity=0.507  Sum_probs=200.0

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      .-..|+.+||++|+.+.| +.+|+..|||+|+.|||.|+.|+|++.+|.||||||.+|.+|+++.+..      ..+|.+
T Consensus         5 t~~~F~~LGl~~Wlve~l-~~l~i~~pTpiQ~~cIpkILeGrdcig~AkTGsGKT~AFaLPil~rLse------dP~giF   77 (442)
T KOG0340|consen    5 TAKPFSILGLSPWLVEQL-KALGIKKPTPIQQACIPKILEGRDCIGCAKTGSGKTAAFALPILNRLSE------DPYGIF   77 (442)
T ss_pred             ccCchhhcCccHHHHHHH-HHhcCCCCCchHhhhhHHHhcccccccccccCCCcchhhhHHHHHhhcc------CCCcce
Confidence            346899999999999999 7899999999999999999999999999999999999999999999976      246889


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcC---CccccCceeE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHT---SSFLHTNLRW  189 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~---~~~~~~~l~~  189 (316)
                      ++|++|||||+-|+.+.+..++... ...+++++||.+.-.+...+...+|++|+|||++.+++.+.   ....+..+++
T Consensus        78 alvlTPTrELA~QiaEQF~alGk~l-~lK~~vivGG~d~i~qa~~L~~rPHvVvatPGRlad~l~sn~~~~~~~~~rlkf  156 (442)
T KOG0340|consen   78 ALVLTPTRELALQIAEQFIALGKLL-NLKVSVIVGGTDMIMQAAILSDRPHVVVATPGRLADHLSSNLGVCSWIFQRLKF  156 (442)
T ss_pred             EEEecchHHHHHHHHHHHHHhcccc-cceEEEEEccHHHhhhhhhcccCCCeEecCccccccccccCCccchhhhhceee
Confidence            9999999999999999999888764 58889999999999999999999999999999999999876   3446789999


Q ss_pred             EEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCC--CEEEEcCCCCC
Q 043110          190 IIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLET--PVLIGLDEKKF  267 (316)
Q Consensus       190 lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~--p~~i~~~~~~~  267 (316)
                      +|+||||++++..|.+.++.+.+.+|.               .+|+++||||+++.+..+..-....  +..+...++..
T Consensus       157 lVlDEADrvL~~~f~d~L~~i~e~lP~---------------~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~vs  221 (442)
T KOG0340|consen  157 LVLDEADRVLAGCFPDILEGIEECLPK---------------PRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDGVS  221 (442)
T ss_pred             EEecchhhhhccchhhHHhhhhccCCC---------------ccceEEEEeehhhHHHHhhcCCcccccceEEeccCCCC
Confidence            999999999999999999999999998               8999999999999999987766654  44555544544


Q ss_pred             CCCCCCcccccccchhhh
Q 043110          268 PEDKSNVHFGSLESDVKE  285 (316)
Q Consensus       268 ~~~~~~~~~~~~~~~~~~  285 (316)
                      .++...+.|..++.++++
T Consensus       222 tvetL~q~yI~~~~~vkd  239 (442)
T KOG0340|consen  222 TVETLYQGYILVSIDVKD  239 (442)
T ss_pred             chhhhhhheeecchhhhH
Confidence            555555566666655544

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

Probab=100.00  E-value=7.6e-40  Score=288.32  Aligned_cols=216  Identities=33%  Similarity=0.562  Sum_probs=196.3

Q ss_pred             cccCCccc-CCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCC
Q 043110           32 FASCCFSS-LGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSG  110 (316)
Q Consensus        32 ~~~~~f~~-~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~  110 (316)
                      ...++|++ ++-.+++++.+ ++.||.+|+|+|++|||.+++|+|++..|+||+|||++|++|.+-++..+........+
T Consensus       216 nP~ctFddAFq~~pevmenI-kK~GFqKPtPIqSQaWPI~LQG~DliGVAQTgtgKtL~~L~pg~ihi~aqp~~~~qr~~  294 (629)
T KOG0336|consen  216 NPVCTFDDAFQCYPEVMENI-KKTGFQKPTPIQSQAWPILLQGIDLIGVAQTGTGKTLAFLLPGFIHIDAQPKRREQRNG  294 (629)
T ss_pred             CCcCcHHHHHhhhHHHHHHH-HhccCCCCCcchhcccceeecCcceEEEEecCCCcCHHHhccceeeeeccchhhhccCC
Confidence            35578875 47899999999 77899999999999999999999999999999999999999999888877776667788


Q ss_pred             eeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEE
Q 043110          111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWI  190 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~l  190 (316)
                      +.+|+++|||+|+.|+.-.+.+..  +...+..|++||.+...+.+.+.++.+|+++||++|.++... +.+.+..+.+|
T Consensus       295 p~~lvl~ptreLalqie~e~~kys--yng~ksvc~ygggnR~eqie~lkrgveiiiatPgrlndL~~~-n~i~l~siTYl  371 (629)
T KOG0336|consen  295 PGVLVLTPTRELALQIEGEVKKYS--YNGLKSVCVYGGGNRNEQIEDLKRGVEIIIATPGRLNDLQMD-NVINLASITYL  371 (629)
T ss_pred             CceEEEeccHHHHHHHHhHHhHhh--hcCcceEEEecCCCchhHHHHHhcCceEEeeCCchHhhhhhc-CeeeeeeeEEE
Confidence            999999999999999988777664  456788899999999999999999999999999999998776 67788999999


Q ss_pred             EEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCC
Q 043110          191 IFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK  266 (316)
Q Consensus       191 ViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~  266 (316)
                      |+||||+|+|+||.++++.|+-.+..               .+|+++.|||+|+.|..++..++++|+.+.+..-.
T Consensus       372 VlDEADrMLDMgFEpqIrkilldiRP---------------DRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLd  432 (629)
T KOG0336|consen  372 VLDEADRMLDMGFEPQIRKILLDIRP---------------DRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLD  432 (629)
T ss_pred             EecchhhhhcccccHHHHHHhhhcCC---------------cceeeeecccCchHHHHHHHHhhhCceEEEecccc
Confidence            99999999999999999999988876               99999999999999999999999999988776654

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.9e-38  Score=306.58  Aligned_cols=221  Identities=33%  Similarity=0.495  Sum_probs=191.8

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCC-CCCCCeeE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRI-DRSSGTFA  113 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~-~~~~~~~~  113 (316)
                      .+|++++|++.+++.| +++||..|||+|.++||.+++|+|++++||||||||++|++|+++.+....... ....++++
T Consensus         9 ~~f~~l~l~~~l~~~L-~~~g~~~ptpiQ~~~ip~~l~G~Dvi~~ApTGSGKTlafllpil~~l~~~~~~~~~~~~~~ra   87 (572)
T PRK04537          9 LTFSSFDLHPALLAGL-ESAGFTRCTPIQALTLPVALPGGDVAGQAQTGTGKTLAFLVAVMNRLLSRPALADRKPEDPRA   87 (572)
T ss_pred             CChhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCcHHHHHHHHHHHHHHhcccccccccCCceE
Confidence            4799999999999999 778999999999999999999999999999999999999999999886532211 12235789


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      |||+||+|||.|+++.+..++...+ +.+..++||.....+...+..+++|+|+||++|++++.....+.+..+++||||
T Consensus        88 LIl~PTreLa~Qi~~~~~~l~~~~~-i~v~~l~Gg~~~~~q~~~l~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~lViD  166 (572)
T PRK04537         88 LILAPTRELAIQIHKDAVKFGADLG-LRFALVYGGVDYDKQRELLQQGVDVIIATPGRLIDYVKQHKVVSLHACEICVLD  166 (572)
T ss_pred             EEEeCcHHHHHHHHHHHHHHhccCC-ceEEEEECCCCHHHHHHHHhCCCCEEEECHHHHHHHHHhccccchhheeeeEec
Confidence            9999999999999999999987654 667788899988888888888899999999999999987556677889999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCC
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPED  270 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~  270 (316)
                      |||+|++++|...+..++..++...             .+|+++||||++..+..+...++.+|..+.+........
T Consensus       167 EAh~lld~gf~~~i~~il~~lp~~~-------------~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~~~~~~  230 (572)
T PRK04537        167 EADRMFDLGFIKDIRFLLRRMPERG-------------TRQTLLFSATLSHRVLELAYEHMNEPEKLVVETETITAA  230 (572)
T ss_pred             CHHHHhhcchHHHHHHHHHhccccc-------------CceEEEEeCCccHHHHHHHHHHhcCCcEEEecccccccc
Confidence            9999999999999999999987522             579999999999999999999999998877766554433

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

Probab=100.00  E-value=3.3e-38  Score=285.35  Aligned_cols=243  Identities=28%  Similarity=0.480  Sum_probs=210.8

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCC---CCCCCCe
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPR---IDRSSGT  111 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~---~~~~~~~  111 (316)
                      .+|++.+++.++++.+ .+.||..|+|+|..+||..++.+|+|..|.||||||++|++|++..+.+..+.   .+...|+
T Consensus       245 rnwEE~~~P~e~l~~I-~~~~y~eptpIqR~aipl~lQ~rD~igvaETgsGktaaf~ipLl~~IsslP~~~~~en~~~gp  323 (673)
T KOG0333|consen  245 RNWEESGFPLELLSVI-KKPGYKEPTPIQRQAIPLGLQNRDPIGVAETGSGKTAAFLIPLLIWISSLPPMARLENNIEGP  323 (673)
T ss_pred             cChhhcCCCHHHHHHH-HhcCCCCCchHHHhhccchhccCCeeeEEeccCCccccchhhHHHHHHcCCCcchhhhcccCc
Confidence            6899999999999988 77899999999999999999999999999999999999999999998775532   2455799


Q ss_pred             eEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEE
Q 043110          112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWII  191 (316)
Q Consensus       112 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lV  191 (316)
                      +++|++|||+|++|+.+.-.+++...+ ..+..++||....++--.+..+|+|+|+|||+|.+.+.+ ..+.++.+.++|
T Consensus       324 yaiilaptReLaqqIeeEt~kf~~~lg-~r~vsvigg~s~EEq~fqls~gceiviatPgrLid~Len-r~lvl~qctyvv  401 (673)
T KOG0333|consen  324 YAIILAPTRELAQQIEEETNKFGKPLG-IRTVSVIGGLSFEEQGFQLSMGCEIVIATPGRLIDSLEN-RYLVLNQCTYVV  401 (673)
T ss_pred             eeeeechHHHHHHHHHHHHHHhccccc-ceEEEEecccchhhhhhhhhccceeeecCchHHHHHHHH-HHHHhccCceEe
Confidence            999999999999999999999998876 677788899999998888999999999999999999987 566778999999


Q ss_pred             EecchhhhcCCcHHHHHHHHHHhccCcccccCCC----------CccccccceEEEEeeecchhHHHHHHHhcCCCEEEE
Q 043110          192 FDEADRILELGFGKEIEEILDILGSRNIASIGEG----------NEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIG  261 (316)
Q Consensus       192 iDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~----------~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~  261 (316)
                      +||||+|+|+||.+++..++..+|..+.......          ...+..-+|+++||||+|+.+..+++.+|++|+++.
T Consensus       402 ldeadrmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~vt  481 (673)
T KOG0333|consen  402 LDEADRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVVT  481 (673)
T ss_pred             ccchhhhhcccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCCeEEE
Confidence            9999999999999999999999998654422211          122334489999999999999999999999999999


Q ss_pred             cCCCCCCCCCCCccccccc
Q 043110          262 LDEKKFPEDKSNVHFGSLE  280 (316)
Q Consensus       262 ~~~~~~~~~~~~~~~~~~~  280 (316)
                      +.....+.....+++.-+.
T Consensus       482 ig~~gk~~~rveQ~v~m~~  500 (673)
T KOG0333|consen  482 IGSAGKPTPRVEQKVEMVS  500 (673)
T ss_pred             eccCCCCccchheEEEEec
Confidence            8887766666665555444

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

Probab=100.00  E-value=9.8e-40  Score=285.91  Aligned_cols=223  Identities=29%  Similarity=0.517  Sum_probs=200.0

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCC--CCCCCCC
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSP--RIDRSSG  110 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~--~~~~~~~  110 (316)
                      ...+|.++.++..+++.|++ .|+.+|||+|-+.+|.+++|+|.+..|-||||||++|++|++.....+.-  ...++.|
T Consensus       168 PIksF~eMKFP~~~L~~lk~-KGI~~PTpIQvQGlPvvLsGRDmIGIAfTGSGKTlvFvLP~imf~LeqE~~lPf~~~EG  246 (610)
T KOG0341|consen  168 PIKSFKEMKFPKPLLRGLKK-KGIVHPTPIQVQGLPVVLSGRDMIGIAFTGSGKTLVFVLPVIMFALEQEMMLPFARGEG  246 (610)
T ss_pred             chhhhhhccCCHHHHHHHHh-cCCCCCCceeecCcceEeecCceeeEEeecCCceEEEeHHHHHHHHHHHhcCccccCCC
Confidence            44689999999999999954 69999999999999999999999999999999999999999887665443  3456789


Q ss_pred             eeEEEEeCChHHHHHHHHHHHHHHhhc-----CCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccC
Q 043110          111 TFALVLVPTSELCLLVYEILQKLLHRF-----RWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHT  185 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~  185 (316)
                      +..||+||+||||.|.++.+..+...+     +.+...+++||.....+...++.+.+|+|+|||||.+++.. +...+.
T Consensus       247 P~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v~~GvHivVATPGRL~DmL~K-K~~sLd  325 (610)
T KOG0341|consen  247 PYGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVVRRGVHIVVATPGRLMDMLAK-KIMSLD  325 (610)
T ss_pred             CeeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHHhcCeeEEEcCcchHHHHHHH-hhccHH
Confidence            999999999999999999998887543     44667788999999999999999999999999999999987 666777


Q ss_pred             ceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          186 NLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                      -+++|++||||+|+|+||.++++.|+..+..               .+|+++||||||..++.|++..+..|+.|.+...
T Consensus       326 ~CRyL~lDEADRmiDmGFEddir~iF~~FK~---------------QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVGRA  390 (610)
T KOG0341|consen  326 ACRYLTLDEADRMIDMGFEDDIRTIFSFFKG---------------QRQTLLFSATMPKKIQNFAKSALVKPVTVNVGRA  390 (610)
T ss_pred             HHHHhhhhhHHHHhhccchhhHHHHHHHHhh---------------hhheeeeeccccHHHHHHHHhhcccceEEecccc
Confidence            7899999999999999999999999999988               9999999999999999999999999999999887


Q ss_pred             CCCCCCC
Q 043110          266 KFPEDKS  272 (316)
Q Consensus       266 ~~~~~~~  272 (316)
                      ..++-..
T Consensus       391 GAAsldV  397 (610)
T KOG0341|consen  391 GAASLDV  397 (610)
T ss_pred             cccchhH
Confidence            6555433

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=100.00  E-value=7.1e-37  Score=288.80  Aligned_cols=211  Identities=36%  Similarity=0.564  Sum_probs=186.7

Q ss_pred             CcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEE
Q 043110           36 CFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALV  115 (316)
Q Consensus        36 ~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~li  115 (316)
                      +|++++|++.+++.| +++||.+|+++|.++||.++.|+|++++||||+|||++|++|+++.+.....  ....++++||
T Consensus         2 ~f~~l~l~~~l~~~l-~~~g~~~p~~iQ~~ai~~~~~g~d~l~~apTGsGKT~~~~lp~l~~l~~~~~--~~~~~~~~li   78 (434)
T PRK11192          2 TFSELELDESLLEAL-QDKGYTRPTAIQAEAIPPALDGRDVLGSAPTGTGKTAAFLLPALQHLLDFPR--RKSGPPRILI   78 (434)
T ss_pred             CHhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHhhccc--cCCCCceEEE
Confidence            699999999999999 7789999999999999999999999999999999999999999999875321  1234578999


Q ss_pred             EeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecc
Q 043110          116 LVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEA  195 (316)
Q Consensus       116 l~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEa  195 (316)
                      ++||++|+.|+++.+..++...+ ..+..+.||.....+...+..+++|+|+||++|++++.. ..+.+.++++||+|||
T Consensus        79 l~Pt~eLa~Q~~~~~~~l~~~~~-~~v~~~~gg~~~~~~~~~l~~~~~IlV~Tp~rl~~~~~~-~~~~~~~v~~lViDEa  156 (434)
T PRK11192         79 LTPTRELAMQVADQARELAKHTH-LDIATITGGVAYMNHAEVFSENQDIVVATPGRLLQYIKE-ENFDCRAVETLILDEA  156 (434)
T ss_pred             ECCcHHHHHHHHHHHHHHHccCC-cEEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHc-CCcCcccCCEEEEECH
Confidence            99999999999999999987655 667778888888888888888899999999999999986 5566788999999999


Q ss_pred             hhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecch-hHHHHHHHhcCCCEEEEcCCCC
Q 043110          196 DRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNE-KVNHLTKISLETPVLIGLDEKK  266 (316)
Q Consensus       196 d~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~-~v~~~~~~~l~~p~~i~~~~~~  266 (316)
                      |+|++++|...+..+...++.               ..|+++||||++. .+..+....+.+|+.+.+....
T Consensus       157 h~~l~~~~~~~~~~i~~~~~~---------------~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~~  213 (434)
T PRK11192        157 DRMLDMGFAQDIETIAAETRW---------------RKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPSR  213 (434)
T ss_pred             HHHhCCCcHHHHHHHHHhCcc---------------ccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCCc
Confidence            999999999999999988876               7899999999985 5888999999999998876654

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

Probab=100.00  E-value=7.2e-38  Score=285.29  Aligned_cols=232  Identities=31%  Similarity=0.475  Sum_probs=197.8

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCC--C--CCCCC
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPR--I--DRSSG  110 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~--~--~~~~~  110 (316)
                      .+|++..+.+.+...+ ++.||..|||+|+.+||.+..|+|++++|+||||||.+|++|++..+......  .  .....
T Consensus        74 ~~f~~~~l~~~l~~ni-~~~~~~~ptpvQk~sip~i~~Grdl~acAqTGsGKT~aFLiPii~~~~~~~~~~~~~~~~~~~  152 (482)
T KOG0335|consen   74 PTFDEAILGEALAGNI-KRSGYTKPTPVQKYSIPIISGGRDLMACAQTGSGKTAAFLIPIISYLLDEGPEDRGESGGGVY  152 (482)
T ss_pred             ccccccchhHHHhhcc-ccccccCCCcceeeccceeecCCceEEEccCCCcchHHHHHHHHHHHHhcCcccCcccCCCCC
Confidence            3788888999999998 77899999999999999999999999999999999999999999999876542  1  11235


Q ss_pred             eeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEE
Q 043110          111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWI  190 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~l  190 (316)
                      +++||++||||||.|+++..+++.-. ..+.....+||.+...+.+.+.++|||+|+|||+|.+++.. +.+.+.+++++
T Consensus       153 P~~lIlapTReL~~Qi~nea~k~~~~-s~~~~~~~ygg~~~~~q~~~~~~gcdIlvaTpGrL~d~~e~-g~i~l~~~k~~  230 (482)
T KOG0335|consen  153 PRALILAPTRELVDQIYNEARKFSYL-SGMKSVVVYGGTDLGAQLRFIKRGCDILVATPGRLKDLIER-GKISLDNCKFL  230 (482)
T ss_pred             CceEEEeCcHHHhhHHHHHHHhhccc-ccceeeeeeCCcchhhhhhhhccCccEEEecCchhhhhhhc-ceeehhhCcEE
Confidence            89999999999999999999998743 55778889999999999999999999999999999999987 67778899999


Q ss_pred             EEecchhhhc-CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCC-CEEEEcCCCCCC
Q 043110          191 IFDEADRILE-LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLET-PVLIGLDEKKFP  268 (316)
Q Consensus       191 ViDEad~l~~-~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~-p~~i~~~~~~~~  268 (316)
                      ||||||+|+| ++|.++|+.|+.....           .....+|+++||||+|.++..++..++.+ .+++.+......
T Consensus       231 vLDEADrMlD~mgF~p~Ir~iv~~~~~-----------~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rvg~~  299 (482)
T KOG0335|consen  231 VLDEADRMLDEMGFEPQIRKIVEQLGM-----------PPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRVGST  299 (482)
T ss_pred             EecchHHhhhhccccccHHHHhcccCC-----------CCccceeEEEEeccCChhhhhhHHHHhhccceEEEEeeeccc
Confidence            9999999999 8999999999988753           22347999999999999999999999886 777776665544


Q ss_pred             CCCCCccccccc
Q 043110          269 EDKSNVHFGSLE  280 (316)
Q Consensus       269 ~~~~~~~~~~~~  280 (316)
                      .....+....+.
T Consensus       300 ~~ni~q~i~~V~  311 (482)
T KOG0335|consen  300 SENITQKILFVN  311 (482)
T ss_pred             cccceeEeeeec
Confidence            444444444443

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=8.5e-36  Score=284.18  Aligned_cols=229  Identities=31%  Similarity=0.443  Sum_probs=190.6

Q ss_pred             cccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCC-CCCC
Q 043110           32 FASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRID-RSSG  110 (316)
Q Consensus        32 ~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~-~~~~  110 (316)
                      .....|.+++|++.++++| .++||..|+++|.++|+.+++|+|+++.+|||||||++|++|+++.+........ ....
T Consensus        84 ~~~~~f~~~~l~~~l~~~l-~~~g~~~~~~iQ~~ai~~~~~G~dvi~~apTGSGKTlay~lpil~~l~~~~~~~~~~~~~  162 (475)
T PRK01297         84 EGKTRFHDFNLAPELMHAI-HDLGFPYCTPIQAQVLGYTLAGHDAIGRAQTGTGKTAAFLISIINQLLQTPPPKERYMGE  162 (475)
T ss_pred             cCCCCHhHCCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhcCcccccccCC
Confidence            3446799999999999999 6689999999999999999999999999999999999999999999876432211 1125


Q ss_pred             eeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHh-cCCcEEEeCcHHHHHHHhcCCccccCceeE
Q 043110          111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLR-KGISILVATPGHLLDHLKHTSSFLHTNLRW  189 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~  189 (316)
                      +++|||+||++|+.|+++.++.+....+ ..+..+.||.+...+...+. ..++|+|+||++|++++.. ....++++++
T Consensus       163 ~~aLil~PtreLa~Q~~~~~~~l~~~~~-~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~-~~~~l~~l~~  240 (475)
T PRK01297        163 PRALIIAPTRELVVQIAKDAAALTKYTG-LNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQR-GEVHLDMVEV  240 (475)
T ss_pred             ceEEEEeCcHHHHHHHHHHHHHhhccCC-CEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHc-CCcccccCce
Confidence            7899999999999999999999887654 55666778877776666654 4589999999999998876 4566789999


Q ss_pred             EEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCC
Q 043110          190 IIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPE  269 (316)
Q Consensus       190 lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~  269 (316)
                      |||||||++++++|...+..++..++...             .+|++++|||++.++.++++.++.+|..+.+..+....
T Consensus       241 lViDEah~l~~~~~~~~l~~i~~~~~~~~-------------~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~~~~~  307 (475)
T PRK01297        241 MVLDEADRMLDMGFIPQVRQIIRQTPRKE-------------ERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPENVAS  307 (475)
T ss_pred             EEechHHHHHhcccHHHHHHHHHhCCCCC-------------CceEEEEEeecCHHHHHHHHHhccCCEEEEeccCcCCC
Confidence            99999999999999999999998886421             57999999999999999999999999998877665444


Q ss_pred             CCCCccc
Q 043110          270 DKSNVHF  276 (316)
Q Consensus       270 ~~~~~~~  276 (316)
                      .....++
T Consensus       308 ~~~~~~~  314 (475)
T PRK01297        308 DTVEQHV  314 (475)
T ss_pred             CcccEEE
Confidence            4333333

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

Probab=100.00  E-value=1.6e-37  Score=274.51  Aligned_cols=227  Identities=36%  Similarity=0.574  Sum_probs=202.6

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      ...|+++||+..+.+++.+ -||+.|+|+|++.||.+++|+|++..|-||||||.||++|+++.+....     ..|.++
T Consensus        20 ~g~fqsmgL~~~v~raI~k-kg~~~ptpiqRKTipliLe~~dvv~martgsgktaaf~ipm~e~Lk~~s-----~~g~Ra   93 (529)
T KOG0337|consen   20 SGGFQSMGLDYKVLRAIHK-KGFNTPTPIQRKTIPLILEGRDVVGMARTGSGKTAAFLIPMIEKLKSHS-----QTGLRA   93 (529)
T ss_pred             CCCccccCCCHHHHHHHHH-hhcCCCCchhcccccceeeccccceeeecCCcchhhHHHHHHHHHhhcc-----ccccce
Confidence            6889999999999999955 4999999999999999999999999999999999999999999998743     357899


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      +++.|||+|+.|..+..+.++...+ ....+++||....++...+..++|||++||+++..+... -.+.++.+.|+|+|
T Consensus        94 lilsptreLa~qtlkvvkdlgrgt~-lr~s~~~ggD~~eeqf~~l~~npDii~ATpgr~~h~~ve-m~l~l~sveyVVfd  171 (529)
T KOG0337|consen   94 LILSPTRELALQTLKVVKDLGRGTK-LRQSLLVGGDSIEEQFILLNENPDIIIATPGRLLHLGVE-MTLTLSSVEYVVFD  171 (529)
T ss_pred             eeccCcHHHHHHHHHHHHHhccccc-hhhhhhcccchHHHHHHHhccCCCEEEecCceeeeeehh-eeccccceeeeeeh
Confidence            9999999999999999999997654 677788999999999999999999999999999887765 33677899999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCCCC
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSN  273 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~~~  273 (316)
                      |||+++++||.+++..++.+++.               .+|+++||||+|..+..+++..+.+|+.|.++.+....+...
T Consensus       172 Eadrlfemgfqeql~e~l~rl~~---------------~~QTllfSatlp~~lv~fakaGl~~p~lVRldvetkise~lk  236 (529)
T KOG0337|consen  172 EADRLFEMGFQEQLHEILSRLPE---------------SRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVETKISELLK  236 (529)
T ss_pred             hhhHHHhhhhHHHHHHHHHhCCC---------------cceEEEEeccCchhhHHHHHccCCCCceEEeehhhhcchhhh
Confidence            99999999999999999999998               889999999999999999999999999999887765555555


Q ss_pred             cccccccchh
Q 043110          274 VHFGSLESDV  283 (316)
Q Consensus       274 ~~~~~~~~~~  283 (316)
                      +.+....++.
T Consensus       237 ~~f~~~~~a~  246 (529)
T KOG0337|consen  237 VRFFRVRKAE  246 (529)
T ss_pred             hheeeeccHH
Confidence            5555444443

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=1e-36  Score=295.59  Aligned_cols=227  Identities=35%  Similarity=0.582  Sum_probs=200.1

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      ..+|.+.|++..++..+ +++||..|+|||.+|||+++.|+|+|..|.||||||++|++|++.++..+.+ ...+.||.+
T Consensus       364 v~sW~q~gl~~~il~tl-kkl~y~k~~~IQ~qAiP~ImsGrdvIgvakTgSGKT~af~LPmirhi~dQr~-~~~gdGPi~  441 (997)
T KOG0334|consen  364 VTSWTQCGLSSKILETL-KKLGYEKPTPIQAQAIPAIMSGRDVIGVAKTGSGKTLAFLLPMIRHIKDQRP-LEEGDGPIA  441 (997)
T ss_pred             cchHhhCCchHHHHHHH-HHhcCCCCcchhhhhcchhccCcceEEeeccCCccchhhhcchhhhhhcCCC-hhhCCCceE
Confidence            36899999999999999 8899999999999999999999999999999999999999999988766544 345569999


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcC--CccccCceeEEE
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHT--SSFLHTNLRWII  191 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~--~~~~~~~l~~lV  191 (316)
                      ||++|||+|+.|+++.++.++.. ..+.+.+++||....++...+..++.|+|||||+..+.+..+  +...+.++.++|
T Consensus       442 li~aPtrela~QI~r~~~kf~k~-l~ir~v~vygg~~~~~qiaelkRg~eIvV~tpGRmiD~l~~n~grvtnlrR~t~lv  520 (997)
T KOG0334|consen  442 LILAPTRELAMQIHREVRKFLKL-LGIRVVCVYGGSGISQQIAELKRGAEIVVCTPGRMIDILCANSGRVTNLRRVTYLV  520 (997)
T ss_pred             EEEcCCHHHHHHHHHHHHHHHhh-cCceEEEecCCccHHHHHHHHhcCCceEEeccchhhhhHhhcCCccccccccceee
Confidence            99999999999999999999987 457888999999999999999999999999999999988543  233555667999


Q ss_pred             EecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCC
Q 043110          192 FDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDK  271 (316)
Q Consensus       192 iDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~  271 (316)
                      +||||+|++++|.+++..|++.++.               .+|+++||||+|..++.+++..++.|+.|.+.....-...
T Consensus       521 ~deaDrmfdmgfePq~~~Ii~nlrp---------------drQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~svV~k~  585 (997)
T KOG0334|consen  521 LDEADRMFDMGFEPQITRILQNLRP---------------DRQTVLFSATFPRSMEALARKVLKKPVEIIVGGRSVVCKE  585 (997)
T ss_pred             echhhhhheeccCcccchHHhhcch---------------hhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccceeEecc
Confidence            9999999999999999999999977               9999999999999999999999999999988866544444


Q ss_pred             CCccccc
Q 043110          272 SNVHFGS  278 (316)
Q Consensus       272 ~~~~~~~  278 (316)
                      ..+.+.+
T Consensus       586 V~q~v~V  592 (997)
T KOG0334|consen  586 VTQVVRV  592 (997)
T ss_pred             ceEEEEE
Confidence            4443333

>PTZ00424 helicase 45; Provisional

Probab=100.00  E-value=9.6e-35  Score=271.76  Aligned_cols=212  Identities=27%  Similarity=0.433  Sum_probs=184.3

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      ..+|+++++++.+.++| .++||..|+|+|.++|+.+++|+|++++||||||||++|++|+++.+...      ..+.++
T Consensus        27 ~~~~~~l~l~~~~~~~l-~~~~~~~~~~~Q~~ai~~i~~~~d~ii~apTGsGKT~~~~l~~l~~~~~~------~~~~~~   99 (401)
T PTZ00424         27 VDSFDALKLNEDLLRGI-YSYGFEKPSAIQQRGIKPILDGYDTIGQAQSGTGKTATFVIAALQLIDYD------LNACQA   99 (401)
T ss_pred             cCCHhhCCCCHHHHHHH-HHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhcCC------CCCceE
Confidence            47899999999999999 77899999999999999999999999999999999999999999887531      235679


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      ||++|+++|+.|+.+.+..++.... ..+....|+.....+...+..+++|+|+||+++.+.+.. ....+++++++|+|
T Consensus       100 lil~Pt~~L~~Q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~-~~~~l~~i~lvViD  177 (401)
T PTZ00424        100 LILAPTRELAQQIQKVVLALGDYLK-VRCHACVGGTVVRDDINKLKAGVHMVVGTPGRVYDMIDK-RHLRVDDLKLFILD  177 (401)
T ss_pred             EEECCCHHHHHHHHHHHHHHhhhcC-ceEEEEECCcCHHHHHHHHcCCCCEEEECcHHHHHHHHh-CCcccccccEEEEe
Confidence            9999999999999999999886543 445566777777777778888899999999999998876 44567899999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCC
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPE  269 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~  269 (316)
                      |||++++.+|...+..++..++.               ..|++++|||+|+.+..+...++.+|..+.+.......
T Consensus       178 Eah~~~~~~~~~~~~~i~~~~~~---------------~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (401)
T PTZ00424        178 EADEMLSRGFKGQIYDVFKKLPP---------------DVQVALFSATMPNEILELTTKFMRDPKRILVKKDELTL  238 (401)
T ss_pred             cHHHHHhcchHHHHHHHHhhCCC---------------CcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCCCccc
Confidence            99999999999999999888876               88999999999999999999999999887766554333

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

Probab=100.00  E-value=2.2e-36  Score=251.87  Aligned_cols=226  Identities=24%  Similarity=0.410  Sum_probs=199.6

Q ss_pred             cccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCe
Q 043110           32 FASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT  111 (316)
Q Consensus        32 ~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~  111 (316)
                      +.+..|.++-|.|++++++ -.+||++|+.+|.+|||...-|.|++++|.+|.|||.+|+++-++.+.-      ....+
T Consensus        39 ihssgfrdfllkpellrai-vdcgfehpsevqhecipqailgmdvlcqaksgmgktavfvl~tlqqiep------v~g~v  111 (387)
T KOG0329|consen   39 IHSSGFRDFLLKPELLRAI-VDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQIEP------VDGQV  111 (387)
T ss_pred             EeccchhhhhcCHHHHHHH-HhccCCCchHhhhhhhhHHhhcchhheecccCCCceeeeehhhhhhcCC------CCCeE
Confidence            3456799999999999999 6689999999999999999999999999999999999999988887753      12356


Q ss_pred             eEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEE
Q 043110          112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWII  191 (316)
Q Consensus       112 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lV  191 (316)
                      -+|++|.|||||-|+.+....+..+++...+.+++||.........+.+.|+|+|+|||+++.+.++ +.+.+++++.+|
T Consensus       112 svlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk~~PhivVgTPGrilALvr~-k~l~lk~vkhFv  190 (387)
T KOG0329|consen  112 SVLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLKNCPHIVVGTPGRILALVRN-RSLNLKNVKHFV  190 (387)
T ss_pred             EEEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHhCCCeEEEcCcHHHHHHHHh-ccCchhhcceee
Confidence            7999999999999999999999999999999999999999988888999999999999999999987 778889999999


Q ss_pred             EecchhhhcC-CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCC-CCC
Q 043110          192 FDEADRILEL-GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK-FPE  269 (316)
Q Consensus       192 iDEad~l~~~-~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~-~~~  269 (316)
                      +||||.|+++ ..+.++..|++..|.               ..|+++||||++++++..++.+|++|..|.++++. ...
T Consensus       191 lDEcdkmle~lDMrRDvQEifr~tp~---------------~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~KLtL  255 (387)
T KOG0329|consen  191 LDECDKMLEQLDMRRDVQEIFRMTPH---------------EKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEAKLTL  255 (387)
T ss_pred             hhhHHHHHHHHHHHHHHHHHhhcCcc---------------cceeeeeeeecchhhHHHHHhhhcCchhhhccchhhhhh
Confidence            9999999976 678889999988887               89999999999999999999999999999988764 233


Q ss_pred             CCCCccccccc
Q 043110          270 DKSNVHFGSLE  280 (316)
Q Consensus       270 ~~~~~~~~~~~  280 (316)
                      ....++|+.+.
T Consensus       256 HGLqQ~YvkLk  266 (387)
T KOG0329|consen  256 HGLQQYYVKLK  266 (387)
T ss_pred             hhHHHHHHhhh
Confidence            33334444444

>cd00268 DEADc DEAD-box helicases

Probab=100.00  E-value=6.2e-34  Score=241.91  Aligned_cols=202  Identities=43%  Similarity=0.688  Sum_probs=178.4

Q ss_pred             cccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEE
Q 043110           37 FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVL  116 (316)
Q Consensus        37 f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil  116 (316)
                      |+++++++.+.+.+ +++|+..|+++|+++++.+.+|+|+++.+|||+|||++|++|+++.+....    ...++++||+
T Consensus         1 ~~~~~~~~~i~~~l-~~~~~~~~~~~Q~~~~~~~~~~~~~li~~~TG~GKT~~~~~~~l~~~~~~~----~~~~~~viii   75 (203)
T cd00268           1 FEELGLSPELLRGI-YALGFEKPTPIQARAIPPLLSGRDVIGQAQTGSGKTAAFLIPILEKLDPSP----KKDGPQALIL   75 (203)
T ss_pred             CCcCCCCHHHHHHH-HHcCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHHHHhhc----ccCCceEEEE
Confidence            78999999999999 568999999999999999999999999999999999999999999987742    1246789999


Q ss_pred             eCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecch
Q 043110          117 VPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEAD  196 (316)
Q Consensus       117 ~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad  196 (316)
                      +|+++|+.|+.+.++.+.... ........|+.........+..+++|+|+||+.+.+.+.+. ...+.+++++|+||+|
T Consensus        76 ~p~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~~-~~~~~~l~~lIvDE~h  153 (203)
T cd00268          76 APTRELALQIAEVARKLGKHT-NLKVVVIYGGTSIDKQIRKLKRGPHIVVATPGRLLDLLERG-KLDLSKVKYLVLDEAD  153 (203)
T ss_pred             cCCHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHhcCCCCEEEEChHHHHHHHHcC-CCChhhCCEEEEeChH
Confidence            999999999999999987653 45666777777776666666668899999999999988864 4667889999999999


Q ss_pred             hhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEE
Q 043110          197 RILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI  260 (316)
Q Consensus       197 ~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i  260 (316)
                      .+.+.++...+..+++.++.               .+|++++|||+++.+..++..++.+|+.|
T Consensus       154 ~~~~~~~~~~~~~~~~~l~~---------------~~~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         154 RMLDMGFEDQIREILKLLPK---------------DRQTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             HhhccChHHHHHHHHHhCCc---------------ccEEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence            99988999999999998876               89999999999999999999999999987

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.

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

Probab=100.00  E-value=3.3e-35  Score=257.89  Aligned_cols=223  Identities=30%  Similarity=0.485  Sum_probs=192.8

Q ss_pred             CcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEE
Q 043110           36 CFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALV  115 (316)
Q Consensus        36 ~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~li  115 (316)
                      +|++++|.+++++.+ ..+||++|+.+|++||+.+..|.|+.+++++|+|||.+|.+++++.+...      ....+||+
T Consensus        27 sfddm~L~e~LLrgi-y~yGFekPSaIQqraI~p~i~G~dv~~qaqsgTgKt~af~i~iLq~iD~~------~ke~qali   99 (397)
T KOG0327|consen   27 SFDDMNLKESLLRGI-YAYGFEKPSAIQQRAILPCIKGHDVIAQAQSGTGKTAAFLISILQQIDMS------VKETQALI   99 (397)
T ss_pred             hhhhcCCCHHHHhHH-HhhccCCchHHHhccccccccCCceeEeeeccccchhhhHHHHHhhcCcc------hHHHHHHH
Confidence            899999999999999 77899999999999999999999999999999999999999999987432      23456999


Q ss_pred             EeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHH-hcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          116 LVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARL-RKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       116 l~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      ++|||+|+.|+.++.+.++...+ ..+..+.||.+...+...+ ...++|+|+|||++.+.+... .+....++++|+||
T Consensus       100 laPtreLa~qi~~v~~~lg~~~~-~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~~-~l~~~~iKmfvlDE  177 (397)
T KOG0327|consen  100 LAPTRELAQQIQKVVRALGDHMD-VSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNRG-SLSTDGIKMFVLDE  177 (397)
T ss_pred             hcchHHHHHHHHHHHHhhhcccc-eeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhccc-cccccceeEEeecc
Confidence            99999999999999999887654 5556666777766444444 455899999999999999874 66667899999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCCCCc
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNV  274 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~~~~  274 (316)
                      ||.++..||.+++..|++.++.               +.|++++|||+|+++..+.+.++++|+.|.+..++.....+.+
T Consensus       178 aDEmLs~gfkdqI~~if~~lp~---------------~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~~ltl~gikq  242 (397)
T KOG0327|consen  178 ADEMLSRGFKDQIYDIFQELPS---------------DVQVVLLSATMPSDVLEVTKKFMREPVRILVKKDELTLEGIKQ  242 (397)
T ss_pred             hHhhhccchHHHHHHHHHHcCc---------------chhheeecccCcHHHHHHHHHhccCceEEEecchhhhhhheee
Confidence            9999999999999999999998               8899999999999999999999999999999887766555555


Q ss_pred             ccccccch
Q 043110          275 HFGSLESD  282 (316)
Q Consensus       275 ~~~~~~~~  282 (316)
                      .|..+..+
T Consensus       243 ~~i~v~k~  250 (397)
T KOG0327|consen  243 FYINVEKE  250 (397)
T ss_pred             eeeecccc
Confidence            55555443

>KOG4284 consensus DEAD box protein [Transcription]

Probab=100.00  E-value=2.8e-35  Score=271.79  Aligned_cols=226  Identities=27%  Similarity=0.397  Sum_probs=204.0

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ...+|+++.|...++..| ++.+|..||++|..|||.++.+.|+|++|..|+|||++|.+.+++.+..      +...++
T Consensus        23 ~~~~fe~l~l~r~vl~gl-rrn~f~~ptkiQaaAIP~~~~kmDliVQaKSGTGKTlVfsv~av~sl~~------~~~~~q   95 (980)
T KOG4284|consen   23 CTPGFEQLALWREVLLGL-RRNAFALPTKIQAAAIPAIFSKMDLIVQAKSGTGKTLVFSVLAVESLDS------RSSHIQ   95 (980)
T ss_pred             CCCCHHHHHHHHHHHHHH-HhhcccCCCchhhhhhhhhhcccceEEEecCCCCceEEEEeeeehhcCc------ccCcce
Confidence            446899999999999999 6679999999999999999999999999999999999999888887754      345778


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      ++||+||||++.|+.+.+..++..+....|.+++||+.......++. .++|+||||||+..++.. ..+..++++++|+
T Consensus        96 ~~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rlk-~~rIvIGtPGRi~qL~el-~~~n~s~vrlfVL  173 (980)
T KOG4284|consen   96 KVIVTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRLK-QTRIVIGTPGRIAQLVEL-GAMNMSHVRLFVL  173 (980)
T ss_pred             eEEEecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhhh-hceEEecCchHHHHHHHh-cCCCccceeEEEe
Confidence            99999999999999999999999998999999999999888777765 479999999999999886 6778899999999


Q ss_pred             ecchhhhcC-CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCC
Q 043110          193 DEADRILEL-GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDK  271 (316)
Q Consensus       193 DEad~l~~~-~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~  271 (316)
                      ||||.|++. .|+++++.|++.+|.               .+|++.||||.|.++.++...+|++|..|....+....-.
T Consensus       174 DEADkL~~t~sfq~~In~ii~slP~---------------~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~d~~L~G  238 (980)
T KOG4284|consen  174 DEADKLMDTESFQDDINIIINSLPQ---------------IRQVAAFSATYPRNLDNLLSKFMRDPALVRFNADDVQLFG  238 (980)
T ss_pred             ccHHhhhchhhHHHHHHHHHHhcch---------------hheeeEEeccCchhHHHHHHHHhcccceeecccCCceeec
Confidence            999999994 699999999999998               9999999999999999999999999999999888766666


Q ss_pred             CCcccccccch
Q 043110          272 SNVHFGSLESD  282 (316)
Q Consensus       272 ~~~~~~~~~~~  282 (316)
                      ..+++..+++.
T Consensus       239 ikQyv~~~~s~  249 (980)
T KOG4284|consen  239 IKQYVVAKCSP  249 (980)
T ss_pred             hhheeeeccCC
Confidence            66666666543

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=5.3e-35  Score=265.89  Aligned_cols=199  Identities=32%  Similarity=0.481  Sum_probs=171.7

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC-CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCC-------C
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG-RDVLVNAATGTGKTVAYLAPIINHLQSYSPRI-------D  106 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g-~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~-------~  106 (316)
                      .-|..++|+.+++++| ..+||.+||+||..++|++..| .|++..|.||||||+||-+|+++.+.......       .
T Consensus       181 sAW~~l~lp~~iL~aL-~~~gFs~Pt~IQsl~lp~ai~gk~DIlGaAeTGSGKTLAFGIPiv~~l~~~s~~s~e~~~~~~  259 (731)
T KOG0347|consen  181 SAWKNLFLPMEILRAL-SNLGFSRPTEIQSLVLPAAIRGKVDILGAAETGSGKTLAFGIPIVERLLESSDDSQELSNTSA  259 (731)
T ss_pred             HHHhcCCCCHHHHHHH-HhcCCCCCccchhhcccHhhccchhcccccccCCCceeeecchhhhhhhhccchHhhhhhHHh
Confidence            4588889999999999 7899999999999999999999 69999999999999999999999665432211       1


Q ss_pred             CCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCcc--cc
Q 043110          107 RSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSF--LH  184 (316)
Q Consensus       107 ~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~--~~  184 (316)
                      +...+.+||++||||||.|+.+-+..++.. ..+.+..+.||.....+.+.++..++|||+|||||+.++......  .+
T Consensus       260 k~~k~~~LV~tPTRELa~QV~~Hl~ai~~~-t~i~v~si~GGLavqKQqRlL~~~p~IVVATPGRlweli~e~n~~l~~~  338 (731)
T KOG0347|consen  260 KYVKPIALVVTPTRELAHQVKQHLKAIAEK-TQIRVASITGGLAVQKQQRLLNQRPDIVVATPGRLWELIEEDNTHLGNF  338 (731)
T ss_pred             ccCcceeEEecChHHHHHHHHHHHHHhccc-cCeEEEEeechhHHHHHHHHHhcCCCEEEecchHHHHHHHhhhhhhhhh
Confidence            122335999999999999999999998876 457788899999999999999999999999999999999876542  56


Q ss_pred             CceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchh
Q 043110          185 TNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEK  245 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~  245 (316)
                      +++++||+||||+|++.|+...+..|++.|..          ++.+.++|++.||||++-.
T Consensus       339 k~vkcLVlDEaDRmvekghF~Els~lL~~L~e----------~~~~~qrQTlVFSATlt~~  389 (731)
T KOG0347|consen  339 KKVKCLVLDEADRMVEKGHFEELSKLLKHLNE----------EQKNRQRQTLVFSATLTLV  389 (731)
T ss_pred             hhceEEEEccHHHHhhhccHHHHHHHHHHhhh----------hhcccccceEEEEEEeehh
Confidence            78999999999999999999999999999863          4556689999999998743

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

Probab=100.00  E-value=5.5e-33  Score=250.33  Aligned_cols=220  Identities=33%  Similarity=0.477  Sum_probs=178.2

Q ss_pred             CcccCCCCHHHHHH----------HHHHcCCCCCcHHHHHHHHHHh---------CCCcEEEEcCCCCchHHHHHHHHHH
Q 043110           36 CFSSLGLDSTLCDQ----------LRERLGFEAPTKVQAQAIPVIL---------SGRDVLVNAATGTGKTVAYLAPIIN   96 (316)
Q Consensus        36 ~f~~~~l~~~l~~~----------l~~~~g~~~p~~~Q~~~i~~il---------~g~d~li~a~TGsGKT~~~~lp~l~   96 (316)
                      -|+.++++......          + .++++.+.+|+|..++|.++         .++|+.+.||||||||++|.+|+++
T Consensus       128 ~~s~l~~se~k~~~d~lea~~~q~l-~k~~is~~FPVQ~aVlp~ll~~~~~p~~~r~rDIcV~ApTGSGKTLaY~iPIVQ  206 (620)
T KOG0350|consen  128 IFSVLGKSEMKNLEDTLEATIDQLL-VKMAISRLFPVQYAVLPSLLEEIRSPPPSRPRDICVNAPTGSGKTLAYVIPIVQ  206 (620)
T ss_pred             eeeccchhHHHHHHHHHHHHHHHHH-HHhhcccccchHHHHHHHHHHhhcCCCCCCCCceEEecCCCCCceeeehhHHHH
Confidence            46666666654443          6 56899999999999999986         2579999999999999999999999


Q ss_pred             HhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcC-----CcEEEeCcHH
Q 043110           97 HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKG-----ISILVATPGH  171 (316)
Q Consensus        97 ~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-----~~IlV~Tp~~  171 (316)
                      .+....-     ...+||||+||++|+.|+++.+..+....+ +.++...|..+..++...+.+.     .||+|+||||
T Consensus       207 ~L~~R~v-----~~LRavVivPtr~L~~QV~~~f~~~~~~tg-L~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGR  280 (620)
T KOG0350|consen  207 LLSSRPV-----KRLRAVVIVPTRELALQVYDTFKRLNSGTG-LAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGR  280 (620)
T ss_pred             HHccCCc-----cceEEEEEeeHHHHHHHHHHHHHHhccCCc-eEEEecccccchHHHHHHHhcCCCccccceEEcCchH
Confidence            9977432     357899999999999999999999998766 4467777888888888888765     3899999999


Q ss_pred             HHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcc--------cccCCC---------C--cccccc
Q 043110          172 LLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNI--------ASIGEG---------N--EVSNVK  232 (316)
Q Consensus       172 l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~--------~~~~~~---------~--~~~~~~  232 (316)
                      |.+|+.+.+.+.+++++|+||||||+|++..|+.++..++..+.....        ...+..         +  ....+.
T Consensus       281 LVDHl~~~k~f~Lk~LrfLVIDEADRll~qsfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~  360 (620)
T KOG0350|consen  281 LVDHLNNTKSFDLKHLRFLVIDEADRLLDQSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPP  360 (620)
T ss_pred             HHHhccCCCCcchhhceEEEechHHHHHHHHHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCch
Confidence            999999989999999999999999999999999999988888765310        000000         0  112334


Q ss_pred             ceEEEEeeecchhHHHHHHHhcCCCEEEEc
Q 043110          233 RQNLLLSATLNEKVNHLTKISLETPVLIGL  262 (316)
Q Consensus       233 ~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~  262 (316)
                      .+.+.+|||++.+-..+...-++.|-...+
T Consensus       361 l~kL~~satLsqdP~Kl~~l~l~~Prl~~v  390 (620)
T KOG0350|consen  361 LWKLVFSATLSQDPSKLKDLTLHIPRLFHV  390 (620)
T ss_pred             hHhhhcchhhhcChHHHhhhhcCCCceEEe
Confidence            568899999999999999999999955544

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

Probab=99.98  E-value=5.1e-31  Score=261.21  Aligned_cols=199  Identities=23%  Similarity=0.313  Sum_probs=157.8

Q ss_pred             CCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCCh
Q 043110           41 GLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTS  120 (316)
Q Consensus        41 ~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~  120 (316)
                      .+++++.++| ++.||.+|+++|.++||.+++|+|+++.+|||||||++|++|+++.+...       .++++|||+||+
T Consensus        20 ~l~~~l~~~L-~~~g~~~p~~~Q~~ai~~il~G~nvvv~apTGSGKTla~~LPiL~~l~~~-------~~~~aL~l~Ptr   91 (742)
T TIGR03817        20 WAHPDVVAAL-EAAGIHRPWQHQARAAELAHAGRHVVVATGTASGKSLAYQLPVLSALADD-------PRATALYLAPTK   91 (742)
T ss_pred             cCCHHHHHHH-HHcCCCcCCHHHHHHHHHHHCCCCEEEECCCCCcHHHHHHHHHHHHHhhC-------CCcEEEEEcChH
Confidence            3899999999 67899999999999999999999999999999999999999999998652       357899999999


Q ss_pred             HHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhc-CC--ccccCceeEEEEecchh
Q 043110          121 ELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKH-TS--SFLHTNLRWIIFDEADR  197 (316)
Q Consensus       121 ~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~-~~--~~~~~~l~~lViDEad~  197 (316)
                      ||+.|+.+.++.++  ...+.+....|+.. ..+...+..+++|+|+||+++...+.. ..  ...+++++++||||||.
T Consensus        92 aLa~q~~~~l~~l~--~~~i~v~~~~Gdt~-~~~r~~i~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l~~vViDEah~  168 (742)
T TIGR03817        92 ALAADQLRAVRELT--LRGVRPATYDGDTP-TEERRWAREHARYVLTNPDMLHRGILPSHARWARFLRRLRYVVIDECHS  168 (742)
T ss_pred             HHHHHHHHHHHHhc--cCCeEEEEEeCCCC-HHHHHHHhcCCCEEEEChHHHHHhhccchhHHHHHHhcCCEEEEeChhh
Confidence            99999999999986  22344444444444 555567777899999999999754322 11  12367899999999999


Q ss_pred             hhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEE
Q 043110          198 ILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI  260 (316)
Q Consensus       198 l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i  260 (316)
                      +.+ .|+..+..+++++....        .....++|++++|||+++... ++..++..|+.+
T Consensus       169 ~~g-~fg~~~~~il~rL~ri~--------~~~g~~~q~i~~SATi~n~~~-~~~~l~g~~~~~  221 (742)
T TIGR03817       169 YRG-VFGSHVALVLRRLRRLC--------ARYGASPVFVLASATTADPAA-AASRLIGAPVVA  221 (742)
T ss_pred             ccC-ccHHHHHHHHHHHHHHH--------HhcCCCCEEEEEecCCCCHHH-HHHHHcCCCeEE
Confidence            977 48888888887775310        112236899999999998765 566777778655

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.

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

Probab=99.97  E-value=6.7e-32  Score=235.74  Aligned_cols=226  Identities=23%  Similarity=0.393  Sum_probs=191.4

Q ss_pred             cccccccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC--CcEEEEcCCCCchHHHHHHHHHHHhhhcCC
Q 043110           26 ETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYLAPIINHLQSYSP  103 (316)
Q Consensus        26 ~~~~~~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g--~d~li~a~TGsGKT~~~~lp~l~~l~~~~~  103 (316)
                      +...++++..+|++++|.|++++++ ..|+|++|+.+|..|+|.++..  +|+|.+++.|+|||.||++.++.++.-.  
T Consensus        81 dpnsPlyS~ksFeeL~LkPellkgl-y~M~F~kPskIQe~aLPlll~~Pp~nlIaQsqsGtGKTaaFvL~MLsrvd~~--  157 (477)
T KOG0332|consen   81 DPNSPLYSAKSFEELRLKPELLKGL-YAMKFQKPSKIQETALPLLLAEPPQNLIAQSQSGTGKTAAFVLTMLSRVDPD--  157 (477)
T ss_pred             CCCCCccccccHHhhCCCHHHHhHH-HHhccCCcchHHHhhcchhhcCCchhhhhhhcCCCchhHHHHHHHHHhcCcc--
Confidence            3556778888999999999999999 6699999999999999999965  6899999999999999999999887542  


Q ss_pred             CCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccc
Q 043110          104 RIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFL  183 (316)
Q Consensus       104 ~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~  183 (316)
                          ...|+++.|+||||||.|+.+++.+++++. .+...+...+.....- ..  -..+|+|+|||.+.+++...+...
T Consensus       158 ----~~~PQ~iCLaPtrELA~Q~~eVv~eMGKf~-~ita~yair~sk~~rG-~~--i~eqIviGTPGtv~Dlm~klk~id  229 (477)
T KOG0332|consen  158 ----VVVPQCICLAPTRELAPQTGEVVEEMGKFT-ELTASYAIRGSKAKRG-NK--LTEQIVIGTPGTVLDLMLKLKCID  229 (477)
T ss_pred             ----ccCCCceeeCchHHHHHHHHHHHHHhcCce-eeeEEEEecCcccccC-Cc--chhheeeCCCccHHHHHHHHHhhC
Confidence                235679999999999999999999999876 4666666665521110 01  114799999999999999877888


Q ss_pred             cCceeEEEEecchhhhcC-CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEc
Q 043110          184 HTNLRWIIFDEADRILEL-GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGL  262 (316)
Q Consensus       184 ~~~l~~lViDEad~l~~~-~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~  262 (316)
                      ++.++.+|+||||.|++. ||+++-..|...+|+               ..|+++||||+...+.+++...+.+|..+.+
T Consensus       230 ~~kikvfVlDEAD~Mi~tqG~~D~S~rI~~~lP~---------------~~QllLFSATf~e~V~~Fa~kivpn~n~i~L  294 (477)
T KOG0332|consen  230 LEKIKVFVLDEADVMIDTQGFQDQSIRIMRSLPR---------------NQQLLLFSATFVEKVAAFALKIVPNANVIIL  294 (477)
T ss_pred             hhhceEEEecchhhhhhcccccccchhhhhhcCC---------------cceEEeeechhHHHHHHHHHHhcCCCceeee
Confidence            899999999999999986 899999999999997               8999999999999999999999999988888


Q ss_pred             CCCCCCCCCCCcccc
Q 043110          263 DEKKFPEDKSNVHFG  277 (316)
Q Consensus       263 ~~~~~~~~~~~~~~~  277 (316)
                      ..++...+...+.+.
T Consensus       295 k~eel~L~~IkQlyv  309 (477)
T KOG0332|consen  295 KREELALDNIKQLYV  309 (477)
T ss_pred             ehhhccccchhhhee
Confidence            877766665555444

>PF00270 DEAD: DEAD/DEAH box helicase; InterPro: IPR011545 Members of this family include the DEAD and DEAH box helicases

Probab=99.97  E-value=6.1e-29  Score=204.78  Aligned_cols=168  Identities=35%  Similarity=0.494  Sum_probs=140.3

Q ss_pred             cHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCC
Q 043110           60 TKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRW  139 (316)
Q Consensus        60 ~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~  139 (316)
                      ||+|.++++.+.+|+++++.||||+|||++|++|+++.+.+.       ...+++|++|+++|+.|+++.+..++.. ..
T Consensus         1 t~~Q~~~~~~i~~~~~~li~aptGsGKT~~~~~~~l~~~~~~-------~~~~~lii~P~~~l~~q~~~~~~~~~~~-~~   72 (169)
T PF00270_consen    1 TPLQQEAIEAIISGKNVLISAPTGSGKTLAYILPALNRLQEG-------KDARVLIIVPTRALAEQQFERLRKFFSN-TN   72 (169)
T ss_dssp             -HHHHHHHHHHHTTSEEEEECSTTSSHHHHHHHHHHHHHHTT-------SSSEEEEEESSHHHHHHHHHHHHHHTTT-TT
T ss_pred             CHHHHHHHHHHHcCCCEEEECCCCCccHHHHHHHHHhhhccC-------CCceEEEEeecccccccccccccccccc-cc
Confidence            689999999999999999999999999999999999988763       1236999999999999999999998876 33


Q ss_pred             ceeEEeeCCCChH-HHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCc
Q 043110          140 IVPGYVMGGGNRS-KEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRN  218 (316)
Q Consensus       140 ~~~~~~~~~~~~~-~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~  218 (316)
                      .....++++.... .....+..+++|+|+||++|.+++..... .+.+++++|+||+|.+.++++...+..+++.+....
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~~~~-~~~~~~~iViDE~h~l~~~~~~~~~~~i~~~~~~~~  151 (169)
T PF00270_consen   73 VRVVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISNGKI-NISRLSLIVIDEAHHLSDETFRAMLKSILRRLKRFK  151 (169)
T ss_dssp             SSEEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHTTSS-TGTTESEEEEETHHHHHHTTHHHHHHHHHHHSHTTT
T ss_pred             cccccccccccccccccccccccccccccCcchhhcccccccc-ccccceeeccCcccccccccHHHHHHHHHHHhcCCC
Confidence            5556667777655 44555666799999999999999987444 556699999999999999889999999999875421


Q ss_pred             ccccCCCCccccccceEEEEeeecchhHHHH
Q 043110          219 IASIGEGNEVSNVKRQNLLLSATLNEKVNHL  249 (316)
Q Consensus       219 ~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~  249 (316)
                                   +.|++++|||++++++++
T Consensus       152 -------------~~~~i~~SAT~~~~~~~~  169 (169)
T PF00270_consen  152 -------------NIQIILLSATLPSNVEKL  169 (169)
T ss_dssp             -------------TSEEEEEESSSTHHHHHH
T ss_pred             -------------CCcEEEEeeCCChhHhhC
Confidence                         589999999999877764

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 ....

>PRK02362 ski2-like helicase; Provisional

Probab=99.96  E-value=8.1e-29  Score=247.25  Aligned_cols=187  Identities=24%  Similarity=0.289  Sum_probs=153.0

Q ss_pred             CcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           36 CFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPV-ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        36 ~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~-il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      .|++++|++.+++.+ +..||.+|+|+|.+|++. +..|+|++++||||||||++|.+|+++.+..         +.++|
T Consensus         2 ~~~~l~lp~~~~~~l-~~~g~~~l~p~Q~~ai~~~~~~g~nvlv~APTGSGKTlia~lail~~l~~---------~~kal   71 (737)
T PRK02362          2 KIAELPLPEGVIEFY-EAEGIEELYPPQAEAVEAGLLDGKNLLAAIPTASGKTLIAELAMLKAIAR---------GGKAL   71 (737)
T ss_pred             ChhhcCCCHHHHHHH-HhCCCCcCCHHHHHHHHHHHhCCCcEEEECCCcchHHHHHHHHHHHHHhc---------CCcEE
Confidence            589999999999999 567999999999999998 7799999999999999999999999998853         45699


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      |++|+++||.|+++.++.+.. + ...+....|+......   ....++|+|+||+++..++++. ...+.+++++|+||
T Consensus        72 ~i~P~raLa~q~~~~~~~~~~-~-g~~v~~~tGd~~~~~~---~l~~~~IiV~Tpek~~~llr~~-~~~l~~v~lvViDE  145 (737)
T PRK02362         72 YIVPLRALASEKFEEFERFEE-L-GVRVGISTGDYDSRDE---WLGDNDIIVATSEKVDSLLRNG-APWLDDITCVVVDE  145 (737)
T ss_pred             EEeChHHHHHHHHHHHHHhhc-C-CCEEEEEeCCcCcccc---ccCCCCEEEECHHHHHHHHhcC-hhhhhhcCEEEEEC
Confidence            999999999999999987653 2 3455556665543322   2345799999999999988763 34467899999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHH
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK  251 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~  251 (316)
                      +|.+.+.+++..++.++..+...            .+..|++++|||+++ ...++.
T Consensus       146 ~H~l~d~~rg~~le~il~rl~~~------------~~~~qii~lSATl~n-~~~la~  189 (737)
T PRK02362        146 VHLIDSANRGPTLEVTLAKLRRL------------NPDLQVVALSATIGN-ADELAD  189 (737)
T ss_pred             ccccCCCcchHHHHHHHHHHHhc------------CCCCcEEEEcccCCC-HHHHHH
Confidence            99999989999999998887642            126899999999985 344443

>PRK00254 ski2-like helicase; Provisional

Probab=99.96  E-value=2.5e-28  Score=243.17  Aligned_cols=185  Identities=24%  Similarity=0.308  Sum_probs=154.4

Q ss_pred             CcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           36 CFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPV-ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        36 ~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~-il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      +|+++++++.+.+.| ++.||.+|+|+|.++++. +++|+|+++++|||||||++|.+|+++.+..        .+.++|
T Consensus         2 ~~~~l~l~~~~~~~l-~~~g~~~l~~~Q~~ai~~~~~~g~nvlv~apTGsGKT~~~~l~il~~l~~--------~~~~~l   72 (720)
T PRK00254          2 KVDELRVDERIKRVL-KERGIEELYPPQAEALKSGVLEGKNLVLAIPTASGKTLVAEIVMVNKLLR--------EGGKAV   72 (720)
T ss_pred             cHHHcCCCHHHHHHH-HhCCCCCCCHHHHHHHHHHHhCCCcEEEECCCCcHHHHHHHHHHHHHHHh--------cCCeEE
Confidence            588999999999999 668999999999999986 7899999999999999999999999998764        245699


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      ||+|+++|+.|+++.++.+.. .+ ..+....|+......   ....++|+|+||+++..++.+ ....+++++++|+||
T Consensus        73 ~l~P~~aLa~q~~~~~~~~~~-~g-~~v~~~~Gd~~~~~~---~~~~~~IiV~Tpe~~~~ll~~-~~~~l~~l~lvViDE  146 (720)
T PRK00254         73 YLVPLKALAEEKYREFKDWEK-LG-LRVAMTTGDYDSTDE---WLGKYDIIIATAEKFDSLLRH-GSSWIKDVKLVVADE  146 (720)
T ss_pred             EEeChHHHHHHHHHHHHHHhh-cC-CEEEEEeCCCCCchh---hhccCCEEEEcHHHHHHHHhC-CchhhhcCCEEEEcC
Confidence            999999999999999887642 33 455566666554322   235689999999999888875 334568999999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHH
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK  251 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~  251 (316)
                      +|.+.+.+++..++.++..+..               ..|++++|||+++ ...++.
T Consensus       147 ~H~l~~~~rg~~le~il~~l~~---------------~~qiI~lSATl~n-~~~la~  187 (720)
T PRK00254        147 IHLIGSYDRGATLEMILTHMLG---------------RAQILGLSATVGN-AEELAE  187 (720)
T ss_pred             cCccCCccchHHHHHHHHhcCc---------------CCcEEEEEccCCC-HHHHHH
Confidence            9999998899999999998876               7899999999985 455555

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.96  E-value=6.9e-28  Score=243.25  Aligned_cols=190  Identities=25%  Similarity=0.296  Sum_probs=150.8

Q ss_pred             CCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           42 LDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        42 l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      +++.+.+.+ +. +|..|+|+|.++||.+++|+|++++||||||||++|++|+++.+...........++++||++|+++
T Consensus        18 l~~~v~~~~-~~-~~~~~tpiQ~~Ai~~il~g~nvli~APTGSGKTlaa~Lpil~~l~~~~~~~~~~~~~~~LyIsPtra   95 (876)
T PRK13767         18 LRPYVREWF-KE-KFGTFTPPQRYAIPLIHEGKNVLISSPTGSGKTLAAFLAIIDELFRLGREGELEDKVYCLYVSPLRA   95 (876)
T ss_pred             cCHHHHHHH-HH-ccCCCCHHHHHHHHHHHcCCCEEEECCCCCcHHHHHHHHHHHHHHhhccccCCCCCeEEEEEcCHHH
Confidence            778888888 44 7889999999999999999999999999999999999999999875432222245788999999999


Q ss_pred             HHHHHHHHHHHHHh-----------hcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCc-cccCceeE
Q 043110          122 LCLLVYEILQKLLH-----------RFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSS-FLHTNLRW  189 (316)
Q Consensus       122 L~~Q~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~-~~~~~l~~  189 (316)
                      |+.|+++.+.....           ......+....|+.........+.+.++|+|+||++|..++.+... ..+.++++
T Consensus        96 La~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l~~~p~IlVtTPE~L~~ll~~~~~~~~l~~l~~  175 (876)
T PRK13767         96 LNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKMLKKPPHILITTPESLAILLNSPKFREKLRTVKW  175 (876)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHHhCCCCEEEecHHHHHHHhcChhHHHHHhcCCE
Confidence            99999987664321           1123456667777777776667777899999999999887765322 24678999


Q ss_pred             EEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecch
Q 043110          190 IIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       190 lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                      ||+||+|.+.+..++..+..+++++...           .....|.+++|||+++
T Consensus       176 VVIDE~H~l~~~~RG~~l~~~L~rL~~l-----------~~~~~q~IglSATl~~  219 (876)
T PRK13767        176 VIVDEIHSLAENKRGVHLSLSLERLEEL-----------AGGEFVRIGLSATIEP  219 (876)
T ss_pred             EEEechhhhccCccHHHHHHHHHHHHHh-----------cCCCCeEEEEecccCC
Confidence            9999999999888888887777776541           1236899999999975

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

Probab=99.95  E-value=5e-27  Score=230.03  Aligned_cols=197  Identities=18%  Similarity=0.118  Sum_probs=151.9

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHhCCC-cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEE-EeCChHHHH
Q 043110           47 CDQLRERLGFEAPTKVQAQAIPVILSGR-DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALV-LVPTSELCL  124 (316)
Q Consensus        47 ~~~l~~~~g~~~p~~~Q~~~i~~il~g~-d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~li-l~Pt~~L~~  124 (316)
                      -+.+.+..||+ |+|+|.+++|.++.|+ ++++++|||||||.++.++++.. ..      ....++.|| ++|||+|+.
T Consensus         5 ~~ff~~~~G~~-PtpiQ~~~i~~il~G~~~v~~~apTGSGKTaa~aafll~~-~~------~~~~~~rLv~~vPtReLa~   76 (844)
T TIGR02621         5 DEWYQGLHGYS-PFPWQLSLAERFVAGQPPESCSTPTGLGKTSIIAAWLLAV-EI------GAKVPRRLVYVVNRRTVVD   76 (844)
T ss_pred             HHHHHHHhCCC-CCHHHHHHHHHHHcCCCcceEecCCCCcccHHHHHhhccc-cc------cccccceEEEeCchHHHHH
Confidence            44554557998 9999999999999998 58889999999999765544422 11      122344555 679999999


Q ss_pred             HHHHHHHHHHhhcC----------------------CceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCcc
Q 043110          125 LVYEILQKLLHRFR----------------------WIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSF  182 (316)
Q Consensus       125 Q~~~~~~~~~~~~~----------------------~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~  182 (316)
                      |+++.+++++..+.                      .+.+..++||.....++..+..+++|||+|++    ++.+...+
T Consensus        77 Qi~~~~~~~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l~~~p~IIVgT~D----~i~sr~L~  152 (844)
T TIGR02621        77 QVTEEAEKIGERLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLDPHRPAVIVGTVD----MIGSRLLF  152 (844)
T ss_pred             HHHHHHHHHHHHhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhcCCCCcEEEECHH----HHcCCccc
Confidence            99999999998652                      26677889999999999999999999999954    44332210


Q ss_pred             ---------------ccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHH
Q 043110          183 ---------------LHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVN  247 (316)
Q Consensus       183 ---------------~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~  247 (316)
                                     .+.+++++|+||||  ++++|.+.+..|++.+...          ....++|+++||||++.++.
T Consensus       153 ~gYg~~~~~~pi~ag~L~~v~~LVLDEAD--Ld~gF~~~l~~Il~~l~rp----------~~~rprQtLLFSAT~p~ei~  220 (844)
T TIGR02621       153 SGYGCGFKSRPLHAGFLGQDALIVHDEAH--LEPAFQELLKQIMNEQQRP----------PDFLPLRVVELTATSRTDGP  220 (844)
T ss_pred             cccccccccccchhhhhccceEEEEehhh--hccccHHHHHHHHHhcccC----------cccccceEEEEecCCCccHH
Confidence                           25789999999999  6789999999999975210          00013799999999999999


Q ss_pred             HHHHHhcCCCEEEEcCCCCC
Q 043110          248 HLTKISLETPVLIGLDEKKF  267 (316)
Q Consensus       248 ~~~~~~l~~p~~i~~~~~~~  267 (316)
                      .+...++.+|..+.+.....
T Consensus       221 ~l~~~~~~~p~~i~V~~~~l  240 (844)
T TIGR02621       221 DRTTLLSAEDYKHPVLKKRL  240 (844)
T ss_pred             HHHHHHccCCceeecccccc
Confidence            99888998888777665443

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.

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

Probab=99.95  E-value=4.2e-28  Score=223.25  Aligned_cols=220  Identities=28%  Similarity=0.404  Sum_probs=174.3

Q ss_pred             CCccc----CCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCC
Q 043110           35 CCFSS----LGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSG  110 (316)
Q Consensus        35 ~~f~~----~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~  110 (316)
                      .+|++    ...++.+++.+ ...+|..|+|+|.+|+|.++.++|++.|+|||||||++|.+|+++++..... .+...|
T Consensus       132 ~~f~~lt~~~~~~~~ll~nl-~~~~F~~Pt~iq~~aipvfl~~r~~lAcapTGsgKtlaf~~Pil~~L~~~~~-~~~~~g  209 (593)
T KOG0344|consen  132 LSFSDLTYDYSMNKRLLENL-QELGFDEPTPIQKQAIPVFLEKRDVLACAPTGSGKTLAFNLPILQHLKDLSQ-EKHKVG  209 (593)
T ss_pred             ccccccchhhhhcHHHHHhH-hhCCCCCCCcccchhhhhhhcccceEEeccCCCcchhhhhhHHHHHHHHhhc-ccCccc
Confidence            35554    46788999999 5679999999999999999999999999999999999999999999976543 234568


Q ss_pred             eeEEEEeCChHHHHHHHHHHHHHHhh--cCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCC-ccccCce
Q 043110          111 TFALVLVPTSELCLLVYEILQKLLHR--FRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTS-SFLHTNL  187 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~-~~~~~~l  187 (316)
                      .+++|+.|+|+|+.|++..+.++...  ........-+...............++|+|+||.++..++.... .+.++.+
T Consensus       210 l~a~Il~ptreLa~Qi~re~~k~~~~~~t~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~~~~~idl~~V  289 (593)
T KOG0344|consen  210 LRALILSPTRELAAQIYREMRKYSIDEGTSLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGLGKLNIDLSKV  289 (593)
T ss_pred             eEEEEecchHHHHHHHHHHHHhcCCCCCCchhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcCCCccchhhee
Confidence            89999999999999999999988722  21111111111111112222223347899999999999997643 3577899


Q ss_pred             eEEEEecchhhhcC-CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCC
Q 043110          188 RWIIFDEADRILEL-GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK  266 (316)
Q Consensus       188 ~~lViDEad~l~~~-~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~  266 (316)
                      .++|+||||++++. .|..++..|+..+...              ...+-+||||++..+.+.+...+.+++.|.++..+
T Consensus       290 ~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~--------------~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~~  355 (593)
T KOG0344|consen  290 EWLVVDEADLLFEPEFFVEQLADIYSACQSP--------------DIRVALFSATISVYVEEWAELIKSDLKRVIVGLRN  355 (593)
T ss_pred             eeEeechHHhhhChhhHHHHHHHHHHHhcCc--------------chhhhhhhccccHHHHHHHHHhhccceeEEEecch
Confidence            99999999999999 8999999999988752              67788999999999999999999999988887765


Q ss_pred             CCCC
Q 043110          267 FPED  270 (316)
Q Consensus       267 ~~~~  270 (316)
                      ....
T Consensus       356 sa~~  359 (593)
T KOG0344|consen  356 SANE  359 (593)
T ss_pred             hHhh
Confidence            4433

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

Probab=99.95  E-value=9.2e-27  Score=227.09  Aligned_cols=203  Identities=29%  Similarity=0.356  Sum_probs=166.7

Q ss_pred             CCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           42 LDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        42 l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      |++.+++.+.++  |..|||.|.+|||.+.+|+|+++.||||||||+++++|++..+.... ......+..+|||+|.|+
T Consensus         8 l~~~v~~~~~~~--~~~~t~~Q~~a~~~i~~G~nvLiiAPTGsGKTeAAfLpil~~l~~~~-~~~~~~~i~~lYIsPLkA   84 (814)
T COG1201           8 LDPRVREWFKRK--FTSLTPPQRYAIPEIHSGENVLIIAPTGSGKTEAAFLPVINELLSLG-KGKLEDGIYALYISPLKA   84 (814)
T ss_pred             cCHHHHHHHHHh--cCCCCHHHHHHHHHHhCCCceEEEcCCCCChHHHHHHHHHHHHHhcc-CCCCCCceEEEEeCcHHH
Confidence            889999999544  99999999999999999999999999999999999999999998864 222345789999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCc-cccCceeEEEEecchhhhc
Q 043110          122 LCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSS-FLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       122 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~-~~~~~l~~lViDEad~l~~  200 (316)
                      |...+...++.++..++..+ .+-+|.+..........+.|||+|+||+.|.-++...+. -.+.+++++|+||.|.+.+
T Consensus        85 Ln~Di~~rL~~~~~~~G~~v-~vRhGDT~~~er~r~~~~PPdILiTTPEsL~lll~~~~~r~~l~~vr~VIVDEiHel~~  163 (814)
T COG1201          85 LNNDIRRRLEEPLRELGIEV-AVRHGDTPQSEKQKMLKNPPHILITTPESLAILLNSPKFRELLRDVRYVIVDEIHALAE  163 (814)
T ss_pred             HHHHHHHHHHHHHHHcCCcc-ceecCCCChHHhhhccCCCCcEEEeChhHHHHHhcCHHHHHHhcCCcEEEeehhhhhhc
Confidence            99999999999999876444 666677776666666777899999999999988876322 2678999999999999999


Q ss_pred             CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcC-C-CEEEE
Q 043110          201 LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLE-T-PVLIG  261 (316)
Q Consensus       201 ~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~-~-p~~i~  261 (316)
                      ...+.++..-++++...           .. ..|.|++|||.. +...+++.... + |+.|.
T Consensus       164 sKRG~~Lsl~LeRL~~l-----------~~-~~qRIGLSATV~-~~~~varfL~g~~~~~~Iv  213 (814)
T COG1201         164 SKRGVQLALSLERLREL-----------AG-DFQRIGLSATVG-PPEEVAKFLVGFGDPCEIV  213 (814)
T ss_pred             cccchhhhhhHHHHHhh-----------Cc-ccEEEeehhccC-CHHHHHHHhcCCCCceEEE
Confidence            99999999888888752           11 789999999998 44444443332 3 65443

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

Probab=99.95  E-value=3.8e-26  Score=227.45  Aligned_cols=214  Identities=20%  Similarity=0.212  Sum_probs=153.0

Q ss_pred             ccCCcc--cCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCC
Q 043110           33 ASCCFS--SLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSG  110 (316)
Q Consensus        33 ~~~~f~--~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~  110 (316)
                      ....|.  .++.+..+...+.+.|||..++|+|.++|+.++.|+|+++.+|||+|||+||++|++..            +
T Consensus       433 ~~~~W~~~~fpw~~~L~~~lk~~FG~~sFRp~Q~eaI~aiL~GrDVLVimPTGSGKSLcYQLPAL~~------------~  500 (1195)
T PLN03137        433 NDKKWSSRNFPWTKKLEVNNKKVFGNHSFRPNQREIINATMSGYDVFVLMPTGGGKSLTYQLPALIC------------P  500 (1195)
T ss_pred             CCccccccCCCchHHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHHHHHHHHHHHc------------C
Confidence            334465  46777888888888899999999999999999999999999999999999999999853            2


Q ss_pred             eeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHh------cCCcEEEeCcHHHHH---HHhcCCc
Q 043110          111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLR------KGISILVATPGHLLD---HLKHTSS  181 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~------~~~~IlV~Tp~~l~~---~l~~~~~  181 (316)
                      ..+|||+|+++|+.++...+...     .+....+.++.....+...+.      ..++||++||++|..   ++.....
T Consensus       501 GiTLVISPLiSLmqDQV~~L~~~-----GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~  575 (1195)
T PLN03137        501 GITLVISPLVSLIQDQIMNLLQA-----NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLEN  575 (1195)
T ss_pred             CcEEEEeCHHHHHHHHHHHHHhC-----CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHh
Confidence            34999999999998655554432     355666777777665554433      357999999999853   1221111


Q ss_pred             c-ccCceeEEEEecchhhhcCC--cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHh--cCC
Q 043110          182 F-LHTNLRWIIFDEADRILELG--FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKIS--LET  256 (316)
Q Consensus       182 ~-~~~~l~~lViDEad~l~~~~--~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~--l~~  256 (316)
                      . ....+.+|||||||++++||  |++.+..+-.....             -+..|++++|||++..+...+...  +.+
T Consensus       576 L~~~~~LslIVIDEAHcVSqWGhDFRpdYr~L~~Lr~~-------------fp~vPilALTATAT~~V~eDI~~~L~l~~  642 (1195)
T PLN03137        576 LNSRGLLARFVIDEAHCVSQWGHDFRPDYQGLGILKQK-------------FPNIPVLALTATATASVKEDVVQALGLVN  642 (1195)
T ss_pred             hhhccccceeccCcchhhhhcccchHHHHHHHHHHHHh-------------CCCCCeEEEEecCCHHHHHHHHHHcCCCC
Confidence            1 22458899999999999997  88877764222111             016789999999999988755443  446


Q ss_pred             CEEEEcCCCCCCCCCCCcccccccc
Q 043110          257 PVLIGLDEKKFPEDKSNVHFGSLES  281 (316)
Q Consensus       257 p~~i~~~~~~~~~~~~~~~~~~~~~  281 (316)
                      |+.+....+     +.++.+.+++.
T Consensus       643 ~~vfr~Sf~-----RpNL~y~Vv~k  662 (1195)
T PLN03137        643 CVVFRQSFN-----RPNLWYSVVPK  662 (1195)
T ss_pred             cEEeecccC-----ccceEEEEecc
Confidence            655443322     23455555543

>PRK09401 reverse gyrase; Reviewed

Probab=99.95  E-value=4.7e-26  Score=233.43  Aligned_cols=205  Identities=20%  Similarity=0.256  Sum_probs=144.7

Q ss_pred             HHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHH
Q 043110           45 TLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCL  124 (316)
Q Consensus        45 ~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~  124 (316)
                      ++.+.+.+.+|+ +|+++|+.++|.++.|+|++++||||+|||. |.++++..+..        .+.++|||+||++|+.
T Consensus        68 ~~~~~f~~~~G~-~pt~iQ~~~i~~il~g~dv~i~ApTGsGKT~-f~l~~~~~l~~--------~g~~alIL~PTreLa~  137 (1176)
T PRK09401         68 EFEKFFKKKTGS-KPWSLQRTWAKRLLLGESFAIIAPTGVGKTT-FGLVMSLYLAK--------KGKKSYIIFPTRLLVE  137 (1176)
T ss_pred             HHHHHHHHhcCC-CCcHHHHHHHHHHHCCCcEEEEcCCCCCHHH-HHHHHHHHHHh--------cCCeEEEEeccHHHHH
Confidence            445566566788 6999999999999999999999999999996 55565555433        2667999999999999


Q ss_pred             HHHHHHHHHHhhcCCceeEEeeCCCC-----hHHHHHHHh-cCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhh
Q 043110          125 LVYEILQKLLHRFRWIVPGYVMGGGN-----RSKEKARLR-KGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRI  198 (316)
Q Consensus       125 Q~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l  198 (316)
                      |+++.++.++...+ ..+..+.++..     .......+. ..++|+|+||++|.+++..   +....++++|+||||++
T Consensus       138 Qi~~~l~~l~~~~~-~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~~---l~~~~~~~lVvDEaD~~  213 (1176)
T PRK09401        138 QVVEKLEKFGEKVG-CGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFDE---LPKKKFDFVFVDDVDAV  213 (1176)
T ss_pred             HHHHHHHHHhhhcC-ceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHHh---ccccccCEEEEEChHHh
Confidence            99999999988765 33344444432     223333444 3589999999999998762   33456999999999999


Q ss_pred             hc-----------CCcH-HHHHHHHHHhccCccc--------ccC-CCCccccccceEEEEeeecchh-HHHHHHHhcCC
Q 043110          199 LE-----------LGFG-KEIEEILDILGSRNIA--------SIG-EGNEVSNVKRQNLLLSATLNEK-VNHLTKISLET  256 (316)
Q Consensus       199 ~~-----------~~~~-~~i~~i~~~l~~~~~~--------~~~-~~~~~~~~~~q~i~~SAT~~~~-v~~~~~~~l~~  256 (316)
                      ++           .||. ++++.+++.++.....        ... .........+|++++|||+++. +..   ..+++
T Consensus       214 L~~~k~id~~l~~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~~~~~~---~l~~~  290 (1176)
T PRK09401        214 LKSSKNIDKLLYLLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRPRGNRV---KLFRE  290 (1176)
T ss_pred             hhcccchhhHHHhCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCccchHH---HHhhc
Confidence            96           5785 6888888888641110        000 0000112268999999999864 432   23455


Q ss_pred             CEEEEcCCCC
Q 043110          257 PVLIGLDEKK  266 (316)
Q Consensus       257 p~~i~~~~~~  266 (316)
                      +..+.+....
T Consensus       291 ll~~~v~~~~  300 (1176)
T PRK09401        291 LLGFEVGSPV  300 (1176)
T ss_pred             cceEEecCcc
Confidence            6556555443

>PRK01172 ski2-like helicase; Provisional

Probab=99.95  E-value=2.4e-26  Score=227.82  Aligned_cols=186  Identities=24%  Similarity=0.328  Sum_probs=150.4

Q ss_pred             CcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEE
Q 043110           36 CFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALV  115 (316)
Q Consensus        36 ~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~li  115 (316)
                      .|++++|++.+.+.+ +..+|. ++++|.++++.+.+|+|++++||||||||+++.+++++.+..         +.++||
T Consensus         2 ~~~~~~l~~~~~~~~-~~~~~~-l~~~Q~~ai~~l~~~~nvlv~apTGSGKTl~a~lail~~l~~---------~~k~v~   70 (674)
T PRK01172          2 KISDLGYDDEFLNLF-TGNDFE-LYDHQRMAIEQLRKGENVIVSVPTAAGKTLIAYSAIYETFLA---------GLKSIY   70 (674)
T ss_pred             cHhhcCCCHHHHHHH-hhCCCC-CCHHHHHHHHHHhcCCcEEEECCCCchHHHHHHHHHHHHHHh---------CCcEEE
Confidence            588999999999999 666887 999999999999999999999999999999999999988754         345999


Q ss_pred             EeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecc
Q 043110          116 LVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEA  195 (316)
Q Consensus       116 l~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEa  195 (316)
                      ++|+++||.|+++.++++.. .+ ..+....|+......   ..+.++|+|+||+++..++.+. ...+.+++++|+|||
T Consensus        71 i~P~raLa~q~~~~~~~l~~-~g-~~v~~~~G~~~~~~~---~~~~~dIiv~Tpek~~~l~~~~-~~~l~~v~lvViDEa  144 (674)
T PRK01172         71 IVPLRSLAMEKYEELSRLRS-LG-MRVKISIGDYDDPPD---FIKRYDVVILTSEKADSLIHHD-PYIINDVGLIVADEI  144 (674)
T ss_pred             EechHHHHHHHHHHHHHHhh-cC-CeEEEEeCCCCCChh---hhccCCEEEECHHHHHHHHhCC-hhHHhhcCEEEEecc
Confidence            99999999999999987642 23 444455555443221   2346799999999998888763 344678999999999


Q ss_pred             hhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHH
Q 043110          196 DRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK  251 (316)
Q Consensus       196 d~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~  251 (316)
                      |.+.+.+++..++.++..+...            ++..|++++|||+++ ..++++
T Consensus       145 H~l~d~~rg~~le~ll~~~~~~------------~~~~riI~lSATl~n-~~~la~  187 (674)
T PRK01172        145 HIIGDEDRGPTLETVLSSARYV------------NPDARILALSATVSN-ANELAQ  187 (674)
T ss_pred             hhccCCCccHHHHHHHHHHHhc------------CcCCcEEEEeCccCC-HHHHHH
Confidence            9999888999999888776531            126899999999974 455554

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.94  E-value=1.8e-26  Score=219.50  Aligned_cols=184  Identities=22%  Similarity=0.283  Sum_probs=133.4

Q ss_pred             HHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHH
Q 043110           50 LRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI  129 (316)
Q Consensus        50 l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~  129 (316)
                      |++.|||..|+|+|.++|+.+++|+|+++.+|||+|||++|++|++..            +..+||++|+++|+.|+.+.
T Consensus         3 l~~~~g~~~~r~~Q~~ai~~~l~g~dvlv~apTGsGKTl~y~lp~l~~------------~~~~lVi~P~~~L~~dq~~~   70 (470)
T TIGR00614         3 LKTVFGLSSFRPVQLEVINAVLLGRDCFVVMPTGGGKSLCYQLPALCS------------DGITLVISPLISLMEDQVLQ   70 (470)
T ss_pred             hHhhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCcHhHHHHHHHHHc------------CCcEEEEecHHHHHHHHHHH
Confidence            567799999999999999999999999999999999999999998752            23499999999999999888


Q ss_pred             HHHHHhhcCCceeEEeeCCCChHHHH---HHH-hcCCcEEEeCcHHHHHHHhcCCcc-ccCceeEEEEecchhhhcCC--
Q 043110          130 LQKLLHRFRWIVPGYVMGGGNRSKEK---ARL-RKGISILVATPGHLLDHLKHTSSF-LHTNLRWIIFDEADRILELG--  202 (316)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~---~~l-~~~~~IlV~Tp~~l~~~l~~~~~~-~~~~l~~lViDEad~l~~~~--  202 (316)
                      +..++     +....+.++.......   ..+ ...++|+++||+++.........+ ...+++++||||||++++||  
T Consensus        71 l~~~g-----i~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~i~~iViDEaH~i~~~g~~  145 (470)
T TIGR00614        71 LKASG-----IPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKGITLIAVDEAHCISQWGHD  145 (470)
T ss_pred             HHHcC-----CcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCCcCEEEEeCCcccCccccc
Confidence            77542     3344444554443222   122 234799999999875422110111 34688999999999999986  


Q ss_pred             cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHh--cCCCEEEEcC
Q 043110          203 FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKIS--LETPVLIGLD  263 (316)
Q Consensus       203 ~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~--l~~p~~i~~~  263 (316)
                      |.+.+..+......             .+..|++++|||+++.+...+...  +.+|..+..+
T Consensus       146 fr~~~~~l~~l~~~-------------~~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~s  195 (470)
T TIGR00614       146 FRPDYKALGSLKQK-------------FPNVPIMALTATASPSVREDILRQLNLKNPQIFCTS  195 (470)
T ss_pred             cHHHHHHHHHHHHH-------------cCCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeCC
Confidence            67766655332221             116789999999999887654433  5577666544

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=99.94  E-value=6e-26  Score=227.73  Aligned_cols=223  Identities=23%  Similarity=0.281  Sum_probs=163.5

Q ss_pred             ccCchhhhhhhhccccccccccc-ccccccc----CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC------
Q 043110            5 PLNSQTISKKKKRNDKMSKKKET-VKEIFAS----CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG------   73 (316)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~----~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g------   73 (316)
                      .|.+..|.+.+.+.+.-.+.-.. .-.+++.    ..+ .++.+..+.+.+.+.++|+ ||+.|.+||+.++++      
T Consensus       395 ~lg~~~w~~~k~~~~~~~~~~a~~l~~l~a~r~~~~~~-~~~~~~~~~~~~~~~~~f~-~T~~Q~~aI~~I~~d~~~~~~  472 (926)
T TIGR00580       395 KLGGKSWEKTKAKVKKSVREIAAKLIELYAKRKAIKGH-AFPPDLEWQQEFEDSFPFE-ETPDQLKAIEEIKADMESPRP  472 (926)
T ss_pred             ccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CCCCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHhhhcccCc
Confidence            57788999998887554443211 1111111    111 2345667777787889996 999999999999875      


Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHH
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSK  153 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (316)
                      +|.+++|+||+|||.+|++|++..+..         +.+++|++||++||.|+++.+++++..++ ..+..+.++.....
T Consensus       473 ~d~Ll~adTGsGKT~val~a~l~al~~---------g~qvlvLvPT~~LA~Q~~~~f~~~~~~~~-i~v~~Lsg~~~~~e  542 (926)
T TIGR00580       473 MDRLVCGDVGFGKTEVAMRAAFKAVLD---------GKQVAVLVPTTLLAQQHFETFKERFANFP-VTIELLSRFRSAKE  542 (926)
T ss_pred             CCEEEECCCCccHHHHHHHHHHHHHHh---------CCeEEEEeCcHHHHHHHHHHHHHHhccCC-cEEEEEeccccHHH
Confidence            799999999999999999999988754         46799999999999999999999887654 44555666555433


Q ss_pred             H---HHHHhc-CCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccc
Q 043110          154 E---KARLRK-GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVS  229 (316)
Q Consensus       154 ~---~~~l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~  229 (316)
                      .   ...+.. .++|+||||..+    .  ..+.+.+++++||||+|++     +......+..++.             
T Consensus       543 ~~~~~~~l~~g~~dIVIGTp~ll----~--~~v~f~~L~llVIDEahrf-----gv~~~~~L~~~~~-------------  598 (926)
T TIGR00580       543 QNEILKELASGKIDILIGTHKLL----Q--KDVKFKDLGLLIIDEEQRF-----GVKQKEKLKELRT-------------  598 (926)
T ss_pred             HHHHHHHHHcCCceEEEchHHHh----h--CCCCcccCCEEEeeccccc-----chhHHHHHHhcCC-------------
Confidence            3   333444 489999999432    2  3456689999999999993     3444555555554             


Q ss_pred             cccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          230 NVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       230 ~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                        ++|+++||||+.+....+....+.++..|.....
T Consensus       599 --~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~  632 (926)
T TIGR00580       599 --SVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPE  632 (926)
T ss_pred             --CCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCC
Confidence              7899999999887777777777888888876544

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.

>PRK14701 reverse gyrase; Provisional

Probab=99.94  E-value=4.4e-25  Score=230.95  Aligned_cols=209  Identities=19%  Similarity=0.191  Sum_probs=144.5

Q ss_pred             CHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHH
Q 043110           43 DSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSEL  122 (316)
Q Consensus        43 ~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L  122 (316)
                      -.++.+.+.+.+|| +|+++|+.++|.++.|+|+++.||||+|||++++++++....         .+.++|||+||++|
T Consensus        65 ~~~~~~~f~~~~G~-~pt~iQ~~~i~~il~G~d~li~APTGsGKTl~~~~~al~~~~---------~g~~aLVl~PTreL  134 (1638)
T PRK14701         65 VEEFEEFFEKITGF-EFWSIQKTWAKRILRGKSFSIVAPTGMGKSTFGAFIALFLAL---------KGKKCYIILPTTLL  134 (1638)
T ss_pred             HHHHHHHHHHhhCC-CCCHHHHHHHHHHHcCCCEEEEEcCCCCHHHHHHHHHHHHHh---------cCCeEEEEECHHHH
Confidence            34566677556899 599999999999999999999999999999976666554322         25679999999999


Q ss_pred             HHHHHHHHHHHHhhcC-CceeEEeeCCCChHHHH---HHHhc-CCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchh
Q 043110          123 CLLVYEILQKLLHRFR-WIVPGYVMGGGNRSKEK---ARLRK-GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADR  197 (316)
Q Consensus       123 ~~Q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~---~~l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~  197 (316)
                      +.|+++.++.++...+ ......++|+.+...+.   ..+.. .++|+|+||++|.+++...  .. .+++++|+||||+
T Consensus       135 a~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~l--~~-~~i~~iVVDEAD~  211 (1638)
T PRK14701        135 VKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPEM--KH-LKFDFIFVDDVDA  211 (1638)
T ss_pred             HHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHHH--hh-CCCCEEEEECcee
Confidence            9999999999987654 24445666777665543   33444 4899999999998877642  12 5789999999999


Q ss_pred             hhc-----------CCcHHHHHH-HHHHhccCcc----------cccCCCCccccccce-EEEEeeecchhHHHHHHHhc
Q 043110          198 ILE-----------LGFGKEIEE-ILDILGSRNI----------ASIGEGNEVSNVKRQ-NLLLSATLNEKVNHLTKISL  254 (316)
Q Consensus       198 l~~-----------~~~~~~i~~-i~~~l~~~~~----------~~~~~~~~~~~~~~q-~i~~SAT~~~~v~~~~~~~l  254 (316)
                      |++           .||.+++.. +++.++....          ..........+..+| ++++|||++.... . ...+
T Consensus       212 ml~~~knid~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~~r~~-~-~~l~  289 (1638)
T PRK14701        212 FLKASKNIDRSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGKAKGD-R-VKLY  289 (1638)
T ss_pred             ccccccccchhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCCchhH-H-HHHh
Confidence            987           478888764 2222210000          000000001122445 6789999996421 1 1344


Q ss_pred             CCCEEEEcCCCC
Q 043110          255 ETPVLIGLDEKK  266 (316)
Q Consensus       255 ~~p~~i~~~~~~  266 (316)
                      ++|..+.++.+.
T Consensus       290 ~~~l~f~v~~~~  301 (1638)
T PRK14701        290 RELLGFEVGSGR  301 (1638)
T ss_pred             hcCeEEEecCCC
Confidence            778878777664

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.93  E-value=7.3e-25  Score=224.28  Aligned_cols=223  Identities=21%  Similarity=0.252  Sum_probs=164.1

Q ss_pred             CccCchhhhhhhhccccccccccc-------cccccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC---
Q 043110            4 QPLNSQTISKKKKRNDKMSKKKET-------VKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG---   73 (316)
Q Consensus         4 ~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g---   73 (316)
                      ..|.+..|.+.+.+.+.-.+.-..       .........|   .-+....+.+.+.++|. ||+.|.+||+.++.+   
T Consensus       543 ~~lg~~~w~~~k~~~~~~~~~~a~~l~~~~a~r~~~~~~~~---~~~~~~~~~~~~~~~~~-~T~~Q~~aI~~il~d~~~  618 (1147)
T PRK10689        543 HKLGGDAWSRARQKAAEKVRDVAAELLDIYAQRAAKEGFAF---KHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQ  618 (1147)
T ss_pred             ccCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCC---CCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHHHhhc
Confidence            357788899988877554443211       1112222222   34455666666889995 999999999999987   


Q ss_pred             ---CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCC
Q 043110           74 ---RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGN  150 (316)
Q Consensus        74 ---~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~  150 (316)
                         +|++++|+||+|||.+|+.++...+..         +.+++|++||++||.|+++.+++.+..++ +.+.++.++.+
T Consensus       619 ~~~~d~Ll~a~TGsGKT~val~aa~~~~~~---------g~qvlvLvPT~eLA~Q~~~~f~~~~~~~~-v~i~~l~g~~s  688 (1147)
T PRK10689        619 PLAMDRLVCGDVGFGKTEVAMRAAFLAVEN---------HKQVAVLVPTTLLAQQHYDNFRDRFANWP-VRIEMLSRFRS  688 (1147)
T ss_pred             CCCCCEEEEcCCCcCHHHHHHHHHHHHHHc---------CCeEEEEeCcHHHHHHHHHHHHHhhccCC-ceEEEEECCCC
Confidence               799999999999999999888776542         66799999999999999999998765543 45556667666


Q ss_pred             hHHHHHHH---h-cCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCC
Q 043110          151 RSKEKARL---R-KGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGN  226 (316)
Q Consensus       151 ~~~~~~~l---~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~  226 (316)
                      ...+...+   . ..++|+||||+.+    .  ..+.+.+++++||||+|++   |+.  ....+..++.          
T Consensus       689 ~~e~~~il~~l~~g~~dIVVgTp~lL----~--~~v~~~~L~lLVIDEahrf---G~~--~~e~lk~l~~----------  747 (1147)
T PRK10689        689 AKEQTQILAEAAEGKIDILIGTHKLL----Q--SDVKWKDLGLLIVDEEHRF---GVR--HKERIKAMRA----------  747 (1147)
T ss_pred             HHHHHHHHHHHHhCCCCEEEECHHHH----h--CCCCHhhCCEEEEechhhc---chh--HHHHHHhcCC----------
Confidence            65554433   2 3589999999743    2  3345678999999999996   332  2344455554          


Q ss_pred             ccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCC
Q 043110          227 EVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK  266 (316)
Q Consensus       227 ~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~  266 (316)
                           ++|+++||||+++....++...+++|..|......
T Consensus       748 -----~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~~  782 (1147)
T PRK10689        748 -----DVDILTLTATPIPRTLNMAMSGMRDLSIIATPPAR  782 (1147)
T ss_pred             -----CCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCCC
Confidence                 88999999999888888888899999988765543

>TIGR01054 rgy reverse gyrase

Probab=99.93  E-value=2e-24  Score=221.80  Aligned_cols=207  Identities=20%  Similarity=0.229  Sum_probs=141.0

Q ss_pred             CHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHH
Q 043110           43 DSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSEL  122 (316)
Q Consensus        43 ~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L  122 (316)
                      ..++.+.+.+..|+ +|+++|+.++|.++.|+|++++||||+|||+ |.+|+...+..        .+.++|||+||++|
T Consensus        64 ~~~f~~~f~~~~g~-~p~~iQ~~~i~~il~G~d~vi~ApTGsGKT~-f~l~~~~~l~~--------~g~~vLIL~PTreL  133 (1171)
T TIGR01054        64 LKEFEEFFKKAVGS-EPWSIQKMWAKRVLRGDSFAIIAPTGVGKTT-FGLAMSLFLAK--------KGKRCYIILPTTLL  133 (1171)
T ss_pred             HHHHHHHHHHhcCC-CCcHHHHHHHHHHhCCCeEEEECCCCCCHHH-HHHHHHHHHHh--------cCCeEEEEeCHHHH
Confidence            34556666445565 6999999999999999999999999999997 66777666543        25679999999999


Q ss_pred             HHHHHHHHHHHHhhcCCce--eEEeeCCCChHHH---HHHHhc-CCcEEEeCcHHHHHHHhcCCccccCceeEEEEecch
Q 043110          123 CLLVYEILQKLLHRFRWIV--PGYVMGGGNRSKE---KARLRK-GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEAD  196 (316)
Q Consensus       123 ~~Q~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~---~~~l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad  196 (316)
                      |.|+++.++.++...+...  ..+.+||.+...+   ...+.+ +++|+|+||++|.+++....    ..++++|+||||
T Consensus       134 a~Qi~~~l~~l~~~~~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~l~----~~~~~iVvDEaD  209 (1171)
T TIGR01054       134 VIQVAEKISSLAEKAGVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDELG----PKFDFIFVDDVD  209 (1171)
T ss_pred             HHHHHHHHHHHHHhcCCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHHhc----CCCCEEEEeChH
Confidence            9999999999987654222  2345677665543   233444 48999999999998876522    178999999999


Q ss_pred             hhhc-----------CCcHHH-HHHHHHHhccCcccc-------cCCCCccccccce--EEEEeee-cchhHHHHHHHhc
Q 043110          197 RILE-----------LGFGKE-IEEILDILGSRNIAS-------IGEGNEVSNVKRQ--NLLLSAT-LNEKVNHLTKISL  254 (316)
Q Consensus       197 ~l~~-----------~~~~~~-i~~i~~~l~~~~~~~-------~~~~~~~~~~~~q--~i~~SAT-~~~~v~~~~~~~l  254 (316)
                      +|++           .||.++ ++.+++.++......       ........+.++|  ++++||| .|..+..   .++
T Consensus       210 ~~L~~~k~vd~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~p~~~~~---~l~  286 (1171)
T TIGR01054       210 ALLKASKNVDKLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGRPRGKRA---KLF  286 (1171)
T ss_pred             hhhhccccHHHHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCCccccHH---HHc
Confidence            9998           577764 666654432100000       0000000112344  6779999 5655442   345


Q ss_pred             CCCEEEEcCCCC
Q 043110          255 ETPVLIGLDEKK  266 (316)
Q Consensus       255 ~~p~~i~~~~~~  266 (316)
                      +++..+.+....
T Consensus       287 r~ll~~~v~~~~  298 (1171)
T TIGR01054       287 RELLGFEVGGGS  298 (1171)
T ss_pred             ccccceEecCcc
Confidence            666666665543

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.

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.93  E-value=1.2e-24  Score=212.66  Aligned_cols=191  Identities=24%  Similarity=0.280  Sum_probs=138.3

Q ss_pred             CCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCC
Q 043110           40 LGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPT  119 (316)
Q Consensus        40 ~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt  119 (316)
                      ++++....+.|++.+||..|+|+|+++|+.+++|+|+++.+|||+|||++|++|++..-            ..+||++|+
T Consensus         7 ~~~~~~~~~~l~~~fG~~~~r~~Q~~ai~~il~g~dvlv~apTGsGKTl~y~lpal~~~------------g~tlVisPl   74 (607)
T PRK11057          7 LNLESLAKQVLQETFGYQQFRPGQQEIIDAVLSGRDCLVVMPTGGGKSLCYQIPALVLD------------GLTLVVSPL   74 (607)
T ss_pred             CCchhHHHHHHHHHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHcC------------CCEEEEecH
Confidence            44666667778778999999999999999999999999999999999999999998531            239999999


Q ss_pred             hHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHH---HHh-cCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecc
Q 043110          120 SELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA---RLR-KGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEA  195 (316)
Q Consensus       120 ~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEa  195 (316)
                      ++|+.|+.+.++..+     +...+..++........   .+. ...+++++||+++...... ..+...+++++|||||
T Consensus        75 ~sL~~dqv~~l~~~g-----i~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~-~~l~~~~l~~iVIDEa  148 (607)
T PRK11057         75 ISLMKDQVDQLLANG-----VAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFL-EHLAHWNPALLAVDEA  148 (607)
T ss_pred             HHHHHHHHHHHHHcC-----CcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHH-HHHhhCCCCEEEEeCc
Confidence            999999988887642     33444445544443322   222 3478999999998732111 1122347899999999


Q ss_pred             hhhhcCC--cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHH--HhcCCCEEEE
Q 043110          196 DRILELG--FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK--ISLETPVLIG  261 (316)
Q Consensus       196 d~l~~~~--~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~--~~l~~p~~i~  261 (316)
                      |++.+||  |.+.+..+......             .+..+++++|||+++.+...+.  ..+.+|....
T Consensus       149 H~i~~~G~~fr~~y~~L~~l~~~-------------~p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~~  205 (607)
T PRK11057        149 HCISQWGHDFRPEYAALGQLRQR-------------FPTLPFMALTATADDTTRQDIVRLLGLNDPLIQI  205 (607)
T ss_pred             cccccccCcccHHHHHHHHHHHh-------------CCCCcEEEEecCCChhHHHHHHHHhCCCCeEEEE
Confidence            9999986  67666554332211             1167899999999988765433  3456776544

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.93  E-value=9.7e-25  Score=213.36  Aligned_cols=183  Identities=19%  Similarity=0.264  Sum_probs=135.8

Q ss_pred             HHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHH
Q 043110           48 DQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY  127 (316)
Q Consensus        48 ~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~  127 (316)
                      +.|++.|||.+|+|+|.++|+.+++|+|+++.+|||+|||++|++|++..            +..++|++|+++|+.|+.
T Consensus         3 ~~l~~~fg~~~fr~~Q~~~i~~il~g~dvlv~~PTG~GKTl~y~lpal~~------------~g~~lVisPl~sL~~dq~   70 (591)
T TIGR01389         3 QVLKRTFGYDDFRPGQEEIISHVLDGRDVLVVMPTGGGKSLCYQVPALLL------------KGLTVVISPLISLMKDQV   70 (591)
T ss_pred             HHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCccHhHHHHHHHHHc------------CCcEEEEcCCHHHHHHHH
Confidence            45767799999999999999999999999999999999999999998742            123899999999999999


Q ss_pred             HHHHHHHhhcCCceeEEeeCCCChHHHHHH----HhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCC-
Q 043110          128 EILQKLLHRFRWIVPGYVMGGGNRSKEKAR----LRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELG-  202 (316)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~-  202 (316)
                      +.++.++     +.+..+.++.+.......    ....++|+++||+++...... ......+++++||||||++.+|| 
T Consensus        71 ~~l~~~g-----i~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~-~~l~~~~l~~iViDEaH~i~~~g~  144 (591)
T TIGR01389        71 DQLRAAG-----VAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFL-NMLQRIPIALVAVDEAHCVSQWGH  144 (591)
T ss_pred             HHHHHcC-----CcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHH-HHHhcCCCCEEEEeCCcccccccC
Confidence            8887753     344455555554433222    234579999999998643221 12234578999999999999876 


Q ss_pred             -cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhc--CCCEEEE
Q 043110          203 -FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISL--ETPVLIG  261 (316)
Q Consensus       203 -~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l--~~p~~i~  261 (316)
                       |++.+..+.......             +..+++++|||.++.+...+...+  .+|..+.
T Consensus       145 ~frp~y~~l~~l~~~~-------------~~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~  193 (591)
T TIGR01389       145 DFRPEYQRLGSLAERF-------------PQVPRIALTATADAETRQDIRELLRLADANEFI  193 (591)
T ss_pred             ccHHHHHHHHHHHHhC-------------CCCCEEEEEeCCCHHHHHHHHHHcCCCCCCeEe
Confidence             777776665543321             145699999999999887665554  3555443

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.

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

Probab=99.92  E-value=7e-24  Score=211.57  Aligned_cols=210  Identities=28%  Similarity=0.330  Sum_probs=158.6

Q ss_pred             CCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           42 LDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        42 l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      .+..+...| .+.|+..|+++|.+|+..+.+|+|+++.++||||||.+|++|+++++.+..       ..++|+|.||++
T Consensus        55 ~~~~l~~~l-~~~g~~~lY~HQ~~A~~~~~~G~~vvVtTgTgSGKTe~FllPIld~~l~~~-------~a~AL~lYPtnA  126 (851)
T COG1205          55 RDESLKSAL-VKAGIERLYSHQVDALRLIREGRNVVVTTGTGSGKTESFLLPILDHLLRDP-------SARALLLYPTNA  126 (851)
T ss_pred             hhhHHHHHH-HHhccccccHHHHHHHHHHHCCCCEEEECCCCCchhHHHHHHHHHHHhhCc-------CccEEEEechhh
Confidence            455567777 445888899999999999999999999999999999999999999998743       336999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHH-HHHhcCCcEEEeCcHHHHHHHhcCC---ccccCceeEEEEecchh
Q 043110          122 LCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK-ARLRKGISILVATPGHLLDHLKHTS---SFLHTNLRWIIFDEADR  197 (316)
Q Consensus       122 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~l~~~~~IlV~Tp~~l~~~l~~~~---~~~~~~l~~lViDEad~  197 (316)
                      |++.+.+.++++....+.......+.|.....+. ....+.++||++||.+|..++....   .+.++++++||+||+|.
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            9999999999999887743444455555555555 6677889999999999998554332   23567899999999998


Q ss_pred             hhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCC
Q 043110          198 ILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPE  269 (316)
Q Consensus       198 l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~  269 (316)
                      .-. .|+.++..++++|...        ....+...|+|+.|||+... ..++..+...+....++++..+.
T Consensus       207 YrG-v~GS~vA~llRRL~~~--------~~~~~~~~q~i~~SAT~~np-~e~~~~l~~~~f~~~v~~~g~~~  268 (851)
T COG1205         207 YRG-VQGSEVALLLRRLLRR--------LRRYGSPLQIICTSATLANP-GEFAEELFGRDFEVPVDEDGSPR  268 (851)
T ss_pred             ccc-cchhHHHHHHHHHHHH--------HhccCCCceEEEEeccccCh-HHHHHHhcCCcceeeccCCCCCC
Confidence            655 3788887777777642        11223478999999999855 44555454444444355554333

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.91  E-value=3e-23  Score=204.96  Aligned_cols=181  Identities=25%  Similarity=0.293  Sum_probs=136.1

Q ss_pred             CHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC------CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEE
Q 043110           43 DSTLCDQLRERLGFEAPTKVQAQAIPVILSG------RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVL  116 (316)
Q Consensus        43 ~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g------~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil  116 (316)
                      +..+.+.+.+.++|. ||++|++|++.+.++      .+.+++|+||||||++|++|++..+..         |.+++|+
T Consensus       247 ~~~~~~~~~~~l~f~-lt~~Q~~ai~~I~~d~~~~~~~~~Ll~~~TGSGKT~va~~~il~~~~~---------g~q~lil  316 (681)
T PRK10917        247 DGELLKKFLASLPFE-LTGAQKRVVAEILADLASPKPMNRLLQGDVGSGKTVVAALAALAAIEA---------GYQAALM  316 (681)
T ss_pred             ChHHHHHHHHhCCCC-CCHHHHHHHHHHHHhhhccCCceEEEECCCCCcHHHHHHHHHHHHHHc---------CCeEEEE
Confidence            356667776889996 999999999999876      479999999999999999999988754         6779999


Q ss_pred             eCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH---HHHHhc-CCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          117 VPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE---KARLRK-GISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       117 ~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      +||++||.|+++.+++++...+ ..+.++.|+......   ...+.. .++|+||||+.+.+      ...+.+++++|+
T Consensus       317 aPT~~LA~Q~~~~l~~l~~~~~-i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~------~v~~~~l~lvVI  389 (681)
T PRK10917        317 APTEILAEQHYENLKKLLEPLG-IRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQD------DVEFHNLGLVII  389 (681)
T ss_pred             eccHHHHHHHHHHHHHHHhhcC-cEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhcc------cchhcccceEEE
Confidence            9999999999999999987654 566777787765433   333444 48999999987743      234578999999


Q ss_pred             ecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEE
Q 043110          193 DEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI  260 (316)
Q Consensus       193 DEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i  260 (316)
                      ||+|++.     ......+.....               .+++++||||..+....+......++..+
T Consensus       390 DE~Hrfg-----~~qr~~l~~~~~---------------~~~iL~~SATp~prtl~~~~~g~~~~s~i  437 (681)
T PRK10917        390 DEQHRFG-----VEQRLALREKGE---------------NPHVLVMTATPIPRTLAMTAYGDLDVSVI  437 (681)
T ss_pred             echhhhh-----HHHHHHHHhcCC---------------CCCEEEEeCCCCHHHHHHHHcCCCceEEE
Confidence            9999852     223333333322               67899999998766555544333344343

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

Probab=99.91  E-value=4.3e-24  Score=190.26  Aligned_cols=160  Identities=20%  Similarity=0.295  Sum_probs=131.5

Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCc--eeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCce
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWI--VPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNL  187 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l  187 (316)
                      .+.+||+-|+|||++|.++.++++-....+.  ...+++||.....+...+..+.+|+|+||+|+.+++.. ..+.+..+
T Consensus       286 ap~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~~g~~ivvGtpgRl~~~is~-g~~~lt~c  364 (725)
T KOG0349|consen  286 APEAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLKDGTHIVVGTPGRLLQPISK-GLVTLTHC  364 (725)
T ss_pred             CcceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhhcCceeeecCchhhhhhhhc-cceeeeee
Confidence            4679999999999999999998887665433  33467788899999999999999999999999999986 56677899


Q ss_pred             eEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecc-hhHHHHHHHhcCCCEEEEcCCCC
Q 043110          188 RWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLN-EKVNHLTKISLETPVLIGLDEKK  266 (316)
Q Consensus       188 ~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~-~~v~~~~~~~l~~p~~i~~~~~~  266 (316)
                      +++|+||||.++..++.+.|..+...+|...         ......|.+++|||+. -+|..+..+.|+-|..|.+..+.
T Consensus       365 rFlvlDead~lL~qgy~d~I~r~h~qip~~t---------sdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkgeD  435 (725)
T KOG0349|consen  365 RFLVLDEADLLLGQGYDDKIYRFHGQIPHMT---------SDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGED  435 (725)
T ss_pred             EEEEecchhhhhhcccHHHHHHHhccchhhh---------cCCcccccceeeeEEeEEEeeehhhhhccCceeEeccccc
Confidence            9999999999999999999999999988632         1124789999999995 46888999999999999988877


Q ss_pred             CCCCCCCcccccc
Q 043110          267 FPEDKSNVHFGSL  279 (316)
Q Consensus       267 ~~~~~~~~~~~~~  279 (316)
                      .-++........+
T Consensus       436 ~vpetvHhvv~lv  448 (725)
T KOG0349|consen  436 LVPETVHHVVKLV  448 (725)
T ss_pred             ccchhhccceeec
Confidence            6665544433333

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.90  E-value=1.5e-22  Score=208.92  Aligned_cols=172  Identities=22%  Similarity=0.195  Sum_probs=128.0

Q ss_pred             EEcCCCCchHHHHHHHHHHHhhhcCCC----CCCCCCeeEEEEeCChHHHHHHHHHHHHHHhh-----------cCCcee
Q 043110           78 VNAATGTGKTVAYLAPIINHLQSYSPR----IDRSSGTFALVLVPTSELCLLVYEILQKLLHR-----------FRWIVP  142 (316)
Q Consensus        78 i~a~TGsGKT~~~~lp~l~~l~~~~~~----~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~-----------~~~~~~  142 (316)
                      ++||||||||++|.+|+++.+......    .....++++|||+|+++|+.|+++.++.....           ...+.+
T Consensus         1 V~APTGSGKTLAA~LpaL~~Ll~~~~~~~~~~~~~~~~raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V   80 (1490)
T PRK09751          1 VIAPTGSGKTLAAFLYALDRLFREGGEDTREAHKRKTSRILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRV   80 (1490)
T ss_pred             CcCCCCcHHHHHHHHHHHHHHHhcccccccccccCCCCEEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEE
Confidence            579999999999999999998764311    11234689999999999999999988753321           123566


Q ss_pred             EEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCccccc
Q 043110          143 GYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASI  222 (316)
Q Consensus       143 ~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~  222 (316)
                      ....|+.+.......+.+.++|||+||++|..++.+.....++++++|||||+|.|.+..++.++...++++...     
T Consensus        81 ~vrtGDt~~~eR~rll~~ppdILVTTPEsL~~LLtsk~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l-----  155 (1490)
T PRK09751         81 GIRTGDTPAQERSKLTRNPPDILITTPESLYLMLTSRARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDAL-----  155 (1490)
T ss_pred             EEEECCCCHHHHHHHhcCCCCEEEecHHHHHHHHhhhhhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHh-----
Confidence            677777777777667777899999999999998875434467899999999999999877777666666665431     


Q ss_pred             CCCCccccccceEEEEeeecchhHHHHHHHhc-CCCEEEE
Q 043110          223 GEGNEVSNVKRQNLLLSATLNEKVNHLTKISL-ETPVLIG  261 (316)
Q Consensus       223 ~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l-~~p~~i~  261 (316)
                            ...+.|+|++|||+++ ..++++... .+|+.|.
T Consensus       156 ------~~~~~QrIgLSATI~n-~eevA~~L~g~~pv~Iv  188 (1490)
T PRK09751        156 ------LHTSAQRIGLSATVRS-ASDVAAFLGGDRPVTVV  188 (1490)
T ss_pred             ------CCCCCeEEEEEeeCCC-HHHHHHHhcCCCCEEEE
Confidence                  1227899999999986 455554322 3577664

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.89  E-value=5.9e-22  Score=194.45  Aligned_cols=172  Identities=20%  Similarity=0.271  Sum_probs=126.6

Q ss_pred             HHHHHHHHHHcCCCCCcHHHHHHHHHHhCC------CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEe
Q 043110           44 STLCDQLRERLGFEAPTKVQAQAIPVILSG------RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLV  117 (316)
Q Consensus        44 ~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g------~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~  117 (316)
                      ......+.+.++| +||+.|++|++.++.+      .+.+++|+||||||++|++|++..+..         |.+++|++
T Consensus       222 ~~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~~~~~~~~~~Ll~g~TGSGKT~va~l~il~~~~~---------g~qvlila  291 (630)
T TIGR00643       222 EELLTKFLASLPF-KLTRAQKRVVKEILQDLKSDVPMNRLLQGDVGSGKTLVAALAMLAAIEA---------GYQVALMA  291 (630)
T ss_pred             hHHHHHHHHhCCC-CCCHHHHHHHHHHHHHhccCCCccEEEECCCCCcHHHHHHHHHHHHHHc---------CCcEEEEC
Confidence            3455555588999 5999999999999876      258999999999999999999988754         56799999


Q ss_pred             CChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHH---HHHHHh-cCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          118 PTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSK---EKARLR-KGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       118 Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      ||++||.|+++.+++++...+ ..+..+.|+.....   ....+. ..++|+|+||+.+.+      ...+.+++++|+|
T Consensus       292 PT~~LA~Q~~~~~~~l~~~~g-i~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~~------~~~~~~l~lvVID  364 (630)
T TIGR00643       292 PTEILAEQHYNSLRNLLAPLG-IEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQE------KVEFKRLALVIID  364 (630)
T ss_pred             CHHHHHHHHHHHHHHHhcccC-cEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHhc------cccccccceEEEe
Confidence            999999999999999987654 56677777766544   233333 347999999998754      2345789999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHH
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHL  249 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~  249 (316)
                      |+|++..    .....+......             ...+++++||||+.+....+
T Consensus       365 EaH~fg~----~qr~~l~~~~~~-------------~~~~~~l~~SATp~prtl~l  403 (630)
T TIGR00643       365 EQHRFGV----EQRKKLREKGQG-------------GFTPHVLVMSATPIPRTLAL  403 (630)
T ss_pred             chhhccH----HHHHHHHHhccc-------------CCCCCEEEEeCCCCcHHHHH
Confidence            9998532    112222222211             01578999999976554433

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=99.89  E-value=2.8e-23  Score=201.52  Aligned_cols=221  Identities=20%  Similarity=0.210  Sum_probs=153.1

Q ss_pred             CCHHHHHHHHHHcCCCCCcHHHHHHHHHHhC-CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCC-CCCCeeEEEEeCC
Q 043110           42 LDSTLCDQLRERLGFEAPTKVQAQAIPVILS-GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRID-RSSGTFALVLVPT  119 (316)
Q Consensus        42 l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~-g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~-~~~~~~~lil~Pt  119 (316)
                      |+.--.+.+   ++|..++.+|+.++|.+.. ..|.+|+||||+|||..|++.+++.+.+...... ...+.+++||+|+
T Consensus        97 ld~~~rk~~---f~f~~fN~iQS~vFp~aY~SneNMLIcAPTGsGKT~la~L~ILr~ik~~~~~~~i~k~~fKiVYIaPm  173 (1230)
T KOG0952|consen   97 LDDVGRKGF---FSFEEFNRIQSEVFPVAYKSNENMLICAPTGSGKTVLAELCILRTIKEHEEQGDIAKDDFKIVYIAPM  173 (1230)
T ss_pred             cchhhhhhc---ccHHHHHHHHHHhhhhhhcCCCCEEEECCCCCCchHHHHHHHHHHHHhhccccccccCCceEEEEech
Confidence            444444455   7999999999999999874 5689999999999999999999999986332221 2357889999999


Q ss_pred             hHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCC--ccccCceeEEEEecchh
Q 043110          120 SELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTS--SFLHTNLRWIIFDEADR  197 (316)
Q Consensus       120 ~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~--~~~~~~l~~lViDEad~  197 (316)
                      ++||.++.+.+.+-+..++ +.+.-+.|........   ...++|+|+||+++--.-+...  ...++.++++||||+|.
T Consensus       174 KALa~Em~~~~~kkl~~~g-i~v~ELTGD~ql~~te---i~~tqiiVTTPEKwDvvTRk~~~d~~l~~~V~LviIDEVHl  249 (1230)
T KOG0952|consen  174 KALAAEMVDKFSKKLAPLG-ISVRELTGDTQLTKTE---IADTQIIVTTPEKWDVVTRKSVGDSALFSLVRLVIIDEVHL  249 (1230)
T ss_pred             HHHHHHHHHHHhhhccccc-ceEEEecCcchhhHHH---HHhcCEEEecccceeeeeeeeccchhhhhheeeEEeeeehh
Confidence            9999877766655554433 4444555554443322   3458999999998744333322  23557899999999998


Q ss_pred             hhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCC-CEEEEcCCCCCCCCCCCccc
Q 043110          198 ILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLET-PVLIGLDEKKFPEDKSNVHF  276 (316)
Q Consensus       198 l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~-p~~i~~~~~~~~~~~~~~~~  276 (316)
                      |-| ..++-++.|+.+....        -+.+-...+++++|||+|. ..+++...-.+ +..+...+....|.....++
T Consensus       250 Lhd-~RGpvlEtiVaRtlr~--------vessqs~IRivgLSATlPN-~eDvA~fL~vn~~~glfsFd~~yRPvpL~~~~  319 (1230)
T KOG0952|consen  250 LHD-DRGPVLETIVARTLRL--------VESSQSMIRIVGLSATLPN-YEDVARFLRVNPYAGLFSFDQRYRPVPLTQGF  319 (1230)
T ss_pred             hcC-cccchHHHHHHHHHHH--------HHhhhhheEEEEeeccCCC-HHHHHHHhcCCCccceeeecccccccceeeeE
Confidence            766 4888899988887631        1122337899999999994 55555533233 56666666666665554444


Q ss_pred             ccc
Q 043110          277 GSL  279 (316)
Q Consensus       277 ~~~  279 (316)
                      ...
T Consensus       320 iG~  322 (1230)
T KOG0952|consen  320 IGI  322 (1230)
T ss_pred             Eee
Confidence            433

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.89  E-value=2.8e-21  Score=161.99  Aligned_cols=188  Identities=40%  Similarity=0.591  Sum_probs=152.9

Q ss_pred             HcCCCCCcHHHHHHHHHHhCC-CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH
Q 043110           53 RLGFEAPTKVQAQAIPVILSG-RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ  131 (316)
Q Consensus        53 ~~g~~~p~~~Q~~~i~~il~g-~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~  131 (316)
                      .+++..|+++|.++++.+..+ +++++.++||+|||.++..+++..+....       ..+++|++|+++++.|+...+.
T Consensus         3 ~~~~~~~~~~Q~~~~~~~~~~~~~~~i~~~~GsGKT~~~~~~~~~~~~~~~-------~~~~l~~~p~~~~~~~~~~~~~   75 (201)
T smart00487        3 KFGFEPLRPYQKEAIEALLSGLRDVILAAPTGSGKTLAALLPALEALKRGK-------GKRVLVLVPTRELAEQWAEELK   75 (201)
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCcEEEECCCCCchhHHHHHHHHHHhcccC-------CCcEEEEeCCHHHHHHHHHHHH
Confidence            357788999999999999998 99999999999999999998888876521       2459999999999999999888


Q ss_pred             HHHhhcCCceeEEeeCCCChHHHHHHHhcCC-cEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHH
Q 043110          132 KLLHRFRWIVPGYVMGGGNRSKEKARLRKGI-SILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEI  210 (316)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~-~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i  210 (316)
                      .++.... .......++.........+..+. +++++|++.+.+.+.... .....++++|+||+|.+....+...+..+
T Consensus        76 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~~~-~~~~~~~~iIiDE~h~~~~~~~~~~~~~~  153 (201)
T smart00487       76 KLGPSLG-LKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLENDL-LELSNVDLVILDEAHRLLDGGFGDQLEKL  153 (201)
T ss_pred             HHhccCC-eEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHcCC-cCHhHCCEEEEECHHHHhcCCcHHHHHHH
Confidence            8765432 23344455555455555566665 999999999999887643 44467889999999999876788888888


Q ss_pred             HHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCC
Q 043110          211 LDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDE  264 (316)
Q Consensus       211 ~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~  264 (316)
                      +..++.               ..+++++|||+++........++.+++.+....
T Consensus       154 ~~~~~~---------------~~~~v~~saT~~~~~~~~~~~~~~~~~~~~~~~  192 (201)
T smart00487      154 LKLLPK---------------NVQLLLLSATPPEEIENLLELFLNDPVFIDVGP  192 (201)
T ss_pred             HHhCCc---------------cceEEEEecCCchhHHHHHHHhcCCCEEEeCCc
Confidence            888755               789999999999999999999999888887665

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.89  E-value=1.8e-22  Score=199.03  Aligned_cols=190  Identities=25%  Similarity=0.288  Sum_probs=150.3

Q ss_pred             CCCHHHHHHHHHHcCCCCCcHHHHHHHHHHh-CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCC
Q 043110           41 GLDSTLCDQLRERLGFEAPTKVQAQAIPVIL-SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPT  119 (316)
Q Consensus        41 ~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il-~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt  119 (316)
                      .+++.+.+.+ +..++.++++-|+.++.... .++|+++++|||||||+.+++.+++.+.+.        +.++||++|+
T Consensus        15 ~~~~~v~~i~-~~~~~~el~~~qq~av~~~~~~~~N~li~aPTgsGKTlIA~lai~~~l~~~--------~~k~vYivPl   85 (766)
T COG1204          15 KLDDRVLEIL-KGDGIDELFNPQQEAVEKGLLSDENVLISAPTGSGKTLIALLAILSTLLEG--------GGKVVYIVPL   85 (766)
T ss_pred             cccHHHHHHh-ccCChHHhhHHHHHHhhccccCCCcEEEEcCCCCchHHHHHHHHHHHHHhc--------CCcEEEEeCh
Confidence            4778888888 66788888888888876654 569999999999999999999999999873        4569999999


Q ss_pred             hHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhh
Q 043110          120 SELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       120 ~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~  199 (316)
                      ++||.|.++.++.+ ..++ +.+....|+.....+.   ..+++|+|+||+++-.++++... ...+++++||||+|.+.
T Consensus        86 kALa~Ek~~~~~~~-~~~G-irV~~~TgD~~~~~~~---l~~~~ViVtT~EK~Dsl~R~~~~-~~~~V~lvViDEiH~l~  159 (766)
T COG1204          86 KALAEEKYEEFSRL-EELG-IRVGISTGDYDLDDER---LARYDVIVTTPEKLDSLTRKRPS-WIEEVDLVVIDEIHLLG  159 (766)
T ss_pred             HHHHHHHHHHhhhH-HhcC-CEEEEecCCcccchhh---hccCCEEEEchHHhhHhhhcCcc-hhhcccEEEEeeeeecC
Confidence            99999999999833 3444 5666666666644422   34679999999999998887555 56799999999999999


Q ss_pred             cCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCE
Q 043110          200 ELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPV  258 (316)
Q Consensus       200 ~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~  258 (316)
                      |...++.++.|+..+...+            ...|++.+|||+| +..+++.+.--+++
T Consensus       160 d~~RG~~lE~iv~r~~~~~------------~~~rivgLSATlp-N~~evA~wL~a~~~  205 (766)
T COG1204         160 DRTRGPVLESIVARMRRLN------------ELIRIVGLSATLP-NAEEVADWLNAKLV  205 (766)
T ss_pred             CcccCceehhHHHHHHhhC------------cceEEEEEeeecC-CHHHHHHHhCCccc
Confidence            8889999999999887632            2479999999999 45666654433333

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.89  E-value=2.9e-22  Score=196.25  Aligned_cols=151  Identities=19%  Similarity=0.291  Sum_probs=127.5

Q ss_pred             cccCCCCHHHHHHHHH----HcCCCCC---cHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCC
Q 043110           37 FSSLGLDSTLCDQLRE----RLGFEAP---TKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSS  109 (316)
Q Consensus        37 f~~~~l~~~l~~~l~~----~~g~~~p---~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~  109 (316)
                      -+.+++..++.+.+..    ..||..|   +|+|.+++|.+..+++++++++||+|||++|++|++..+...        
T Consensus        64 ~eafal~re~~~r~lg~~~~~~G~~~p~~~tp~qvQ~I~~i~l~~gvIAeaqTGeGKTLAf~LP~l~~aL~g--------  135 (970)
T PRK12899         64 PEAYGVVKNVCRRLAGTPVEVSGYHQQWDMVPYDVQILGAIAMHKGFITEMQTGEGKTLTAVMPLYLNALTG--------  135 (970)
T ss_pred             HHHhCCCHHHHHHHhccccccccccCCCCCChHHHHHhhhhhcCCCeEEEeCCCCChHHHHHHHHHHHHhhc--------
Confidence            3567899998888842    5689999   999999999999999999999999999999999999877641        


Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcCCcccc----
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHTSSFLH----  184 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~~~~~~----  184 (316)
                       ..++||+||++||.|.++++..+...++ +.+.++.||.+...+...+  +++|+||||++| +++++.. .+.+    
T Consensus       136 -~~v~IVTpTrELA~Qdae~m~~L~k~lG-LsV~~i~GG~~~~eq~~~y--~~DIVygTPgRLgfDyLrd~-~~~~~~~~  210 (970)
T PRK12899        136 -KPVHLVTVNDYLAQRDCEWVGSVLRWLG-LTTGVLVSGSPLEKRKEIY--QCDVVYGTASEFGFDYLRDN-SIATRKEE  210 (970)
T ss_pred             -CCeEEEeCCHHHHHHHHHHHHHHHhhcC-CeEEEEeCCCCHHHHHHHc--CCCEEEECCChhHHHHhhCC-CCCcCHHH
Confidence             1289999999999999999999998765 7778888998887776554  589999999999 9999863 2322    


Q ss_pred             ---CceeEEEEecchhhhc
Q 043110          185 ---TNLRWIIFDEADRILE  200 (316)
Q Consensus       185 ---~~l~~lViDEad~l~~  200 (316)
                         ..+.++||||||.|+-
T Consensus       211 ~vqr~~~~~IIDEADsmLi  229 (970)
T PRK12899        211 QVGRGFYFAIIDEVDSILI  229 (970)
T ss_pred             hhcccccEEEEechhhhhh
Confidence               3568999999999873

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.87  E-value=3.7e-21  Score=187.42  Aligned_cols=175  Identities=19%  Similarity=0.164  Sum_probs=126.7

Q ss_pred             HHHHHHHHHHhCCCcEEEEcCCCCchHHH---------HHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH
Q 043110           61 KVQAQAIPVILSGRDVLVNAATGTGKTVA---------YLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ  131 (316)
Q Consensus        61 ~~Q~~~i~~il~g~d~li~a~TGsGKT~~---------~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~  131 (316)
                      .+|+++++.+++|++++++|+||||||.+         |++|.+..+....+   ...+.+++|++|||+||.|+...+.
T Consensus       167 ~iQ~qil~~i~~gkdvIv~A~TGSGKTtqvPq~l~~~~flf~~l~~l~~~~~---~~~~~~ilvt~PrreLa~qi~~~i~  243 (675)
T PHA02653        167 DVQLKIFEAWISRKPVVLTGGTGVGKTSQVPKLLLWFNYLFGGFDNLDKIDP---NFIERPIVLSLPRVALVRLHSITLL  243 (675)
T ss_pred             HHHHHHHHHHHhCCCEEEECCCCCCchhHHHHHHHHhhhccchhhhhhhccc---ccCCcEEEEECcHHHHHHHHHHHHH
Confidence            58999999999999999999999999997         55556655532111   1234579999999999999999887


Q ss_pred             HHHhhc--CCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHH
Q 043110          132 KLLHRF--RWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEE  209 (316)
Q Consensus       132 ~~~~~~--~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~  209 (316)
                      +...+.  ....+...+||... .......+..+|+|+|++..        ...+++++++||||||.+...+  +.+..
T Consensus       244 ~~vg~~~~~g~~v~v~~Gg~~~-~~~~t~~k~~~Ilv~T~~L~--------l~~L~~v~~VVIDEaHEr~~~~--DllL~  312 (675)
T PHA02653        244 KSLGFDEIDGSPISLKYGSIPD-ELINTNPKPYGLVFSTHKLT--------LNKLFDYGTVIIDEVHEHDQIG--DIIIA  312 (675)
T ss_pred             HHhCccccCCceEEEEECCcch-HHhhcccCCCCEEEEeCccc--------ccccccCCEEEccccccCccch--hHHHH
Confidence            766432  23344566777663 22222234679999997621        1235689999999999987754  55555


Q ss_pred             HHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCC
Q 043110          210 ILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDE  264 (316)
Q Consensus       210 i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~  264 (316)
                      ++..+...              .+|+++||||+++++..+ ..++.+|..|.+..
T Consensus       313 llk~~~~~--------------~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~g  352 (675)
T PHA02653        313 VARKHIDK--------------IRSLFLMTATLEDDRDRI-KEFFPNPAFVHIPG  352 (675)
T ss_pred             HHHHhhhh--------------cCEEEEEccCCcHhHHHH-HHHhcCCcEEEeCC
Confidence            55544321              459999999999988887 57888999888764

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.85  E-value=3.4e-20  Score=177.68  Aligned_cols=151  Identities=19%  Similarity=0.172  Sum_probs=112.0

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhh
Q 043110           57 EAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHR  136 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~  136 (316)
                      ..|+++|.++++.++.+++.++++|||+|||+++...+...+..        ...++|||+||++|+.|+.+.+++++..
T Consensus       113 ~~~r~~Q~~av~~~l~~~~~il~apTGsGKT~i~~~l~~~~~~~--------~~~~vLilvpt~eL~~Q~~~~l~~~~~~  184 (501)
T PHA02558        113 IEPHWYQYDAVYEGLKNNRRLLNLPTSAGKSLIQYLLSRYYLEN--------YEGKVLIIVPTTSLVTQMIDDFVDYRLF  184 (501)
T ss_pred             CCCCHHHHHHHHHHHhcCceEEEeCCCCCHHHHHHHHHHHHHhc--------CCCeEEEEECcHHHHHHHHHHHHHhccc
Confidence            47999999999999999999999999999999865422222222        1236999999999999999999987643


Q ss_pred             cCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          137 FRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      .. .....+.+|....       .+.+|+|+||+++.....    ..+.+++++|+||||++.+    ..+..++..+++
T Consensus       185 ~~-~~~~~i~~g~~~~-------~~~~I~VaT~qsl~~~~~----~~~~~~~~iIvDEaH~~~~----~~~~~il~~~~~  248 (501)
T PHA02558        185 PR-EAMHKIYSGTAKD-------TDAPIVVSTWQSAVKQPK----EWFDQFGMVIVDECHLFTG----KSLTSIITKLDN  248 (501)
T ss_pred             cc-cceeEEecCcccC-------CCCCEEEeeHHHHhhchh----hhccccCEEEEEchhcccc----hhHHHHHHhhhc
Confidence            22 2233344444321       346899999999876432    1346889999999999875    345667777755


Q ss_pred             CcccccCCCCccccccceEEEEeeecchhH
Q 043110          217 RNIASIGEGNEVSNVKRQNLLLSATLNEKV  246 (316)
Q Consensus       217 ~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v  246 (316)
                                     .+++++||||+++..
T Consensus       249 ---------------~~~~lGLTATp~~~~  263 (501)
T PHA02558        249 ---------------CKFKFGLTGSLRDGK  263 (501)
T ss_pred             ---------------cceEEEEeccCCCcc
Confidence                           678999999997543

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

Probab=99.84  E-value=2.6e-20  Score=176.21  Aligned_cols=200  Identities=22%  Similarity=0.303  Sum_probs=148.8

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH
Q 043110           46 LCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL  125 (316)
Q Consensus        46 l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q  125 (316)
                      +...|.+.|||..+++-|.++|..+++|+|+++..|||+||++||.+|++-.-           | .+|||+|..+|+..
T Consensus         5 ~~~~L~~~fGy~~FR~gQ~evI~~~l~g~d~lvvmPTGgGKSlCyQiPAll~~-----------G-~TLVVSPLiSLM~D   72 (590)
T COG0514           5 AQQVLKQVFGYASFRPGQQEIIDALLSGKDTLVVMPTGGGKSLCYQIPALLLE-----------G-LTLVVSPLISLMKD   72 (590)
T ss_pred             HHHHHHHHhCccccCCCHHHHHHHHHcCCcEEEEccCCCCcchHhhhHHHhcC-----------C-CEEEECchHHHHHH
Confidence            34567777999999999999999999999999999999999999999997641           2 39999999999998


Q ss_pred             HHHHHHHHHhhcCCceeEEeeCCCChHHHH---HHHhc-CCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcC
Q 043110          126 VYEILQKLLHRFRWIVPGYVMGGGNRSKEK---ARLRK-GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL  201 (316)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~  201 (316)
                      +.+.++..+     +...++.+..+..+..   ..+.. ..+++.-+|+++...-.. ..+.-..+.++|||||||+.+|
T Consensus        73 QV~~l~~~G-----i~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~-~~L~~~~i~l~vIDEAHCiSqW  146 (590)
T COG0514          73 QVDQLEAAG-----IRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFL-ELLKRLPISLVAIDEAHCISQW  146 (590)
T ss_pred             HHHHHHHcC-----ceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHH-HHHHhCCCceEEechHHHHhhc
Confidence            888887754     3444444443433322   22233 378999999988543221 1112346889999999999999


Q ss_pred             C--cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHH--HhcCCCEEEEcCCCCCCCCCCCcccc
Q 043110          202 G--FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK--ISLETPVLIGLDEKKFPEDKSNVHFG  277 (316)
Q Consensus       202 ~--~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~--~~l~~p~~i~~~~~~~~~~~~~~~~~  277 (316)
                      |  |++.+..+-.......             +.+++++|||.++.+..-+.  +.+.+|..+..+.+     ..|+.+.
T Consensus       147 GhdFRP~Y~~lg~l~~~~~-------------~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~sfd-----RpNi~~~  208 (590)
T COG0514         147 GHDFRPDYRRLGRLRAGLP-------------NPPVLALTATATPRVRDDIREQLGLQDANIFRGSFD-----RPNLALK  208 (590)
T ss_pred             CCccCHhHHHHHHHHhhCC-------------CCCEEEEeCCCChHHHHHHHHHhcCCCcceEEecCC-----Cchhhhh
Confidence            7  9999998887765421             68999999999999987655  45567755544433     4566666


Q ss_pred             cccc
Q 043110          278 SLES  281 (316)
Q Consensus       278 ~~~~  281 (316)
                      +++.
T Consensus       209 v~~~  212 (590)
T COG0514         209 VVEK  212 (590)
T ss_pred             hhhc
Confidence            6663

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.83  E-value=2.5e-19  Score=164.60  Aligned_cols=171  Identities=18%  Similarity=0.197  Sum_probs=116.2

Q ss_pred             HHHHHHHHHhCCCc--EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcC-
Q 043110           62 VQAQAIPVILSGRD--VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFR-  138 (316)
Q Consensus        62 ~Q~~~i~~il~g~d--~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~-  138 (316)
                      +|.++++.+.++.+  +++.||||||||.+|++|++..            +.+++|++|+++|+.|+++.++.+...+. 
T Consensus         1 hQ~~~~~~~~~~~~~~~~i~apTGsGKT~~~~~~~l~~------------~~~~~~~~P~~aL~~~~~~~~~~~~~~~~~   68 (357)
T TIGR03158         1 HQVATFEALQSKDADIIFNTAPTGAGKTLAWLTPLLHG------------ENDTIALYPTNALIEDQTEAIKEFVDVFKP   68 (357)
T ss_pred             CHHHHHHHHHcCCCCEEEEECCCCCCHHHHHHHHHHHc------------CCCEEEEeChHHHHHHHHHHHHHHHHhcCC
Confidence            49999999998875  7899999999999999998842            12389999999999999999999886442 


Q ss_pred             --CceeEEeeCCCChHH---H-----------------H-HHHhcCCcEEEeCcHHHHHHHhcC---Cc----cccCcee
Q 043110          139 --WIVPGYVMGGGNRSK---E-----------------K-ARLRKGISILVATPGHLLDHLKHT---SS----FLHTNLR  188 (316)
Q Consensus       139 --~~~~~~~~~~~~~~~---~-----------------~-~~l~~~~~IlV~Tp~~l~~~l~~~---~~----~~~~~l~  188 (316)
                        .... ....|....+   .                 . ......++|+++||+.|..+++..   ..    ..+..++
T Consensus        69 ~~~~~v-~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p~~l~~llr~~~~~~~~~~~~~~~~~~  147 (357)
T TIGR03158        69 ERDVNL-LHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNPDIFVYLTRFAYIDRGDIAAGFYTKFS  147 (357)
T ss_pred             CCCceE-EEecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecHHHHHHHHhhhccCcccchhhhhcCCC
Confidence              1222 2222322111   0                 0 111235789999999998766532   11    1246899


Q ss_pred             EEEEecchhhhcCCcH-----HHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHh--cCCCEEE
Q 043110          189 WIIFDEADRILELGFG-----KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKIS--LETPVLI  260 (316)
Q Consensus       189 ~lViDEad~l~~~~~~-----~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~--l~~p~~i  260 (316)
                      ++|+||+|.+..+...     -....++.....               ..+++++|||+++.+.......  +..|+.+
T Consensus       148 ~iV~DE~H~~~~~~~~~~~~~l~~~~~~~~~~~---------------~~~~i~lSAT~~~~~~~~l~~~~~~~~~~~~  211 (357)
T TIGR03158       148 TVIFDEFHLYDAKQLVGMLFLLAYMQLIRFFEC---------------RRKFVFLSATPDPALILRLQNAKQAGVKIAP  211 (357)
T ss_pred             EEEEecccccCcccchhhhhhhHHHHHHHhhhc---------------CCcEEEEecCCCHHHHHHHHhccccCceeee
Confidence            9999999997643211     122233333222               4699999999999888777654  5556533

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

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

Probab=99.83  E-value=8.7e-20  Score=168.00  Aligned_cols=200  Identities=23%  Similarity=0.224  Sum_probs=155.3

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPV-ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~-il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      ...+++++++++.+.| ++.|++++.|+|..|+.. +++|.|.++.++|+||||+..-++-+..+..        .|.+.
T Consensus       194 ~~vdeLdipe~fk~~l-k~~G~~eLlPVQ~laVe~GLLeG~nllVVSaTasGKTLIgElAGi~~~l~--------~g~Km  264 (830)
T COG1202         194 VPVDELDIPEKFKRML-KREGIEELLPVQVLAVEAGLLEGENLLVVSATASGKTLIGELAGIPRLLS--------GGKKM  264 (830)
T ss_pred             ccccccCCcHHHHHHH-HhcCcceecchhhhhhhhccccCCceEEEeccCCCcchHHHhhCcHHHHh--------CCCeE
Confidence            4678899999999999 667999999999999977 6799999999999999999999988888776        35569


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHH----HHHhcCCcEEEeCcHHHHHHHhcCCccccCceeE
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK----ARLRKGISILVATPGHLLDHLKHTSSFLHTNLRW  189 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~  189 (316)
                      |+++|..+||+|-++.++.....++ ..+..-.|........    ......+||+|||.+-+-.+++..  ..+.++..
T Consensus       265 lfLvPLVALANQKy~dF~~rYs~Lg-lkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRtg--~~lgdiGt  341 (830)
T COG1202         265 LFLVPLVALANQKYEDFKERYSKLG-LKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRTG--KDLGDIGT  341 (830)
T ss_pred             EEEehhHHhhcchHHHHHHHhhccc-ceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHcC--Ccccccce
Confidence            9999999999999999988776655 3333333332221111    111234799999999998888763  55679999


Q ss_pred             EEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEE
Q 043110          190 IIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVL  259 (316)
Q Consensus       190 lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~  259 (316)
                      +||||+|.|-|...++.+..++.++....            +..|+|.+|||+.+ ...+++..--+++.
T Consensus       342 VVIDEiHtL~deERG~RLdGLI~RLr~l~------------~~AQ~i~LSATVgN-p~elA~~l~a~lV~  398 (830)
T COG1202         342 VVIDEIHTLEDEERGPRLDGLIGRLRYLF------------PGAQFIYLSATVGN-PEELAKKLGAKLVL  398 (830)
T ss_pred             EEeeeeeeccchhcccchhhHHHHHHHhC------------CCCeEEEEEeecCC-hHHHHHHhCCeeEe
Confidence            99999999998888888888888887532            27899999999974 35555544333433

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.82  E-value=6.9e-20  Score=168.96  Aligned_cols=156  Identities=21%  Similarity=0.190  Sum_probs=107.8

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCC----
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGN----  150 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~----  150 (316)
                      ++++.||||||||++|++|++..+..       ..+.+++|++|+++|+.|+++.+..++..    .....+++..    
T Consensus         1 ~vvi~apTGsGKT~~~~~~~l~~~~~-------~~~~~ii~v~P~~~L~~q~~~~l~~~f~~----~~~~~~~~~~~~~~   69 (358)
T TIGR01587         1 LLVIEAPTGYGKTEAALLWALHSIKS-------QKADRVIIALPTRATINAMYRRAKELFGS----NLGLLHSSSSFKRI   69 (358)
T ss_pred             CEEEEeCCCCCHHHHHHHHHHHHHhh-------CCCCeEEEEeehHHHHHHHHHHHHHHhCc----ccEEeeccHHHHHH
Confidence            58999999999999999999987643       22456999999999999999999987532    1112222111    


Q ss_pred             --------hHHHHHHHh------cCCcEEEeCcHHHHHHHhcC-Cc--cccC--ceeEEEEecchhhhcCCcHHHHHHHH
Q 043110          151 --------RSKEKARLR------KGISILVATPGHLLDHLKHT-SS--FLHT--NLRWIIFDEADRILELGFGKEIEEIL  211 (316)
Q Consensus       151 --------~~~~~~~l~------~~~~IlV~Tp~~l~~~l~~~-~~--~~~~--~l~~lViDEad~l~~~~~~~~i~~i~  211 (316)
                              .........      ...+|+|+||+++...+... ..  ..+.  ..+++|+||+|.+.++++.. +..++
T Consensus        70 ~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~-l~~~l  148 (358)
T TIGR01587        70 KEMGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLKSVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLAL-ILAVL  148 (358)
T ss_pred             hccCCchhHHHHHHHHhhchhhhhhCCeeeCCHHHHHHHHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHH-HHHHH
Confidence                    011111111      13579999999998877651 11  1111  23789999999998865444 66666


Q ss_pred             HHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCC
Q 043110          212 DILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLET  256 (316)
Q Consensus       212 ~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~  256 (316)
                      +.+...              +.|++++|||+|+.+.++.......
T Consensus       149 ~~l~~~--------------~~~~i~~SATlp~~l~~~~~~~~~~  179 (358)
T TIGR01587       149 EVLKDN--------------DVPILLMSATLPKFLKEYAEKIGYV  179 (358)
T ss_pred             HHHHHc--------------CCCEEEEecCchHHHHHHHhcCCCc
Confidence            666531              6899999999998888877665443

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.

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.82  E-value=5.2e-19  Score=176.20  Aligned_cols=168  Identities=20%  Similarity=0.222  Sum_probs=121.0

Q ss_pred             HHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCcee
Q 043110           63 QAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVP  142 (316)
Q Consensus        63 Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~  142 (316)
                      -.+.+..+.++.+++++|+||||||.+|.+++++...         .+.+++|+.|+|++|.|+++.+...........+
T Consensus         7 ~~~i~~~l~~~~~vIi~a~TGSGKTT~vpl~lL~~~~---------~~~~ilvlqPrR~aA~qiA~rva~~~~~~~g~~V   77 (819)
T TIGR01970         7 LPALRDALAAHPQVVLEAPPGAGKSTAVPLALLDAPG---------IGGKIIMLEPRRLAARSAAQRLASQLGEAVGQTV   77 (819)
T ss_pred             HHHHHHHHHcCCcEEEECCCCCCHHHHHHHHHHHhhc---------cCCeEEEEeCcHHHHHHHHHHHHHHhCCCcCcEE
Confidence            3455566678889999999999999999999988652         1346999999999999999988544322122334


Q ss_pred             EEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecch-hhhcCCcHHH-HHHHHHHhccCccc
Q 043110          143 GYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEAD-RILELGFGKE-IEEILDILGSRNIA  220 (316)
Q Consensus       143 ~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad-~l~~~~~~~~-i~~i~~~l~~~~~~  220 (316)
                      ++.+++..      ....+.+|+|+|||+|++.+.+  ...++++++|||||+| ++++.++.-. +..+...++.    
T Consensus        78 Gy~vr~~~------~~s~~t~I~v~T~G~Llr~l~~--d~~L~~v~~VIiDEaHER~L~~Dl~L~ll~~i~~~lr~----  145 (819)
T TIGR01970        78 GYRVRGEN------KVSRRTRLEVVTEGILTRMIQD--DPELDGVGALIFDEFHERSLDADLGLALALDVQSSLRE----  145 (819)
T ss_pred             EEEEcccc------ccCCCCcEEEECCcHHHHHHhh--CcccccCCEEEEeccchhhhccchHHHHHHHHHHhcCC----
Confidence            44444432      2234578999999999999875  3457899999999999 5777665433 3445555554    


Q ss_pred             ccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          221 SIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       221 ~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                                 ..|+++||||++...   ...++.++..|.+...
T Consensus       146 -----------dlqlIlmSATl~~~~---l~~~l~~~~vI~~~gr  176 (819)
T TIGR01970       146 -----------DLKILAMSATLDGER---LSSLLPDAPVVESEGR  176 (819)
T ss_pred             -----------CceEEEEeCCCCHHH---HHHHcCCCcEEEecCc
Confidence                       789999999999653   3456666655655543

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=99.81  E-value=1.2e-18  Score=173.90  Aligned_cols=167  Identities=20%  Similarity=0.223  Sum_probs=118.0

Q ss_pred             HHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeE
Q 043110           64 AQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPG  143 (316)
Q Consensus        64 ~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~  143 (316)
                      .+.+..+.++++++++|+||||||.+|.+++++....         ..+++|+.|+|++|.|+++.+...........++
T Consensus        11 ~~i~~~l~~~~~vvv~A~TGSGKTt~~pl~lL~~~~~---------~~~ilvlqPrR~aA~qia~rva~~l~~~~g~~VG   81 (812)
T PRK11664         11 PELLTALKTAPQVLLKAPTGAGKSTWLPLQLLQHGGI---------NGKIIMLEPRRLAARNVAQRLAEQLGEKPGETVG   81 (812)
T ss_pred             HHHHHHHHhCCCEEEEcCCCCCHHHHHHHHHHHcCCc---------CCeEEEECChHHHHHHHHHHHHHHhCcccCceEE
Confidence            3455666688999999999999999999998875321         2369999999999999999885543222234455


Q ss_pred             EeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchh-hhcCCcH-HHHHHHHHHhccCcccc
Q 043110          144 YVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADR-ILELGFG-KEIEEILDILGSRNIAS  221 (316)
Q Consensus       144 ~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~-l~~~~~~-~~i~~i~~~l~~~~~~~  221 (316)
                      +..++.+..      ....+|+|+|||+|.+++..  ...+++++++||||+|. .++..+. ..+..+++.++.     
T Consensus        82 y~vr~~~~~------~~~t~I~v~T~G~Llr~l~~--d~~L~~v~~IIlDEaHER~l~~Dl~L~ll~~i~~~lr~-----  148 (812)
T PRK11664         82 YRMRAESKV------GPNTRLEVVTEGILTRMIQR--DPELSGVGLVILDEFHERSLQADLALALLLDVQQGLRD-----  148 (812)
T ss_pred             EEecCcccc------CCCCcEEEEChhHHHHHHhh--CCCcCcCcEEEEcCCCccccccchHHHHHHHHHHhCCc-----
Confidence            555554321      23458999999999998875  34678999999999996 4443322 223444555544     


Q ss_pred             cCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          222 IGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       222 ~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                                ..|+++||||++..  .+ ..++.++..|.+...
T Consensus       149 ----------~lqlilmSATl~~~--~l-~~~~~~~~~I~~~gr  179 (812)
T PRK11664        149 ----------DLKLLIMSATLDND--RL-QQLLPDAPVIVSEGR  179 (812)
T ss_pred             ----------cceEEEEecCCCHH--HH-HHhcCCCCEEEecCc
Confidence                      78999999999864  23 456666666665543

>COG4581 Superfamily II RNA helicase [DNA replication, recombination, and repair]

Probab=99.79  E-value=3.6e-18  Score=169.67  Aligned_cols=180  Identities=25%  Similarity=0.287  Sum_probs=144.3

Q ss_pred             HHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH
Q 043110           52 ERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ  131 (316)
Q Consensus        52 ~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~  131 (316)
                      ..++|+ |.++|++++-.+..|..++++||||+|||++.-.++...+..         +.+++|.+|.++|.+|.+..+.
T Consensus       114 ~~~~F~-LD~fQ~~a~~~Ler~esVlV~ApTssGKTvVaeyAi~~al~~---------~qrviYTsPIKALsNQKyrdl~  183 (1041)
T COG4581         114 REYPFE-LDPFQQEAIAILERGESVLVCAPTSSGKTVVAEYAIALALRD---------GQRVIYTSPIKALSNQKYRDLL  183 (1041)
T ss_pred             HhCCCC-cCHHHHHHHHHHhCCCcEEEEccCCCCcchHHHHHHHHHHHc---------CCceEeccchhhhhhhHHHHHH
Confidence            557887 999999999999999999999999999999988877777665         4449999999999999998877


Q ss_pred             HHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHH
Q 043110          132 KLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEIL  211 (316)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~  211 (316)
                      ...... .-.+++..|..+.       +.++.++|.|.+.|-.++.. ....+.++.++|+||+|.|.|...+.-++.++
T Consensus       184 ~~fgdv-~~~vGL~TGDv~I-------N~~A~clvMTTEILRnMlyr-g~~~~~~i~~ViFDEvHyi~D~eRG~VWEE~I  254 (1041)
T COG4581         184 AKFGDV-ADMVGLMTGDVSI-------NPDAPCLVMTTEILRNMLYR-GSESLRDIEWVVFDEVHYIGDRERGVVWEEVI  254 (1041)
T ss_pred             HHhhhh-hhhccceecceee-------CCCCceEEeeHHHHHHHhcc-CcccccccceEEEEeeeeccccccchhHHHHH
Confidence            765433 1223444444433       34578999999999998887 45666899999999999999999999999999


Q ss_pred             HHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhc---CCCEEEEcCCCC
Q 043110          212 DILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISL---ETPVLIGLDEKK  266 (316)
Q Consensus       212 ~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l---~~p~~i~~~~~~  266 (316)
                      -.+|.               ..|++++|||+|...+ |..+.-   ..|+++...+..
T Consensus       255 i~lP~---------------~v~~v~LSATv~N~~E-F~~Wi~~~~~~~~~vv~t~~R  296 (1041)
T COG4581         255 ILLPD---------------HVRFVFLSATVPNAEE-FAEWIQRVHSQPIHVVSTEHR  296 (1041)
T ss_pred             HhcCC---------------CCcEEEEeCCCCCHHH-HHHHHHhccCCCeEEEeecCC
Confidence            99998               8899999999996544 443322   467777766654

>PRK13766 Hef nuclease; Provisional

Probab=99.78  E-value=9e-18  Score=169.47  Aligned_cols=163  Identities=25%  Similarity=0.191  Sum_probs=120.7

Q ss_pred             CCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           56 FEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        56 ~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      .-+|+++|.+++..++.+ |+++++|||+|||+++++++...+..        .+.++|||+||++|+.|+.+.++.++.
T Consensus        13 ~~~~r~yQ~~~~~~~l~~-n~lv~~ptG~GKT~~a~~~i~~~l~~--------~~~~vLvl~Pt~~L~~Q~~~~~~~~~~   83 (773)
T PRK13766         13 TIEARLYQQLLAATALKK-NTLVVLPTGLGKTAIALLVIAERLHK--------KGGKVLILAPTKPLVEQHAEFFRKFLN   83 (773)
T ss_pred             cCCccHHHHHHHHHHhcC-CeEEEcCCCccHHHHHHHHHHHHHHh--------CCCeEEEEeCcHHHHHHHHHHHHHHhC
Confidence            346899999999888877 99999999999999999988887732        245699999999999999999988764


Q ss_pred             hcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhc
Q 043110          136 RFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILG  215 (316)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~  215 (316)
                      .. ...+..+.|+.... +...+..+.+|+|+||+.+...+.. ....+.+++++|+||||++........+...+....
T Consensus        84 ~~-~~~v~~~~g~~~~~-~r~~~~~~~~iiv~T~~~l~~~l~~-~~~~~~~~~liVvDEaH~~~~~~~~~~i~~~~~~~~  160 (773)
T PRK13766         84 IP-EEKIVVFTGEVSPE-KRAELWEKAKVIVATPQVIENDLIA-GRISLEDVSLLIFDEAHRAVGNYAYVYIAERYHEDA  160 (773)
T ss_pred             CC-CceEEEEeCCCCHH-HHHHHHhCCCEEEECHHHHHHHHHc-CCCChhhCcEEEEECCccccccccHHHHHHHHHhcC
Confidence            22 12344455555443 4455666789999999999877754 455667899999999999876533333333322222


Q ss_pred             cCcccccCCCCccccccceEEEEeeecchh
Q 043110          216 SRNIASIGEGNEVSNVKRQNLLLSATLNEK  245 (316)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~  245 (316)
                      .               ..+++++|||....
T Consensus       161 ~---------------~~~il~lTaTP~~~  175 (773)
T PRK13766        161 K---------------NPLVLGLTASPGSD  175 (773)
T ss_pred             C---------------CCEEEEEEcCCCCC
Confidence            2               56799999997544

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

Probab=99.78  E-value=2.8e-18  Score=164.67  Aligned_cols=183  Identities=20%  Similarity=0.223  Sum_probs=134.0

Q ss_pred             CCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           42 LDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        42 l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      +++...... ..-..-.++.+|.+....++ |+|+++++|||+|||+.+..-+.+++....       ..++|+++|++-
T Consensus        47 ~~~s~~~~~-~~p~~~~lR~YQ~eivq~AL-gkNtii~lPTG~GKTfIAa~Vm~nh~rw~p-------~~KiVF~aP~~p  117 (746)
T KOG0354|consen   47 LDESAAQRW-IYPTNLELRNYQEELVQPAL-GKNTIIALPTGSGKTFIAAVIMKNHFEWRP-------KGKVVFLAPTRP  117 (746)
T ss_pred             CChhhhccc-cccCcccccHHHHHHhHHhh-cCCeEEEeecCCCccchHHHHHHHHHhcCC-------cceEEEeeCCch
Confidence            444444433 11233468999999998888 999999999999999999998999887632       367999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcC
Q 043110          122 LCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL  201 (316)
Q Consensus       122 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~  201 (316)
                      |+.|+...+..++..   .......||.....-...+.+..+|+++||..+...+.+.....++++.++||||||+-...
T Consensus       118 Lv~QQ~a~~~~~~~~---~~~T~~l~~~~~~~~r~~i~~s~~vff~TpQil~ndL~~~~~~~ls~fs~iv~DE~Hra~kn  194 (746)
T KOG0354|consen  118 LVNQQIACFSIYLIP---YSVTGQLGDTVPRSNRGEIVASKRVFFRTPQILENDLKSGLHDELSDFSLIVFDECHRTSKN  194 (746)
T ss_pred             HHHHHHHHHhhccCc---ccceeeccCccCCCchhhhhcccceEEeChHhhhhhcccccccccceEEEEEEccccccccc
Confidence            999998777766643   22334444533333334566778999999999999998755445788999999999998776


Q ss_pred             C-cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHH
Q 043110          202 G-FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK  251 (316)
Q Consensus       202 ~-~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~  251 (316)
                      . |...+...+..-..               ..|++++|||+.++......
T Consensus       195 ~~Y~~Vmr~~l~~k~~---------------~~qILgLTASpG~~~~~v~~  230 (746)
T KOG0354|consen  195 HPYNNIMREYLDLKNQ---------------GNQILGLTASPGSKLEQVQN  230 (746)
T ss_pred             ccHHHHHHHHHHhhhc---------------cccEEEEecCCCccHHHHHH
Confidence            4 44444455544332               44999999999876655444

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.78  E-value=3.5e-18  Score=167.92  Aligned_cols=140  Identities=22%  Similarity=0.300  Sum_probs=112.1

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH
Q 043110           46 LCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL  125 (316)
Q Consensus        46 l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q  125 (316)
                      +.++..+.+|. .|+++|..+++.+..|+  ++++.||+|||+++++|++.....         |..++|++||++||.|
T Consensus        67 vrea~~R~~g~-~p~~vQl~~~~~l~~G~--Iaem~TGeGKTL~a~lp~~l~al~---------G~~v~VvTpt~~LA~q  134 (790)
T PRK09200         67 VREAAKRVLGM-RPYDVQLIGALVLHEGN--IAEMQTGEGKTLTATMPLYLNALE---------GKGVHLITVNDYLAKR  134 (790)
T ss_pred             HHHHHHHHhCC-CCchHHHHhHHHHcCCc--eeeecCCCcchHHHHHHHHHHHHc---------CCCeEEEeCCHHHHHH
Confidence            34445456788 59999999999998887  999999999999999999866554         5569999999999999


Q ss_pred             HHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcCC-----ccccCceeEEEEecchhhh
Q 043110          126 VYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHTS-----SFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~~-----~~~~~~l~~lViDEad~l~  199 (316)
                      .++.+..+...++ +.++++.|+.+...+.+.. .+++|++|||+++ ++++...-     ...+..+.++|+||||.++
T Consensus       135 d~e~~~~l~~~lG-l~v~~i~g~~~~~~~r~~~-y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~r~~~~~IvDEaDsiL  212 (790)
T PRK09200        135 DAEEMGQVYEFLG-LTVGLNFSDIDDASEKKAI-YEADIIYTTNSELGFDYLRDNLADSKEDKVQRPLNYAIIDEIDSIL  212 (790)
T ss_pred             HHHHHHHHHhhcC-CeEEEEeCCCCcHHHHHHh-cCCCEEEECCccccchhHHhccccchhhhcccccceEEEeccccce
Confidence            9999999998865 6777788887744444444 4589999999999 56554321     1345788999999999876

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.78  E-value=1e-17  Score=165.33  Aligned_cols=159  Identities=21%  Similarity=0.202  Sum_probs=113.6

Q ss_pred             CCcHHHHHHHHHHhCC---CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSG---RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g---~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      .+++.|+++++.+.++   +++++.++||||||.+|+.++...+..         |.++||++|+++|+.|+++.+++.+
T Consensus       144 ~Lt~~Q~~ai~~i~~~~~~~~~Ll~~~TGSGKT~v~l~~i~~~l~~---------g~~vLvLvPt~~L~~Q~~~~l~~~f  214 (679)
T PRK05580        144 TLNPEQAAAVEAIRAAAGFSPFLLDGVTGSGKTEVYLQAIAEVLAQ---------GKQALVLVPEIALTPQMLARFRARF  214 (679)
T ss_pred             CCCHHHHHHHHHHHhccCCCcEEEECCCCChHHHHHHHHHHHHHHc---------CCeEEEEeCcHHHHHHHHHHHHHHh
Confidence            4899999999999874   789999999999999998887776654         4569999999999999999998754


Q ss_pred             hhcCCceeEEeeCCCChHHHH---HHHh-cCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCC---cHHHH
Q 043110          135 HRFRWIVPGYVMGGGNRSKEK---ARLR-KGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELG---FGKEI  207 (316)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~---~~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~---~~~~i  207 (316)
                         + ..+..++++.+.....   ..+. ..++|+||||+.++        ..+.++.++|+||+|.....+   ...+.
T Consensus       215 ---g-~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~--------~p~~~l~liVvDEeh~~s~~~~~~p~y~~  282 (679)
T PRK05580        215 ---G-APVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF--------LPFKNLGLIIVDEEHDSSYKQQEGPRYHA  282 (679)
T ss_pred             ---C-CCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc--------ccccCCCEEEEECCCccccccCcCCCCcH
Confidence               2 3455666666554332   2333 45799999998764        234688999999999765321   11122


Q ss_pred             HHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHH
Q 043110          208 EEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLT  250 (316)
Q Consensus       208 ~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~  250 (316)
                      +.+......             ..+.|++++|||.+.+....+
T Consensus       283 r~va~~ra~-------------~~~~~~il~SATps~~s~~~~  312 (679)
T PRK05580        283 RDLAVVRAK-------------LENIPVVLGSATPSLESLANA  312 (679)
T ss_pred             HHHHHHHhh-------------ccCCCEEEEcCCCCHHHHHHH
Confidence            222221111             117899999999876655443

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.77  E-value=3.5e-18  Score=165.68  Aligned_cols=140  Identities=21%  Similarity=0.282  Sum_probs=112.2

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH
Q 043110           46 LCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL  125 (316)
Q Consensus        46 l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q  125 (316)
                      +.++..+.+|.. |+++|..+.+.+..|+  +++++||+|||++|.+|++.....         |..++|++||++||.|
T Consensus        45 vrEa~~R~lg~~-p~~vQlig~~~l~~G~--Iaem~TGeGKTLva~lpa~l~aL~---------G~~V~VvTpt~~LA~q  112 (745)
T TIGR00963        45 VREASKRVLGMR-PFDVQLIGGIALHKGK--IAEMKTGEGKTLTATLPAYLNALT---------GKGVHVVTVNDYLAQR  112 (745)
T ss_pred             HHHHHHHHhCCC-ccchHHhhhhhhcCCc--eeeecCCCccHHHHHHHHHHHHHh---------CCCEEEEcCCHHHHHH
Confidence            344554567886 9999999999988887  999999999999999999644433         3349999999999999


Q ss_pred             HHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcCC-----ccccCceeEEEEecchhhh
Q 043110          126 VYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHTS-----SFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~~-----~~~~~~l~~lViDEad~l~  199 (316)
                      .++.+..+...++ +.+.++.++.+.......  ..++|++|||++| +++++..-     ...+..+.++|+||+|+++
T Consensus       113 dae~~~~l~~~LG-Lsv~~i~g~~~~~~r~~~--y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~r~l~~aIIDEaDs~L  189 (745)
T TIGR00963       113 DAEWMGQVYRFLG-LSVGLILSGMSPEERREA--YACDITYGTNNELGFDYLRDNMAHSKEEKVQRPFHFAIIDEVDSIL  189 (745)
T ss_pred             HHHHHHHHhccCC-CeEEEEeCCCCHHHHHHh--cCCCEEEECCCchhhHHHhcccccchhhhhccccceeEeecHHHHh
Confidence            9999999998765 677788888775443333  3479999999999 88887642     2356789999999999987


Q ss_pred             c
Q 043110          200 E  200 (316)
Q Consensus       200 ~  200 (316)
                      -
T Consensus       190 I  190 (745)
T TIGR00963       190 I  190 (745)
T ss_pred             H
Confidence            4

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.

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.77  E-value=5.7e-18  Score=163.18  Aligned_cols=137  Identities=27%  Similarity=0.322  Sum_probs=109.5

Q ss_pred             HHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHH
Q 043110           48 DQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY  127 (316)
Q Consensus        48 ~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~  127 (316)
                      ++..+.+|.. |+++|..++|.++.|+  ++++.||+|||++|.+|++.....         |..++|++||++||.|.+
T Consensus        94 Ea~~R~lg~~-p~~VQ~~~~~~ll~G~--Iae~~TGeGKTla~~lp~~~~al~---------G~~v~VvTptreLA~qda  161 (656)
T PRK12898         94 EASGRVLGQR-HFDVQLMGGLALLSGR--LAEMQTGEGKTLTATLPAGTAALA---------GLPVHVITVNDYLAERDA  161 (656)
T ss_pred             HHHHHHhCCC-CChHHHHHHHHHhCCC--eeeeeCCCCcHHHHHHHHHHHhhc---------CCeEEEEcCcHHHHHHHH
Confidence            3444456886 9999999999999999  999999999999999999987654         567999999999999999


Q ss_pred             HHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcCC------------------------cc
Q 043110          128 EILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHTS------------------------SF  182 (316)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~~------------------------~~  182 (316)
                      +.+..+...++ +.+++++||.+.  +.+....+++|++||...| +++++..-                        ..
T Consensus       162 e~~~~l~~~lG-lsv~~i~gg~~~--~~r~~~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~~~~~~~l~~~~~~~~~~  238 (656)
T PRK12898        162 ELMRPLYEALG-LTVGCVVEDQSP--DERRAAYGADITYCTNKELVFDYLRDRLALGQRASDARLALESLHGRSSRSTQL  238 (656)
T ss_pred             HHHHHHHhhcC-CEEEEEeCCCCH--HHHHHHcCCCEEEECCCchhhhhccccccccccccchhhhhhhhccccCchhhh
Confidence            99999998765 677788888654  3344455789999999877 55554321                        11


Q ss_pred             ccCceeEEEEecchhhh
Q 043110          183 LHTNLRWIIFDEADRIL  199 (316)
Q Consensus       183 ~~~~l~~lViDEad~l~  199 (316)
                      ....+.+.||||+|.++
T Consensus       239 v~r~~~~aIvDEvDSiL  255 (656)
T PRK12898        239 LLRGLHFAIVDEADSVL  255 (656)
T ss_pred             cccccceeEeeccccee
Confidence            23567899999999765

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

Probab=99.77  E-value=5e-18  Score=151.56  Aligned_cols=188  Identities=25%  Similarity=0.303  Sum_probs=134.1

Q ss_pred             HHHHHHHHHHcCCCCC-cHHHHHHHHHHhCC-CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           44 STLCDQLRERLGFEAP-TKVQAQAIPVILSG-RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        44 ~~l~~~l~~~~g~~~p-~~~Q~~~i~~il~g-~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      ..+.++|++.||+..+ ++.|..|+..+..+ +|+.+++|||+||++||.+|.+..-           | ..||+.|..+
T Consensus         5 r~VreaLKK~FGh~kFKs~LQE~A~~c~VK~k~DVyVsMPTGaGKSLCyQLPaL~~~-----------g-ITIV~SPLiA   72 (641)
T KOG0352|consen    5 RKVREALKKLFGHKKFKSRLQEQAINCIVKRKCDVYVSMPTGAGKSLCYQLPALVHG-----------G-ITIVISPLIA   72 (641)
T ss_pred             HHHHHHHHHHhCchhhcChHHHHHHHHHHhccCcEEEeccCCCchhhhhhchHHHhC-----------C-eEEEehHHHH
Confidence            3467788888888755 79999999998866 5999999999999999999997532           2 4899999999


Q ss_pred             HHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHH---HH---hcCCcEEEeCcHHHH-----HHHhcCCccccCceeEE
Q 043110          122 LCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA---RL---RKGISILVATPGHLL-----DHLKHTSSFLHTNLRWI  190 (316)
Q Consensus       122 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~l---~~~~~IlV~Tp~~l~-----~~l~~~~~~~~~~l~~l  190 (316)
                      |...+.+-+..+.-     .+..+....+..+..+   .+   .....++..||+...     .+++.  ...-..++++
T Consensus        73 LIkDQiDHL~~LKV-----p~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn~--L~~r~~L~Y~  145 (641)
T KOG0352|consen   73 LIKDQIDHLKRLKV-----PCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLNG--LANRDVLRYI  145 (641)
T ss_pred             HHHHHHHHHHhcCC-----chhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHHH--HhhhceeeeE
Confidence            99887777766532     2222222222222111   11   123579999998643     22221  1122458999


Q ss_pred             EEecchhhhcCC--cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHH--HHHHhcCCCEEEEcC
Q 043110          191 IFDEADRILELG--FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNH--LTKISLETPVLIGLD  263 (316)
Q Consensus       191 ViDEad~l~~~~--~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~--~~~~~l~~p~~i~~~  263 (316)
                      |+||||++..||  |++++..+-.......             ...-+.++||.+..|++  +..+.|++||-|.-.
T Consensus       146 vVDEAHCVSQWGHDFRPDYL~LG~LRS~~~-------------~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkT  209 (641)
T KOG0352|consen  146 VVDEAHCVSQWGHDFRPDYLTLGSLRSVCP-------------GVPWVALTATANAKVQEDIAFQLKLRNPVAIFKT  209 (641)
T ss_pred             EechhhhHhhhccccCcchhhhhhHHhhCC-------------CCceEEeecccChhHHHHHHHHHhhcCcHHhccC
Confidence            999999999996  8888887765544321             67889999999999987  456788999977543

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

Probab=99.76  E-value=4.7e-17  Score=148.62  Aligned_cols=182  Identities=24%  Similarity=0.188  Sum_probs=133.0

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhh
Q 043110           57 EAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHR  136 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~  136 (316)
                      -+++.+|.......+.+ |++++.|||-|||+.+++-+...+...       .+ ++|+++||+.|+.|.++.+.+...-
T Consensus        14 ie~R~YQ~~i~a~al~~-NtLvvlPTGLGKT~IA~~V~~~~l~~~-------~~-kvlfLAPTKPLV~Qh~~~~~~v~~i   84 (542)
T COG1111          14 IEPRLYQLNIAAKALFK-NTLVVLPTGLGKTFIAAMVIANRLRWF-------GG-KVLFLAPTKPLVLQHAEFCRKVTGI   84 (542)
T ss_pred             ccHHHHHHHHHHHHhhc-CeEEEecCCccHHHHHHHHHHHHHHhc-------CC-eEEEecCCchHHHHHHHHHHHHhCC
Confidence            36888998888777665 999999999999999988888888662       23 6999999999999999999998754


Q ss_pred             cCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          137 FRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      .. .....+. |....++........+|+|+||..+.+-+.. +.+++.++.++|+||||+-.+..-...+..-.-.-.+
T Consensus        85 p~-~~i~~lt-Gev~p~~R~~~w~~~kVfvaTPQvveNDl~~-Grid~~dv~~lifDEAHRAvGnyAYv~Va~~y~~~~k  161 (542)
T COG1111          85 PE-DEIAALT-GEVRPEEREELWAKKKVFVATPQVVENDLKA-GRIDLDDVSLLIFDEAHRAVGNYAYVFVAKEYLRSAK  161 (542)
T ss_pred             Ch-hheeeec-CCCChHHHHHHHhhCCEEEeccHHHHhHHhc-CccChHHceEEEechhhhccCcchHHHHHHHHHHhcc
Confidence            22 2333444 4444455556666779999999999888876 6777889999999999998765433333332222222


Q ss_pred             CcccccCCCCccccccceEEEEeeecchhHHHH---HHHhcCCCEEEEcCCC
Q 043110          217 RNIASIGEGNEVSNVKRQNLLLSATLNEKVNHL---TKISLETPVLIGLDEK  265 (316)
Q Consensus       217 ~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~---~~~~l~~p~~i~~~~~  265 (316)
                                     ++.++++|||...+...+   +...--.-+.|..+.+
T Consensus       162 ---------------~~~ilgLTASPGs~~ekI~eV~~nLgIe~vevrTE~d  198 (542)
T COG1111         162 ---------------NPLILGLTASPGSDLEKIQEVVENLGIEKVEVRTEED  198 (542)
T ss_pred             ---------------CceEEEEecCCCCCHHHHHHHHHhCCcceEEEecCCC
Confidence                           788999999997665554   4433334455555444

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.76  E-value=1.2e-17  Score=162.86  Aligned_cols=141  Identities=20%  Similarity=0.230  Sum_probs=102.9

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           47 CDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        47 ~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .++..+.+|. .|+++|......+..|  .+++++||+|||++|++|++.....         +..++|++|+++||.|.
T Consensus        60 rEa~~R~lgl-rpydVQlig~l~l~~G--~Iaem~TGeGKTLta~Lpa~l~aL~---------g~~V~VVTpn~yLA~Rd  127 (762)
T TIGR03714        60 READKRVLGM-FPYDVQVLGAIVLHQG--NIAEMKTGEGKTLTATMPLYLNALT---------GKGAMLVTTNDYLAKRD  127 (762)
T ss_pred             HHHHHhhcCC-CccHHHHHHHHHhcCC--ceeEecCCcchHHHHHHHHHHHhhc---------CCceEEeCCCHHHHHHH
Confidence            3344445677 4777777766666555  6999999999999999998766654         33499999999999999


Q ss_pred             HHHHHHHHhhcCCceeEEeeCCC---ChHHHHHHHhcCCcEEEeCcHHH-HHHHhcC-----CccccCceeEEEEecchh
Q 043110          127 YEILQKLLHRFRWIVPGYVMGGG---NRSKEKARLRKGISILVATPGHL-LDHLKHT-----SSFLHTNLRWIIFDEADR  197 (316)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~-----~~~~~~~l~~lViDEad~  197 (316)
                      ++++..+...++. .+.+..++.   ....+......+++|++|||++| .+++...     ....+..+.++|+||||.
T Consensus       128 ae~m~~l~~~LGL-sv~~~~~~s~~~~~~~~~rr~~y~~dIvygTp~~LgfDyLrD~l~~~~~~~~~r~l~~~IVDEaDs  206 (762)
T TIGR03714       128 AEEMGPVYEWLGL-TVSLGVVDDPDEEYDANEKRKIYNSDIVYTTNSALGFDYLIDNLASNKEGKFLRPFNYVIVDEVDS  206 (762)
T ss_pred             HHHHHHHHhhcCC-cEEEEECCCCccccCHHHHHHhCCCCEEEECchhhhhhHHHHHhhcchhhcccccCcEEEEecHhh
Confidence            9999999988764 444444432   23333344445799999999999 5655321     223457899999999999


Q ss_pred             hhc
Q 043110          198 ILE  200 (316)
Q Consensus       198 l~~  200 (316)
                      |+-
T Consensus       207 ILi  209 (762)
T TIGR03714       207 VLL  209 (762)
T ss_pred             Hhh
Confidence            863

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.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.74  E-value=1.2e-16  Score=126.23  Aligned_cols=144  Identities=44%  Similarity=0.583  Sum_probs=105.4

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHH
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSK  153 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (316)
                      +++++.++||+|||..++..+......       +...+++|++|++.++.|..+.+......  ........++.....
T Consensus         1 ~~~~i~~~~G~GKT~~~~~~~~~~~~~-------~~~~~~lv~~p~~~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~   71 (144)
T cd00046           1 RDVLLAAPTGSGKTLAALLPILELLDS-------LKGGQVLVLAPTRELANQVAERLKELFGE--GIKVGYLIGGTSIKQ   71 (144)
T ss_pred             CCEEEECCCCCchhHHHHHHHHHHHhc-------ccCCCEEEEcCcHHHHHHHHHHHHHHhhC--CcEEEEEecCcchhH
Confidence            468999999999999998887776654       12345999999999999999988887753  344556666666555


Q ss_pred             HHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccc
Q 043110          154 EKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKR  233 (316)
Q Consensus       154 ~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~  233 (316)
                      .........+|+++|++.+...+.... ......+++|+||+|.+....+.............               ..
T Consensus        72 ~~~~~~~~~~i~i~t~~~~~~~~~~~~-~~~~~~~~iiiDE~h~~~~~~~~~~~~~~~~~~~~---------------~~  135 (144)
T cd00046          72 QEKLLSGKTDIVVGTPGRLLDELERLK-LSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPK---------------DR  135 (144)
T ss_pred             HHHHhcCCCCEEEECcHHHHHHHHcCC-cchhcCCEEEEeCHHHHhhcchHHHHHHHHhhCCc---------------cc
Confidence            555556778999999999988776532 23356889999999998876544432112222222               78


Q ss_pred             eEEEEeeec
Q 043110          234 QNLLLSATL  242 (316)
Q Consensus       234 q~i~~SAT~  242 (316)
                      +++++|||+
T Consensus       136 ~~i~~saTp  144 (144)
T cd00046         136 QVLLLSATP  144 (144)
T ss_pred             eEEEEeccC
Confidence            899999995

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

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

Probab=99.74  E-value=1.3e-17  Score=166.23  Aligned_cols=203  Identities=24%  Similarity=0.258  Sum_probs=149.8

Q ss_pred             HHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHH
Q 043110           45 TLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCL  124 (316)
Q Consensus        45 ~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~  124 (316)
                      +....+...||...+++-|.++|..++.|+|+++.+|||.||++||.+|++-.            +...|||.|..+|++
T Consensus       251 ~~~~~l~~~Fg~~~FR~~Q~eaI~~~l~Gkd~fvlmpTG~GKSLCYQlPA~l~------------~gitvVISPL~SLm~  318 (941)
T KOG0351|consen  251 ELELLLKEVFGHKGFRPNQLEAINATLSGKDCFVLMPTGGGKSLCYQLPALLL------------GGVTVVISPLISLMQ  318 (941)
T ss_pred             HHHHHHHHHhccccCChhHHHHHHHHHcCCceEEEeecCCceeeEeecccccc------------CCceEEeccHHHHHH
Confidence            56777878899999999999999999999999999999999999999998642            225999999999997


Q ss_pred             HHHHHHHHHHhhcCCceeEEeeCCCChH---HHHHHHhcC---CcEEEeCcHHHHHHHhcC-CccccCc---eeEEEEec
Q 043110          125 LVYEILQKLLHRFRWIVPGYVMGGGNRS---KEKARLRKG---ISILVATPGHLLDHLKHT-SSFLHTN---LRWIIFDE  194 (316)
Q Consensus       125 Q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~l~~~---~~IlV~Tp~~l~~~l~~~-~~~~~~~---l~~lViDE  194 (316)
                      .+...+..     ..+....+.++....   ...+.+.++   ++|+..||+++...-.-. ....+..   +.++||||
T Consensus       319 DQv~~L~~-----~~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~~~~~lal~vIDE  393 (941)
T KOG0351|consen  319 DQVTHLSK-----KGIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLYARGLLALFVIDE  393 (941)
T ss_pred             HHHHhhhh-----cCcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhccCCCeeEEEEecH
Confidence            66655532     235555666665554   333444444   789999999875432211 1112223   88999999


Q ss_pred             chhhhcCC--cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHH--HHhcCCCEEEEcCCCCCCCC
Q 043110          195 ADRILELG--FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLT--KISLETPVLIGLDEKKFPED  270 (316)
Q Consensus       195 ad~l~~~~--~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~--~~~l~~p~~i~~~~~~~~~~  270 (316)
                      ||+...||  |++.+..+-....+..             ...+|.+|||.+..|..-+  .+.+++|..+.-..     +
T Consensus       394 AHCVSqWgHdFRp~Yk~l~~l~~~~~-------------~vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~sf-----n  455 (941)
T KOG0351|consen  394 AHCVSQWGHDFRPSYKRLGLLRIRFP-------------GVPFIALTATATERVREDVIRSLGLRNPELFKSSF-----N  455 (941)
T ss_pred             HHHhhhhcccccHHHHHHHHHHhhCC-------------CCCeEEeehhccHHHHHHHHHHhCCCCcceecccC-----C
Confidence            99999995  8998888776665421             4799999999999887643  45677888665443     3


Q ss_pred             CCCcccccccch
Q 043110          271 KSNVHFGSLESD  282 (316)
Q Consensus       271 ~~~~~~~~~~~~  282 (316)
                      +.|+++.+....
T Consensus       456 R~NL~yeV~~k~  467 (941)
T KOG0351|consen  456 RPNLKYEVSPKT  467 (941)
T ss_pred             CCCceEEEEecc
Confidence            466777766654

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.74  E-value=3e-17  Score=161.45  Aligned_cols=136  Identities=21%  Similarity=0.249  Sum_probs=108.4

Q ss_pred             HHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           49 QLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        49 ~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      +-.+.+|.. |+++|...--.+..|+  ++.++||+|||++|.+|++.....         |..++|++||++||.|.++
T Consensus        74 a~~R~lg~~-~ydvQliGg~~Lh~G~--Iaem~TGeGKTL~a~Lpa~~~al~---------G~~V~VvTpn~yLA~qd~e  141 (896)
T PRK13104         74 VSLRTLGLR-HFDVQLIGGMVLHEGN--IAEMRTGEGKTLVATLPAYLNAIS---------GRGVHIVTVNDYLAKRDSQ  141 (896)
T ss_pred             HHHHHcCCC-cchHHHhhhhhhccCc--cccccCCCCchHHHHHHHHHHHhc---------CCCEEEEcCCHHHHHHHHH
Confidence            333456775 8899977665555554  899999999999999999977654         2349999999999999999


Q ss_pred             HHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcCCcccc-----CceeEEEEecchhhh
Q 043110          129 ILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHTSSFLH-----TNLRWIIFDEADRIL  199 (316)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~~~~~~-----~~l~~lViDEad~l~  199 (316)
                      ++..+...++ +.++++.||.+.......+  .++|++|||++| +++++..-.+.+     ..+.++||||||.|+
T Consensus       142 ~m~~l~~~lG-Ltv~~i~gg~~~~~r~~~y--~~dIvygT~grlgfDyLrd~~~~~~~~~v~r~l~~~IvDEaDsiL  215 (896)
T PRK13104        142 WMKPIYEFLG-LTVGVIYPDMSHKEKQEAY--KADIVYGTNNEYGFDYLRDNMAFSLTDKVQRELNFAIVDEVDSIL  215 (896)
T ss_pred             HHHHHhcccC-ceEEEEeCCCCHHHHHHHh--CCCEEEECChhhhHHHHhcCCccchHhhhccccceEEeccHhhhh
Confidence            9999998765 6777888887766554433  589999999999 999986533333     588999999999886

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

Probab=99.72  E-value=1.7e-17  Score=163.84  Aligned_cols=227  Identities=18%  Similarity=0.169  Sum_probs=161.4

Q ss_pred             CCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCC-cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCC--CCCCeeEEEE
Q 043110           40 LGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGR-DVLVNAATGTGKTVAYLAPIINHLQSYSPRID--RSSGTFALVL  116 (316)
Q Consensus        40 ~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~-d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~--~~~~~~~lil  116 (316)
                      ..++.+-..++   +|...++++|.+..+..+.+. ++++|||||+|||..+++.+++.+........  .....+++|+
T Consensus       294 selP~Wnq~aF---~g~~sLNrIQS~v~daAl~~~EnmLlCAPTGaGKTNVAvLtiLqel~~h~r~dgs~nl~~fKIVYI  370 (1674)
T KOG0951|consen  294 SELPKWNQPAF---FGKQSLNRIQSKVYDAALRGDENMLLCAPTGAGKTNVAVLTILQELGNHLREDGSVNLAPFKIVYI  370 (1674)
T ss_pred             cCCcchhhhhc---ccchhhhHHHHHHHHHHhcCcCcEEEeccCCCCchHHHHHHHHHHHhcccccccceecccceEEEE
Confidence            35777788888   688889999999999998775 79999999999999999999999977544211  1234689999


Q ss_pred             eCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCcc-ccCceeEEEEecc
Q 043110          117 VPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSF-LHTNLRWIIFDEA  195 (316)
Q Consensus       117 ~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~-~~~~l~~lViDEa  195 (316)
                      +|.++|+..+...+.+....++ +.+.-..|..+...+.   ..+.+|+||||+..--.-++.+.. ..+-++++|+||.
T Consensus       371 APmKaLvqE~VgsfSkRla~~G-I~V~ElTgD~~l~~~q---ieeTqVIV~TPEK~DiITRk~gdraY~qlvrLlIIDEI  446 (1674)
T KOG0951|consen  371 APMKALVQEMVGSFSKRLAPLG-ITVLELTGDSQLGKEQ---IEETQVIVTTPEKWDIITRKSGDRAYEQLVRLLIIDEI  446 (1674)
T ss_pred             eeHHHHHHHHHHHHHhhccccC-cEEEEecccccchhhh---hhcceeEEeccchhhhhhcccCchhHHHHHHHHhhhhh
Confidence            9999999998888777777665 3333333433322211   234689999999875444432222 2245789999999


Q ss_pred             hhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCCCCcc
Q 043110          196 DRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNVH  275 (316)
Q Consensus       196 d~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~~~~~  275 (316)
                      |.+-| ..++.++.|..+....        .+.....++.+++|||+|+ -.+.+.-...+|..+.-.+....|.+..++
T Consensus       447 HLLhD-dRGpvLESIVaRt~r~--------ses~~e~~RlVGLSATLPN-y~DV~~Fl~v~~~glf~fd~syRpvPL~qq  516 (1674)
T KOG0951|consen  447 HLLHD-DRGPVLESIVARTFRR--------SESTEEGSRLVGLSATLPN-YEDVASFLRVDPEGLFYFDSSYRPVPLKQQ  516 (1674)
T ss_pred             hhccc-ccchHHHHHHHHHHHH--------hhhcccCceeeeecccCCc-hhhhHHHhccCcccccccCcccCcCCccce
Confidence            97655 5888888888777642        2233447899999999995 344444334456666666666777778887


Q ss_pred             cccccchh
Q 043110          276 FGSLESDV  283 (316)
Q Consensus       276 ~~~~~~~~  283 (316)
                      +..+....
T Consensus       517 ~Igi~ek~  524 (1674)
T KOG0951|consen  517 YIGITEKK  524 (1674)
T ss_pred             EeccccCC
Confidence            77665433

>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=99.70  E-value=1.6e-16  Score=132.19  Aligned_cols=154  Identities=24%  Similarity=0.258  Sum_probs=101.9

Q ss_pred             CCcHHHHHHHHHHhC-------CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILS-------GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEIL  130 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~-------g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~  130 (316)
                      +|+++|.+++..+..       ++++++.+|||+|||.+++..+.....            ++++++|+..|+.|+.+.+
T Consensus         3 ~lr~~Q~~ai~~i~~~~~~~~~~~~~ll~~~tGsGKT~~~~~~~~~l~~------------~~l~~~p~~~l~~Q~~~~~   70 (184)
T PF04851_consen    3 KLRPYQQEAIARIINSLENKKEERRVLLNAPTGSGKTIIALALILELAR------------KVLIVAPNISLLEQWYDEF   70 (184)
T ss_dssp             EE-HHHHHHHHHHHHHHHTTSGCSEEEEEESTTSSHHHHHHHHHHHHHC------------EEEEEESSHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHhcCCCCCEEEEECCCCCcChhhhhhhhcccc------------ceeEecCHHHHHHHHHHHH
Confidence            489999999988883       588999999999999998765554443            3999999999999999998


Q ss_pred             HHHHhhcCCcee----------EEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCC----------ccccCceeEE
Q 043110          131 QKLLHRFRWIVP----------GYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTS----------SFLHTNLRWI  190 (316)
Q Consensus       131 ~~~~~~~~~~~~----------~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~----------~~~~~~l~~l  190 (316)
                      ..+.........          ....................+++++|...+........          .......+++
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~v  150 (184)
T PF04851_consen   71 DDFGSEKYNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEKKIDESARRSYKLLKNKFDLV  150 (184)
T ss_dssp             HHHSTTSEEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH---------GCHHGGGGSESEE
T ss_pred             HHhhhhhhhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhcccccccccchhhhhhhccccCCEE
Confidence            666543211100          00111111122222334457899999999988765421          1233467899


Q ss_pred             EEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecc
Q 043110          191 IFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLN  243 (316)
Q Consensus       191 ViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~  243 (316)
                      |+||||++....   ....++.  ..               ...+++||||++
T Consensus       151 I~DEaH~~~~~~---~~~~i~~--~~---------------~~~~l~lTATp~  183 (184)
T PF04851_consen  151 IIDEAHHYPSDS---SYREIIE--FK---------------AAFILGLTATPF  183 (184)
T ss_dssp             EEETGGCTHHHH---HHHHHHH--SS---------------CCEEEEEESS-S
T ss_pred             EEehhhhcCCHH---HHHHHHc--CC---------------CCeEEEEEeCcc
Confidence            999999975532   1455555  22               678999999975

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 ....

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

Probab=99.70  E-value=1e-16  Score=154.88  Aligned_cols=164  Identities=24%  Similarity=0.240  Sum_probs=133.3

Q ss_pred             HHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHH
Q 043110           50 LRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI  129 (316)
Q Consensus        50 l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~  129 (316)
                      +...++|+ |..+|++||-++..|..+++.|+|.+|||+++-.++.....         .+.+++|-+|-++|.+|-++.
T Consensus       290 ~a~~~pFe-lD~FQk~Ai~~lerg~SVFVAAHTSAGKTvVAEYAialaq~---------h~TR~iYTSPIKALSNQKfRD  359 (1248)
T KOG0947|consen  290 MALIYPFE-LDTFQKEAIYHLERGDSVFVAAHTSAGKTVVAEYAIALAQK---------HMTRTIYTSPIKALSNQKFRD  359 (1248)
T ss_pred             HHhhCCCC-ccHHHHHHHHHHHcCCeEEEEecCCCCcchHHHHHHHHHHh---------hccceEecchhhhhccchHHH
Confidence            33456886 99999999999999999999999999999997665544332         256699999999999999998


Q ss_pred             HHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHH
Q 043110          130 LQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEE  209 (316)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~  209 (316)
                      +++-+...+     .+.|.....       ....++|.|.+.|-.++.+. ....+++.++|+||+|.+.|...+--++.
T Consensus       360 Fk~tF~Dvg-----LlTGDvqin-------PeAsCLIMTTEILRsMLYrg-adliRDvE~VIFDEVHYiND~eRGvVWEE  426 (1248)
T KOG0947|consen  360 FKETFGDVG-----LLTGDVQIN-------PEASCLIMTTEILRSMLYRG-ADLIRDVEFVIFDEVHYINDVERGVVWEE  426 (1248)
T ss_pred             HHHhccccc-----eeecceeeC-------CCcceEeehHHHHHHHHhcc-cchhhccceEEEeeeeeccccccccccee
Confidence            887654322     455554443       34579999999999999874 44457899999999999999999999999


Q ss_pred             HHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHH
Q 043110          210 ILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKI  252 (316)
Q Consensus       210 i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~  252 (316)
                      ++-.+|.               ..++|++|||+|... +|+.+
T Consensus       427 ViIMlP~---------------HV~~IlLSATVPN~~-EFA~W  453 (1248)
T KOG0947|consen  427 VIIMLPR---------------HVNFILLSATVPNTL-EFADW  453 (1248)
T ss_pred             eeeeccc---------------cceEEEEeccCCChH-HHHHH
Confidence            9999998               899999999999654 45544

>PRK09694 helicase Cas3; Provisional

Probab=99.69  E-value=7.6e-16  Score=153.94  Aligned_cols=174  Identities=20%  Similarity=0.110  Sum_probs=115.9

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           54 LGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        54 ~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      ++...|+|+|+.+......+.-+++.||||+|||.+++..+...+..       +...+++|..||+++++|+++++.++
T Consensus       282 ~~~~~p~p~Q~~~~~~~~~pgl~ileApTGsGKTEAAL~~A~~l~~~-------~~~~gi~~aLPT~Atan~m~~Rl~~~  354 (878)
T PRK09694        282 DNGYQPRQLQTLVDALPLQPGLTIIEAPTGSGKTEAALAYAWRLIDQ-------GLADSIIFALPTQATANAMLSRLEAL  354 (878)
T ss_pred             cCCCCChHHHHHHHhhccCCCeEEEEeCCCCCHHHHHHHHHHHHHHh-------CCCCeEEEECcHHHHHHHHHHHHHHH
Confidence            33447999999886544445679999999999999987766544332       12345999999999999999999876


Q ss_pred             Hhhc-CCceeEEeeCCCChHHHH---------------------HHHh---c---CCcEEEeCcHHHHHHHhcCCccccC
Q 043110          134 LHRF-RWIVPGYVMGGGNRSKEK---------------------ARLR---K---GISILVATPGHLLDHLKHTSSFLHT  185 (316)
Q Consensus       134 ~~~~-~~~~~~~~~~~~~~~~~~---------------------~~l~---~---~~~IlV~Tp~~l~~~l~~~~~~~~~  185 (316)
                      .... ....+.+.+|........                     .-+.   +   -.+|+|||..+++...-..+...+.
T Consensus       355 ~~~~f~~~~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi~V~TiDQlL~a~l~~kh~~lR  434 (878)
T PRK09694        355 ASKLFPSPNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQIGVCTIDQVLISVLPVKHRFIR  434 (878)
T ss_pred             HHHhcCCCceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCEEEcCHHHHHHHHHccchHHHH
Confidence            5532 223344444443211100                     0111   1   1589999999988655443322222


Q ss_pred             c----eeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHH
Q 043110          186 N----LRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHL  249 (316)
Q Consensus       186 ~----l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~  249 (316)
                      .    -++|||||+|.+ +......+..+++.+...              ...+|+||||+|....+.
T Consensus       435 ~~~La~svvIiDEVHAy-D~ym~~lL~~~L~~l~~~--------------g~~vIllSATLP~~~r~~  487 (878)
T PRK09694        435 GFGLGRSVLIVDEVHAY-DAYMYGLLEAVLKAQAQA--------------GGSVILLSATLPATLKQK  487 (878)
T ss_pred             HHhhccCeEEEechhhC-CHHHHHHHHHHHHHHHhc--------------CCcEEEEeCCCCHHHHHH
Confidence            2    258999999986 544556677777766542              567999999999887653

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

Probab=99.69  E-value=3e-16  Score=138.46  Aligned_cols=186  Identities=21%  Similarity=0.240  Sum_probs=138.1

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      ++=++++.+.+..+.|++.|..++++|.|..+|...+.|+|+++..|||.||++||.+|++-.            ...+|
T Consensus        71 wdkd~fpws~e~~~ilk~~f~lekfrplq~~ain~~ma~ed~~lil~tgggkslcyqlpal~a------------dg~al  138 (695)
T KOG0353|consen   71 WDKDDFPWSDEAKDILKEQFHLEKFRPLQLAAINATMAGEDAFLILPTGGGKSLCYQLPALCA------------DGFAL  138 (695)
T ss_pred             cccCCCCCchHHHHHHHHHhhHHhcChhHHHHhhhhhccCceEEEEeCCCccchhhhhhHHhc------------CCceE
Confidence            455788999999999999999999999999999999999999999999999999999999753            23499


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHH-----HHhc--CCcEEEeCcHHHHHHH---hcC-Cccc
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA-----RLRK--GISILVATPGHLLDHL---KHT-SSFL  183 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~l~~--~~~IlV~Tp~~l~~~l---~~~-~~~~  183 (316)
                      |++|..+|++.+.-++++++....     .+....+. .+..     ...+  ...++..||+.+...-   ... +...
T Consensus       139 vi~plislmedqil~lkqlgi~as-----~lnanssk-e~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka~~  212 (695)
T KOG0353|consen  139 VICPLISLMEDQILQLKQLGIDAS-----MLNANSSK-EEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKALE  212 (695)
T ss_pred             eechhHHHHHHHHHHHHHhCcchh-----hccCcccH-HHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHHhh
Confidence            999999999988888888764322     22222222 2211     1122  2569999999875422   111 2233


Q ss_pred             cCceeEEEEecchhhhcCC--cHHHHHHH--H-HHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhc
Q 043110          184 HTNLRWIIFDEADRILELG--FGKEIEEI--L-DILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISL  254 (316)
Q Consensus       184 ~~~l~~lViDEad~l~~~~--~~~~i~~i--~-~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l  254 (316)
                      ...+.++-+||+|+...||  |++++..+  + +.++                ...++.++||.+..|..-++..+
T Consensus       213 ~~~~~~iaidevhccsqwghdfr~dy~~l~ilkrqf~----------------~~~iigltatatn~vl~d~k~il  272 (695)
T KOG0353|consen  213 AGFFKLIAIDEVHCCSQWGHDFRPDYKALGILKRQFK----------------GAPIIGLTATATNHVLDDAKDIL  272 (695)
T ss_pred             cceeEEEeecceeehhhhCcccCcchHHHHHHHHhCC----------------CCceeeeehhhhcchhhHHHHHH
Confidence            4568899999999999986  77766543  2 2222                67899999999988877665443

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.63  E-value=3.7e-15  Score=146.54  Aligned_cols=138  Identities=22%  Similarity=0.275  Sum_probs=108.4

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           47 CDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        47 ~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .++..+.+|.. |+++|-...-.+..|+  ++.++||+|||+++.+|++-....         |..+-|++||.+||.|.
T Consensus        71 rEa~~R~lg~~-~~dvQlig~l~L~~G~--Iaem~TGeGKTLva~lpa~l~aL~---------G~~V~IvTpn~yLA~rd  138 (830)
T PRK12904         71 REASKRVLGMR-HFDVQLIGGMVLHEGK--IAEMKTGEGKTLVATLPAYLNALT---------GKGVHVVTVNDYLAKRD  138 (830)
T ss_pred             HHHHHHHhCCC-CCccHHHhhHHhcCCc--hhhhhcCCCcHHHHHHHHHHHHHc---------CCCEEEEecCHHHHHHH
Confidence            34444456876 8999988776776775  999999999999999999633333         22377999999999999


Q ss_pred             HHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcCCc-----cccCceeEEEEecchhhh
Q 043110          127 YEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHTSS-----FLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~~~-----~~~~~l~~lViDEad~l~  199 (316)
                      ++.+..+...++ +.++++.++.+.......+  .++|++|||++| +++++....     .....+.++||||||.|+
T Consensus       139 ~e~~~~l~~~LG-lsv~~i~~~~~~~er~~~y--~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r~~~~aIvDEaDsiL  214 (830)
T PRK12904        139 AEWMGPLYEFLG-LSVGVILSGMSPEERREAY--AADITYGTNNEFGFDYLRDNMVFSLEERVQRGLNYAIVDEVDSIL  214 (830)
T ss_pred             HHHHHHHHhhcC-CeEEEEcCCCCHHHHHHhc--CCCeEEECCcchhhhhhhcccccchhhhcccccceEEEechhhhe
Confidence            999999998765 6777888887776655543  489999999999 999976432     235678999999999876

>KOG0948 consensus Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification]

Probab=99.62  E-value=2.6e-15  Score=142.26  Aligned_cols=170  Identities=25%  Similarity=0.283  Sum_probs=135.0

Q ss_pred             CcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcC
Q 043110           59 PTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFR  138 (316)
Q Consensus        59 p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~  138 (316)
                      +.|+|+.+|..+-++..+++.|.|.+|||.++-.++.+.+..         .-++||-+|-++|.+|-|+.+..-+... 
T Consensus       130 LDpFQ~~aI~Cidr~eSVLVSAHTSAGKTVVAeYAIA~sLr~---------kQRVIYTSPIKALSNQKYREl~~EF~DV-  199 (1041)
T KOG0948|consen  130 LDPFQSTAIKCIDRGESVLVSAHTSAGKTVVAEYAIAMSLRE---------KQRVIYTSPIKALSNQKYRELLEEFKDV-  199 (1041)
T ss_pred             cCchHhhhhhhhcCCceEEEEeecCCCcchHHHHHHHHHHHh---------cCeEEeeChhhhhcchhHHHHHHHhccc-
Confidence            789999999999999999999999999999998888888865         3349999999999999998776654432 


Q ss_pred             CceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCc
Q 043110          139 WIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRN  218 (316)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~  218 (316)
                          ++..|..+.       ...+..+|.|.+.|-.++.+ +.-.+..+.|+|+||+|.|-|...+--++.-+-.+|.  
T Consensus       200 ----GLMTGDVTI-------nP~ASCLVMTTEILRsMLYR-GSEvmrEVaWVIFDEIHYMRDkERGVVWEETIIllP~--  265 (1041)
T KOG0948|consen  200 ----GLMTGDVTI-------NPDASCLVMTTEILRSMLYR-GSEVMREVAWVIFDEIHYMRDKERGVVWEETIILLPD--  265 (1041)
T ss_pred             ----ceeecceee-------CCCCceeeeHHHHHHHHHhc-cchHhheeeeEEeeeehhccccccceeeeeeEEeccc--
Confidence                344444433       23457999999999999987 4445578999999999999998888777777777777  


Q ss_pred             ccccCCCCccccccceEEEEeeecchhHHHHHHHhc---CCCEEEEcCCCC
Q 043110          219 IASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISL---ETPVLIGLDEKK  266 (316)
Q Consensus       219 ~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l---~~p~~i~~~~~~  266 (316)
                                   +.+.+++|||+|.. .+|+++..   +.|++|.-.+-.
T Consensus       266 -------------~vr~VFLSATiPNA-~qFAeWI~~ihkQPcHVVYTdyR  302 (1041)
T KOG0948|consen  266 -------------NVRFVFLSATIPNA-RQFAEWICHIHKQPCHVVYTDYR  302 (1041)
T ss_pred             -------------cceEEEEeccCCCH-HHHHHHHHHHhcCCceEEeecCC
Confidence                         89999999999955 45555433   478877655443

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

Probab=99.61  E-value=3.7e-15  Score=140.55  Aligned_cols=148  Identities=30%  Similarity=0.350  Sum_probs=100.6

Q ss_pred             CCcHHHHHHHHHHhC----CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILS----GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~----g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .|+++|++++..+.+    ++..++++|||+|||..++..+......            +|||+|+++|+.|+.+.+...
T Consensus        36 ~lr~yQ~~al~a~~~~~~~~~~gvivlpTGaGKT~va~~~~~~~~~~------------~Lvlv~~~~L~~Qw~~~~~~~  103 (442)
T COG1061          36 ELRPYQEEALDALVKNRRTERRGVIVLPTGAGKTVVAAEAIAELKRS------------TLVLVPTKELLDQWAEALKKF  103 (442)
T ss_pred             CCcHHHHHHHHHHHhhcccCCceEEEeCCCCCHHHHHHHHHHHhcCC------------EEEEECcHHHHHHHHHHHHHh
Confidence            499999999999998    8899999999999999876544332222            999999999999998777665


Q ss_pred             HhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHH
Q 043110          134 LHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDI  213 (316)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~  213 (316)
                      ....   .....++|......     . ..|.|+|-..+...- ....+......+||+||||++.+..+    ..+.+.
T Consensus       104 ~~~~---~~~g~~~~~~~~~~-----~-~~i~vat~qtl~~~~-~l~~~~~~~~~liI~DE~Hh~~a~~~----~~~~~~  169 (442)
T COG1061         104 LLLN---DEIGIYGGGEKELE-----P-AKVTVATVQTLARRQ-LLDEFLGNEFGLIIFDEVHHLPAPSY----RRILEL  169 (442)
T ss_pred             cCCc---cccceecCceeccC-----C-CcEEEEEhHHHhhhh-hhhhhcccccCEEEEEccccCCcHHH----HHHHHh
Confidence            5321   11222333332211     0 369999988876632 01222334688999999999876433    444444


Q ss_pred             hccCcccccCCCCccccccceEEEEeeecchhH
Q 043110          214 LGSRNIASIGEGNEVSNVKRQNLLLSATLNEKV  246 (316)
Q Consensus       214 l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v  246 (316)
                      +..               ....+++|||++...
T Consensus       170 ~~~---------------~~~~LGLTATp~R~D  187 (442)
T COG1061         170 LSA---------------AYPRLGLTATPERED  187 (442)
T ss_pred             hhc---------------ccceeeeccCceeec
Confidence            442               222899999987444

>TIGR00595 priA primosomal protein N'

Probab=99.60  E-value=4.2e-15  Score=142.03  Aligned_cols=137  Identities=24%  Similarity=0.202  Sum_probs=93.1

Q ss_pred             EEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH--
Q 043110           77 LVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE--  154 (316)
Q Consensus        77 li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--  154 (316)
                      ++.|+||||||.+|+..+...+..         |.++||++|+++|+.|+++.+++.+.    ......+++.+..+.  
T Consensus         1 LL~g~TGsGKT~v~l~~i~~~l~~---------g~~vLvlvP~i~L~~Q~~~~l~~~f~----~~v~vlhs~~~~~er~~   67 (505)
T TIGR00595         1 LLFGVTGSGKTEVYLQAIEKVLAL---------GKSVLVLVPEIALTPQMIQRFKYRFG----SQVAVLHSGLSDSEKLQ   67 (505)
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHc---------CCeEEEEeCcHHHHHHHHHHHHHHhC----CcEEEEECCCCHHHHHH
Confidence            468999999999997665555433         45699999999999999999987542    233455665544332  


Q ss_pred             -HHHHh-cCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCC---cH---HHHHHHHHHhccCcccccCCCC
Q 043110          155 -KARLR-KGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELG---FG---KEIEEILDILGSRNIASIGEGN  226 (316)
Q Consensus       155 -~~~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~---~~---~~i~~i~~~l~~~~~~~~~~~~  226 (316)
                       +..+. ..++|+|||+..++.        .+.+++++||||+|.....+   ..   .++........           
T Consensus        68 ~~~~~~~g~~~IVVGTrsalf~--------p~~~l~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra~~~-----------  128 (505)
T TIGR00595        68 AWRKVKNGEILVVIGTRSALFL--------PFKNLGLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKKF-----------  128 (505)
T ss_pred             HHHHHHcCCCCEEECChHHHcC--------cccCCCEEEEECCCccccccccCCCCcHHHHHHHHHHhc-----------
Confidence             33333 347899999987642        34688999999999866322   11   22333333322           


Q ss_pred             ccccccceEEEEeeecchhHHHHH
Q 043110          227 EVSNVKRQNLLLSATLNEKVNHLT  250 (316)
Q Consensus       227 ~~~~~~~q~i~~SAT~~~~v~~~~  250 (316)
                           +.+++++|||.+.+....+
T Consensus       129 -----~~~vil~SATPsles~~~~  147 (505)
T TIGR00595       129 -----NCPVVLGSATPSLESYHNA  147 (505)
T ss_pred             -----CCCEEEEeCCCCHHHHHHH
Confidence                 7899999999775544443

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).

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

Probab=99.60  E-value=6.1e-14  Score=133.30  Aligned_cols=175  Identities=28%  Similarity=0.366  Sum_probs=134.8

Q ss_pred             cCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC------CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           39 SLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG------RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        39 ~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g------~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      .++.+.++++.+.+.++|+ +|.-|++++..|...      .+-++++.-|||||++++++++..+..         |.+
T Consensus       244 ~~~~~~~l~~~~~~~LPF~-LT~aQ~~vi~EI~~Dl~~~~~M~RLlQGDVGSGKTvVA~laml~ai~~---------G~Q  313 (677)
T COG1200         244 PLPANGELLAKFLAALPFK-LTNAQKRVIKEILADLASPVPMNRLLQGDVGSGKTVVALLAMLAAIEA---------GYQ  313 (677)
T ss_pred             CCCccHHHHHHHHHhCCCC-ccHHHHHHHHHHHhhhcCchhhHHHhccCcCCCHHHHHHHHHHHHHHc---------CCe
Confidence            4556677777777889998 999999999999854      356999999999999999999998866         778


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCCh---HHHHHHHhcC-CcEEEeCcHHHHHHHhcCCccccCcee
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR---SKEKARLRKG-ISILVATPGHLLDHLKHTSSFLHTNLR  188 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~l~~~-~~IlV~Tp~~l~~~l~~~~~~~~~~l~  188 (316)
                      +..++||--||.|.++.+.+++..++ +.+..+.|....   ......+.++ .+|+|||..-+.+      .+.+.++.
T Consensus       314 ~ALMAPTEILA~QH~~~~~~~l~~~~-i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQd------~V~F~~Lg  386 (677)
T COG1200         314 AALMAPTEILAEQHYESLRKWLEPLG-IRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQD------KVEFHNLG  386 (677)
T ss_pred             eEEeccHHHHHHHHHHHHHHHhhhcC-CeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhhc------ceeeccee
Confidence            99999999999999999999998876 556666665433   3344445555 8999999754433      44557999


Q ss_pred             EEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHH
Q 043110          189 WIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHL  249 (316)
Q Consensus       189 ~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~  249 (316)
                      ++|+||=|+     |+-.=+..+..-...              .+.++.||||.=+....+
T Consensus       387 LVIiDEQHR-----FGV~QR~~L~~KG~~--------------~Ph~LvMTATPIPRTLAl  428 (677)
T COG1200         387 LVIIDEQHR-----FGVHQRLALREKGEQ--------------NPHVLVMTATPIPRTLAL  428 (677)
T ss_pred             EEEEecccc-----ccHHHHHHHHHhCCC--------------CCcEEEEeCCCchHHHHH
Confidence            999999999     666666555544320              467899999975544433

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

Probab=99.59  E-value=4.1e-14  Score=141.38  Aligned_cols=225  Identities=22%  Similarity=0.268  Sum_probs=168.4

Q ss_pred             ccCchhhhhhhhccccccccc-cccccccccCCc---ccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhC----C--C
Q 043110            5 PLNSQTISKKKKRNDKMSKKK-ETVKEIFASCCF---SSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILS----G--R   74 (316)
Q Consensus         5 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~f---~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~----g--~   74 (316)
                      .|++..|.+.|.|.+.-.+.- ...-++.+...-   -.++-+.+....+...|+|. -|+-|..||..+..    +  .
T Consensus       538 kLG~~~W~k~K~K~~~~v~diA~eLi~lyA~R~~~~G~af~~d~~~q~~F~~~FPye-ET~DQl~AI~eVk~DM~~~kpM  616 (1139)
T COG1197         538 KLGGGAWKKAKAKARKKVRDIAAELIKLYAKRQAKKGFAFPPDTEWQEEFEASFPYE-ETPDQLKAIEEVKRDMESGKPM  616 (1139)
T ss_pred             ccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhcCCCc-CCHHHHHHHHHHHHHhccCCcc
Confidence            567888999888775544432 222222222111   13567888888998999998 69999999999873    3  3


Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE  154 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (316)
                      |-++||.-|-|||.+++=++......         |.+|.|++||--||+|-++.++..+..++ +.+..+..=.+..++
T Consensus       617 DRLiCGDVGFGKTEVAmRAAFkAV~~---------GKQVAvLVPTTlLA~QHy~tFkeRF~~fP-V~I~~LSRF~s~kE~  686 (1139)
T COG1197         617 DRLICGDVGFGKTEVAMRAAFKAVMD---------GKQVAVLVPTTLLAQQHYETFKERFAGFP-VRIEVLSRFRSAKEQ  686 (1139)
T ss_pred             hheeecCcCCcHHHHHHHHHHHHhcC---------CCeEEEEcccHHhHHHHHHHHHHHhcCCC-eeEEEecccCCHHHH
Confidence            88999999999999998888887765         67899999999999999999999888776 444455444444443


Q ss_pred             H---HHHhc-CCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCcccc
Q 043110          155 K---ARLRK-GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSN  230 (316)
Q Consensus       155 ~---~~l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~  230 (316)
                      .   ..+.. ..||||||..    ++.  +.+.++++.++||||-|+     |+-.-+.-++.+..              
T Consensus       687 ~~il~~la~G~vDIvIGTHr----LL~--kdv~FkdLGLlIIDEEqR-----FGVk~KEkLK~Lr~--------------  741 (1139)
T COG1197         687 KEILKGLAEGKVDIVIGTHR----LLS--KDVKFKDLGLLIIDEEQR-----FGVKHKEKLKELRA--------------  741 (1139)
T ss_pred             HHHHHHHhcCCccEEEechH----hhC--CCcEEecCCeEEEechhh-----cCccHHHHHHHHhc--------------
Confidence            3   33333 4899999953    333  566778999999999999     66666666666666              


Q ss_pred             ccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCC
Q 043110          231 VKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK  266 (316)
Q Consensus       231 ~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~  266 (316)
                       +.-++-+|||.=+...+++...+++=-.|.+.+.+
T Consensus       742 -~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~  776 (1139)
T COG1197         742 -NVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPED  776 (1139)
T ss_pred             -cCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCC
Confidence             88999999999888888888888877777766554

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.57  E-value=7.9e-14  Score=142.84  Aligned_cols=164  Identities=22%  Similarity=0.271  Sum_probs=102.9

Q ss_pred             HHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeC----ChHHHHHHHHHHHHHHhhcCC
Q 043110           64 AQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVP----TSELCLLVYEILQKLLHRFRW  139 (316)
Q Consensus        64 ~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~P----t~~L~~Q~~~~~~~~~~~~~~  139 (316)
                      .+.+..+..++.++++|+||||||.  .+|.+.....      .+....+++.-|    +++||.++.+.+..-.   +.
T Consensus        80 ~~Il~ai~~~~VviI~GeTGSGKTT--qlPq~lle~g------~g~~g~I~~TQPRRlAArsLA~RVA~El~~~l---G~  148 (1294)
T PRK11131         80 QDILEAIRDHQVVIVAGETGSGKTT--QLPKICLELG------RGVKGLIGHTQPRRLAARTVANRIAEELETEL---GG  148 (1294)
T ss_pred             HHHHHHHHhCCeEEEECCCCCCHHH--HHHHHHHHcC------CCCCCceeeCCCcHHHHHHHHHHHHHHHhhhh---cc
Confidence            4455566666778999999999998  4774332211      011112333446    4688888877765421   11


Q ss_pred             ceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecch-hhhcCCcHHHHHHHHHHhccCc
Q 043110          140 IVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEAD-RILELGFGKEIEEILDILGSRN  218 (316)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad-~l~~~~~~~~i~~i~~~l~~~~  218 (316)
                       .+++...   ...   ....+++|+|+|||+|++.+...  ..+++++++|||||| ++++.+|...  .+...++.  
T Consensus       149 -~VGY~vr---f~~---~~s~~t~I~v~TpG~LL~~l~~d--~~Ls~~~~IIIDEAHERsLn~DfLLg--~Lk~lL~~--  215 (1294)
T PRK11131        149 -CVGYKVR---FND---QVSDNTMVKLMTDGILLAEIQQD--RLLMQYDTIIIDEAHERSLNIDFILG--YLKELLPR--  215 (1294)
T ss_pred             -eeceeec---Ccc---ccCCCCCEEEEChHHHHHHHhcC--CccccCcEEEecCccccccccchHHH--HHHHhhhc--
Confidence             1112111   111   11356899999999999998753  347899999999999 6888777642  22223332  


Q ss_pred             ccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          219 IASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       219 ~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                                 .+..|+|+||||++.  ..+.+.+...|+ |.+...
T Consensus       216 -----------rpdlKvILmSATid~--e~fs~~F~~apv-I~V~Gr  248 (1294)
T PRK11131        216 -----------RPDLKVIITSATIDP--ERFSRHFNNAPI-IEVSGR  248 (1294)
T ss_pred             -----------CCCceEEEeeCCCCH--HHHHHHcCCCCE-EEEcCc
Confidence                       126799999999974  477777777775 555543

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.56  E-value=4.8e-14  Score=137.75  Aligned_cols=150  Identities=15%  Similarity=0.161  Sum_probs=101.1

Q ss_pred             CCcHHHHHHHHHHh-CC--CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVIL-SG--RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        58 ~p~~~Q~~~i~~il-~g--~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      .++|+|.+++..+. +|  +..++++|||+|||+..+..+. .+.           ..+|||||+..|+.|+.+.+.++.
T Consensus       255 ~LRpYQ~eAl~~~~~~gr~r~GIIvLPtGaGKTlvai~aa~-~l~-----------k~tLILvps~~Lv~QW~~ef~~~~  322 (732)
T TIGR00603       255 QIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKSLVGVTAAC-TVK-----------KSCLVLCTSAVSVEQWKQQFKMWS  322 (732)
T ss_pred             CcCHHHHHHHHHHHhcCCCCCcEEEeCCCCChHHHHHHHHH-HhC-----------CCEEEEeCcHHHHHHHHHHHHHhc
Confidence            47999999998887 34  3689999999999999765443 221           229999999999999999999875


Q ss_pred             hhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcC-------CccccCceeEEEEecchhhhcCCcHHHH
Q 043110          135 HRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHT-------SSFLHTNLRWIIFDEADRILELGFGKEI  207 (316)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~-------~~~~~~~l~~lViDEad~l~~~~~~~~i  207 (316)
                      .. ....+....|+...     ......+|+|+|+..+.....+.       ..+.-....++|+||||++..    ..+
T Consensus       323 ~l-~~~~I~~~tg~~k~-----~~~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~~~~gLII~DEvH~lpA----~~f  392 (732)
T TIGR00603       323 TI-DDSQICRFTSDAKE-----RFHGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTNREWGLILLDEVHVVPA----AMF  392 (732)
T ss_pred             CC-CCceEEEEecCccc-----ccccCCcEEEEEHHHhhcccccchhhhHHHHHhccccCCEEEEEccccccH----HHH
Confidence            32 22233333333211     11223689999998775332211       011123578999999999854    445


Q ss_pred             HHHHHHhccCcccccCCCCccccccceEEEEeeecchh
Q 043110          208 EEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEK  245 (316)
Q Consensus       208 ~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~  245 (316)
                      ..++..+.                ....+++|||+...
T Consensus       393 r~il~~l~----------------a~~RLGLTATP~Re  414 (732)
T TIGR00603       393 RRVLTIVQ----------------AHCKLGLTATLVRE  414 (732)
T ss_pred             HHHHHhcC----------------cCcEEEEeecCccc
Confidence            55666654                34569999998643

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).

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=99.55  E-value=4.4e-14  Score=139.06  Aligned_cols=137  Identities=22%  Similarity=0.233  Sum_probs=104.8

Q ss_pred             HHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           49 QLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        49 ~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      +..+.+|.. |+++|...--.+..|+  ++.++||.|||+++.+|++.....         |..|.||+|+++||.|..+
T Consensus        74 aa~R~lgm~-~ydVQliGgl~L~~G~--IaEm~TGEGKTL~a~lp~~l~al~---------g~~VhIvT~ndyLA~RD~e  141 (908)
T PRK13107         74 ASKRVFEMR-HFDVQLLGGMVLDSNR--IAEMRTGEGKTLTATLPAYLNALT---------GKGVHVITVNDYLARRDAE  141 (908)
T ss_pred             HHHHHhCCC-cCchHHhcchHhcCCc--cccccCCCCchHHHHHHHHHHHhc---------CCCEEEEeCCHHHHHHHHH
Confidence            333456775 8999976554555554  899999999999999999877765         3339999999999999999


Q ss_pred             HHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcCCccc-----cCceeEEEEecchhhhc
Q 043110          129 ILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHTSSFL-----HTNLRWIIFDEADRILE  200 (316)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~~~~~-----~~~l~~lViDEad~l~~  200 (316)
                      ++..+...++ +.+.++.++.+... .... -+++|++|||+.| +++++..-...     ...+.+.||||+|.++-
T Consensus       142 ~m~~l~~~lG-lsv~~i~~~~~~~~-r~~~-Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr~~~~aIvDEvDsiLi  216 (908)
T PRK13107        142 NNRPLFEFLG-LTVGINVAGLGQQE-KKAA-YNADITYGTNNEFGFDYLRDNMAFSPQERVQRPLHYALIDEVDSILI  216 (908)
T ss_pred             HHHHHHHhcC-CeEEEecCCCCHHH-HHhc-CCCCeEEeCCCcccchhhhccCccchhhhhccccceeeecchhhhcc
Confidence            9999998865 66677777766532 2222 2589999999999 88887642222     26788999999998874

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=99.53  E-value=3.2e-13  Score=137.19  Aligned_cols=83  Identities=27%  Similarity=0.328  Sum_probs=65.0

Q ss_pred             CCHHHHHHHHHHcCCCCCcHHHHHHHH----HHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEe
Q 043110           42 LDSTLCDQLRERLGFEAPTKVQAQAIP----VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLV  117 (316)
Q Consensus        42 l~~~l~~~l~~~~g~~~p~~~Q~~~i~----~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~  117 (316)
                      +++.+.+.+ ...||+ +++.|.+.+.    .+..|+++++.||||+|||++|++|++.....         +.+++|.+
T Consensus       231 ~~~~~~~~~-~~~~~~-~r~~Q~~~~~~i~~~~~~~~~~~~eA~TG~GKT~ayLlp~~~~~~~---------~~~vvi~t  299 (850)
T TIGR01407       231 LSSLFSKNI-DRLGLE-YRPEQLKLAELVLDQLTHSEKSLIEAPTGTGKTLGYLLPALYYAIT---------EKPVVIST  299 (850)
T ss_pred             ccHHHHHhh-hhcCCc-cCHHHHHHHHHHHHHhccCCcEEEECCCCCchhHHHHHHHHHHhcC---------CCeEEEEe
Confidence            344666666 457888 8999998665    55678999999999999999999999886642         23599999


Q ss_pred             CChHHHHHHHH-HHHHHHh
Q 043110          118 PTSELCLLVYE-ILQKLLH  135 (316)
Q Consensus       118 Pt~~L~~Q~~~-~~~~~~~  135 (316)
                      ||++|..|+.. .+..+.+
T Consensus       300 ~t~~Lq~Ql~~~~~~~l~~  318 (850)
T TIGR01407       300 NTKVLQSQLLEKDIPLLNE  318 (850)
T ss_pred             CcHHHHHHHHHHHHHHHHH
Confidence            99999999865 4555443

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.

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.48  E-value=1.3e-12  Score=134.44  Aligned_cols=177  Identities=20%  Similarity=0.225  Sum_probs=111.4

Q ss_pred             cCCCCCcHHHH---HHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHH
Q 043110           54 LGFEAPTKVQA---QAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEIL  130 (316)
Q Consensus        54 ~g~~~p~~~Q~---~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~  130 (316)
                      ..|...-|+..   +.+..+.+++.++++|+||||||..  +|.+..-..      .+...++++.-|.|--|..++..+
T Consensus        60 ~~~~~~LPi~~~~~~Il~~l~~~~vvii~g~TGSGKTTq--lPq~lle~~------~~~~~~I~~tQPRRlAA~svA~Rv  131 (1283)
T TIGR01967        60 IRYPDNLPVSAKREDIAEAIAENQVVIIAGETGSGKTTQ--LPKICLELG------RGSHGLIGHTQPRRLAARTVAQRI  131 (1283)
T ss_pred             ccCCCCCCHHHHHHHHHHHHHhCceEEEeCCCCCCcHHH--HHHHHHHcC------CCCCceEecCCccHHHHHHHHHHH
Confidence            45555556654   3445555667789999999999984  565432211      111234666678888777777655


Q ss_pred             HHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecch-hhhcCCcHHH-HH
Q 043110          131 QKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEAD-RILELGFGKE-IE  208 (316)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad-~l~~~~~~~~-i~  208 (316)
                      ...........+++.....+.      ...+..|.++|+|+|+..+...  ..++++++||||||| +.++.+|.-. +.
T Consensus       132 A~elg~~lG~~VGY~vR~~~~------~s~~T~I~~~TdGiLLr~l~~d--~~L~~~~~IIIDEaHERsL~~D~LL~lLk  203 (1283)
T TIGR01967       132 AEELGTPLGEKVGYKVRFHDQ------VSSNTLVKLMTDGILLAETQQD--RFLSRYDTIIIDEAHERSLNIDFLLGYLK  203 (1283)
T ss_pred             HHHhCCCcceEEeeEEcCCcc------cCCCceeeeccccHHHHHhhhC--cccccCcEEEEcCcchhhccchhHHHHHH
Confidence            544321111222222211111      1345789999999999988753  346789999999999 5888776643 44


Q ss_pred             HHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          209 EILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       209 ~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                      .++...+                ..|+|+||||++.  ..+.+.+...|+ |.+...
T Consensus       204 ~il~~rp----------------dLKlIlmSATld~--~~fa~~F~~apv-I~V~Gr  241 (1283)
T TIGR01967       204 QLLPRRP----------------DLKIIITSATIDP--ERFSRHFNNAPI-IEVSGR  241 (1283)
T ss_pred             HHHhhCC----------------CCeEEEEeCCcCH--HHHHHHhcCCCE-EEECCC
Confidence            4443322                6799999999974  577777766675 445443

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.

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

Probab=99.45  E-value=1.1e-12  Score=134.98  Aligned_cols=161  Identities=20%  Similarity=0.151  Sum_probs=102.9

Q ss_pred             CCcHHHHHHHHHHh----CC-CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVIL----SG-RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        58 ~p~~~Q~~~i~~il----~g-~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      .++++|.+|+..+.    .| +..+++++||||||.+.+ .++..+.+..      ...++|+|+|+++|+.|..+.++.
T Consensus       413 ~lR~YQ~~AI~ai~~a~~~g~r~~Ll~maTGSGKT~tai-~li~~L~~~~------~~~rVLfLvDR~~L~~Qa~~~F~~  485 (1123)
T PRK11448        413 GLRYYQEDAIQAVEKAIVEGQREILLAMATGTGKTRTAI-ALMYRLLKAK------RFRRILFLVDRSALGEQAEDAFKD  485 (1123)
T ss_pred             CCCHHHHHHHHHHHHHHHhccCCeEEEeCCCCCHHHHHH-HHHHHHHhcC------ccCeEEEEecHHHHHHHHHHHHHh
Confidence            48999999998775    33 579999999999998854 3445444321      234699999999999999998887


Q ss_pred             HHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcC----CccccCceeEEEEecchhhhc------C-
Q 043110          133 LLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHT----SSFLHTNLRWIIFDEADRILE------L-  201 (316)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~----~~~~~~~l~~lViDEad~l~~------~-  201 (316)
                      +..... ......++......  ........|+|+|...+...+...    ....+..+++||+||||+-..      . 
T Consensus       486 ~~~~~~-~~~~~i~~i~~L~~--~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~fdlIIiDEaHRs~~~d~~~~~~  562 (1123)
T PRK11448        486 TKIEGD-QTFASIYDIKGLED--KFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQYDCIIVDEAHRGYTLDKEMSEG  562 (1123)
T ss_pred             cccccc-cchhhhhchhhhhh--hcccCCCCEEEEEHHHHHHhhhccccccccCCCCcccEEEEECCCCCCccccccccc
Confidence            632111 00000111100000  111234689999999987765321    113456788999999999531      0 


Q ss_pred             --C------cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchh
Q 043110          202 --G------FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEK  245 (316)
Q Consensus       202 --~------~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~  245 (316)
                        +      +...+..++.++                 ....|+||||....
T Consensus       563 ~~~~~~~~~~~~~yr~iL~yF-----------------dA~~IGLTATP~r~  597 (1123)
T PRK11448        563 ELQFRDQLDYVSKYRRVLDYF-----------------DAVKIGLTATPALH  597 (1123)
T ss_pred             hhccchhhhHHHHHHHHHhhc-----------------CccEEEEecCCccc
Confidence              1      134566666654                 34679999998643

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=99.43  E-value=3.1e-12  Score=128.79  Aligned_cols=132  Identities=23%  Similarity=0.324  Sum_probs=91.6

Q ss_pred             CCCCCcHHHHHHHHH----HhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHH-HH
Q 043110           55 GFEAPTKVQAQAIPV----ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY-EI  129 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~----il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~-~~  129 (316)
                      ||+ +++-|.+....    +.++++++++|+||+|||++|++|++...          .+.++||++||++|++|+. +.
T Consensus       243 ~~e-~R~~Q~~ma~~V~~~l~~~~~~~~eA~tGtGKT~ayllp~l~~~----------~~~~vvI~t~T~~Lq~Ql~~~~  311 (820)
T PRK07246        243 GLE-ERPKQESFAKLVGEDFHDGPASFIEAQTGIGKTYGYLLPLLAQS----------DQRQIIVSVPTKILQDQIMAEE  311 (820)
T ss_pred             CCc-cCHHHHHHHHHHHHHHhCCCcEEEECCCCCcHHHHHHHHHHHhc----------CCCcEEEEeCcHHHHHHHHHHH
Confidence            665 89999884433    44678899999999999999999988753          1345999999999999994 66


Q ss_pred             HHHHHhhcCCceeEEeeCCCChH---------------------------------------------------------
Q 043110          130 LQKLLHRFRWIVPGYVMGGGNRS---------------------------------------------------------  152 (316)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~---------------------------------------------------------  152 (316)
                      +..+...++ +....+.|+.+.-                                                         
T Consensus       312 i~~l~~~~~-~~~~~~kg~~~ylcl~k~~~~l~~~~~~~~~~~~~~~il~Wl~~T~tGD~~El~~~~~~~~~w~~i~~~~  390 (820)
T PRK07246        312 VKAIQEVFH-IDCHSLKGPQNYLKLDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLDEIKQKQRYAAYFDQLKHDG  390 (820)
T ss_pred             HHHHHHhcC-CcEEEEECCcccccHHHHHHHhhccCcchHHHHHHHHHHHHHhcCCCCCHhhccCCccccHHHHHhhccC
Confidence            777665543 2233333332100                                                         


Q ss_pred             --------------HHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          153 --------------KEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       153 --------------~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                                    ...+.-...++|+|+....|+..+....  .+...+++||||||++.+
T Consensus       391 ~~~~~cp~~~~cf~~~ar~~a~~AdivItNHall~~~~~~~~--~~p~~~~lIiDEAH~l~~  450 (820)
T PRK07246        391 NLSQSSLFYDYDFWKRSYEKAKTARLLITNHAYFLTRVQDDK--DFARNKVLVFDEAQKLML  450 (820)
T ss_pred             CCCCCCCcchhhHHHHHHHHHHhCCEEEEchHHHHHHHhhcc--CCCCCCEEEEECcchhHH
Confidence                          0000011236899999998888765432  245789999999999874

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=99.43  E-value=3e-12  Score=124.06  Aligned_cols=62  Identities=24%  Similarity=0.333  Sum_probs=52.1

Q ss_pred             HHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           66 AIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        66 ~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      +...+.+++.+++.|+||+|||++|++|++..+...       .+.++||++||++|+.|+.+.+..+.
T Consensus         9 i~~al~~~~~lliEA~TGtGKTlAYLlpal~~~~~~-------~~~rvlIstpT~~Lq~Ql~~~l~~l~   70 (636)
T TIGR03117         9 CLTSLRQKRIGMLEASTGVGKTLAMIMAALTMLKER-------PDQKIAIAVPTLALMGQLWSELERLT   70 (636)
T ss_pred             HHHHHhcCCeEEEEcCCCCcHHHHHHHHHHHHHHhc-------cCceEEEECCcHHHHHHHHHHHHHHH
Confidence            344556788899999999999999999999877531       24569999999999999999888776

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.

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=99.42  E-value=7.3e-12  Score=123.02  Aligned_cols=157  Identities=25%  Similarity=0.370  Sum_probs=111.5

Q ss_pred             HHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           44 STLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        44 ~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      +++.+.+.+..|+ +|...|+.....+..|+++-+.||||.|||..-++..+- +..        .|.+++||+||..|+
T Consensus        69 e~~~~fF~k~~G~-~~ws~QR~WakR~~rg~SFaiiAPTGvGKTTfg~~~sl~-~a~--------kgkr~yii~PT~~Lv  138 (1187)
T COG1110          69 EEFEEFFKKATGF-RPWSAQRVWAKRLVRGKSFAIIAPTGVGKTTFGLLMSLY-LAK--------KGKRVYIIVPTTTLV  138 (1187)
T ss_pred             HHHHHHHHHhhCC-CchHHHHHHHHHHHcCCceEEEcCCCCchhHHHHHHHHH-HHh--------cCCeEEEEecCHHHH
Confidence            3455566566677 699999999999999999999999999999754433333 222        245699999999999


Q ss_pred             HHHHHHHHHHHhhcCCceeEEeeCCC-Ch---HHHHHHHhc-CCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhh
Q 043110          124 LLVYEILQKLLHRFRWIVPGYVMGGG-NR---SKEKARLRK-GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRI  198 (316)
Q Consensus       124 ~Q~~~~~~~~~~~~~~~~~~~~~~~~-~~---~~~~~~l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l  198 (316)
                      .|.++.+++++...+.....+.+.+. ..   ..-...+.+ +.||+|+|...|...+.....   -+++++++|++|.+
T Consensus       139 ~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L~~---~kFdfifVDDVDA~  215 (1187)
T COG1110         139 RQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEELSK---LKFDFIFVDDVDAI  215 (1187)
T ss_pred             HHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHHhcc---cCCCEEEEccHHHH
Confidence            99999999999876633333323332 22   222334443 589999999888776664322   26789999999999


Q ss_pred             hcCCcHHHHHHHHHHhc
Q 043110          199 LELGFGKEIEEILDILG  215 (316)
Q Consensus       199 ~~~~~~~~i~~i~~~l~  215 (316)
                      +..+  ..++.++..+.
T Consensus       216 Lkas--kNvDriL~LlG  230 (1187)
T COG1110         216 LKAS--KNVDRLLRLLG  230 (1187)
T ss_pred             Hhcc--ccHHHHHHHcC
Confidence            8754  44555554443

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

Probab=99.39  E-value=2.3e-12  Score=125.75  Aligned_cols=181  Identities=19%  Similarity=0.196  Sum_probs=134.9

Q ss_pred             CCCHHHHHHHHHHcCCCCCcHHHHHHH--HHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeC
Q 043110           41 GLDSTLCDQLRERLGFEAPTKVQAQAI--PVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVP  118 (316)
Q Consensus        41 ~l~~~l~~~l~~~~g~~~p~~~Q~~~i--~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~P  118 (316)
                      .+.+.+.+......|...++.||.+|+  |.++.++|.+..+||+.|||++.-+-++..+.....        .++.+.|
T Consensus       206 ~~~~k~~~~~~~~kgi~~~fewq~ecls~~~~~e~~nliys~Pts~gktlvaeilml~~~l~~rr--------~~llilp  277 (1008)
T KOG0950|consen  206 RLPTKVSHLYAKDKGILKLFEWQAECLSLPRLLERKNLIYSLPTSAGKTLVAEILMLREVLCRRR--------NVLLILP  277 (1008)
T ss_pred             cCchHHHHHHHHhhhHHHHHHHHHHHhcchhhhcccceEEeCCCccchHHHHHHHHHHHHHHHhh--------ceeEecc
Confidence            466666666657779999999999997  778899999999999999999998888877765333        2899999


Q ss_pred             ChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcC-CccccCceeEEEEecchh
Q 043110          119 TSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHT-SSFLHTNLRWIIFDEADR  197 (316)
Q Consensus       119 t~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~-~~~~~~~l~~lViDEad~  197 (316)
                      ..+.+..-...+..+....+..+-++. |......    ..+.-++.|||-++-..++... ..-.+..+.++|+||.|.
T Consensus       278 ~vsiv~Ek~~~l~~~~~~~G~~ve~y~-g~~~p~~----~~k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhm  352 (1008)
T KOG0950|consen  278 YVSIVQEKISALSPFSIDLGFPVEEYA-GRFPPEK----RRKRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHM  352 (1008)
T ss_pred             eeehhHHHHhhhhhhccccCCcchhhc-ccCCCCC----cccceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeee
Confidence            988887777777777776664443333 3322211    1233579999999876666432 112345789999999999


Q ss_pred             hhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecch
Q 043110          198 ILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       198 l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                      +.|.+.+..++.++..+--.+.          ....|+|+||||+|+
T Consensus       353 i~d~~rg~~lE~~l~k~~y~~~----------~~~~~iIGMSATi~N  389 (1008)
T KOG0950|consen  353 IGDKGRGAILELLLAKILYENL----------ETSVQIIGMSATIPN  389 (1008)
T ss_pred             eeccccchHHHHHHHHHHHhcc----------ccceeEeeeecccCC
Confidence            9999999999999887754221          113789999999985

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family

Probab=99.38  E-value=7.5e-12  Score=123.76  Aligned_cols=152  Identities=22%  Similarity=0.209  Sum_probs=97.7

Q ss_pred             CcHHHHHHHHHHh----C------CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           59 PTKVQAQAIPVIL----S------GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        59 p~~~Q~~~i~~il----~------g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      |+..|..|+..+.    .      .+..++..+||||||++.+..+...+..       ....++|+|+|+.+|..|+.+
T Consensus       239 ~r~~Q~~av~~~~~~~~~~~~~~~~~~gli~~~TGsGKT~t~~~la~~l~~~-------~~~~~vl~lvdR~~L~~Q~~~  311 (667)
T TIGR00348       239 QRYMQYRAVKKIVESITRKTWGKDERGGLIWHTQGSGKTLTMLFAARKALEL-------LKNPKVFFVVDRRELDYQLMK  311 (667)
T ss_pred             hHHHHHHHHHHHHHHHHhcccCCCCceeEEEEecCCCccHHHHHHHHHHHhh-------cCCCeEEEEECcHHHHHHHHH
Confidence            6888999987764    2      2469999999999999876544433321       235679999999999999999


Q ss_pred             HHHHHHhhcCCceeEEeeCCCChHHHHHHHhc-CCcEEEeCcHHHHHHHhcC-CccccC-ceeEEEEecchhhhcCCcHH
Q 043110          129 ILQKLLHRFRWIVPGYVMGGGNRSKEKARLRK-GISILVATPGHLLDHLKHT-SSFLHT-NLRWIIFDEADRILELGFGK  205 (316)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~IlV~Tp~~l~~~l~~~-~~~~~~-~l~~lViDEad~l~~~~~~~  205 (316)
                      .+..++...       ..+..+.......+.. ...|+|+|...+...+... ...... .--++|+||||+..   ++.
T Consensus       312 ~f~~~~~~~-------~~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~lvIvDEaHrs~---~~~  381 (667)
T TIGR00348       312 EFQSLQKDC-------AERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVVVIFDEAHRSQ---YGE  381 (667)
T ss_pred             HHHhhCCCC-------CcccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEEEEEEcCcccc---chH
Confidence            988875310       1111222223333332 3589999999997644321 111111 11289999999853   333


Q ss_pred             HHHHHHHHhccCcccccCCCCccccccceEEEEeeecc
Q 043110          206 EIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLN  243 (316)
Q Consensus       206 ~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~  243 (316)
                      ....+.+.++                +...++||||.-
T Consensus       382 ~~~~l~~~~p----------------~a~~lGfTaTP~  403 (667)
T TIGR00348       382 LAKNLKKALK----------------NASFFGFTGTPI  403 (667)
T ss_pred             HHHHHHhhCC----------------CCcEEEEeCCCc
Confidence            2333334554                568999999974

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=99.35  E-value=4.1e-12  Score=123.85  Aligned_cols=164  Identities=21%  Similarity=0.225  Sum_probs=114.5

Q ss_pred             CCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           55 GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      +|. |..||.+.+...-.+..+++.|||.+|||++-...+-..+...+       .-.+|+++||++|+.|+...+....
T Consensus       509 dF~-Pd~WQ~elLDsvDr~eSavIVAPTSaGKTfisfY~iEKVLResD-------~~VVIyvaPtKaLVnQvsa~VyaRF  580 (1330)
T KOG0949|consen  509 DFC-PDEWQRELLDSVDRNESAVIVAPTSAGKTFISFYAIEKVLRESD-------SDVVIYVAPTKALVNQVSANVYARF  580 (1330)
T ss_pred             ccC-CcHHHHHHhhhhhcccceEEEeeccCCceeccHHHHHHHHhhcC-------CCEEEEecchHHHhhhhhHHHHHhh
Confidence            344 88999999999999999999999999999985454444444322       3348999999999999988777665


Q ss_pred             hhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcC--CccccCceeEEEEecchhhhcCCcHHHHHHHHH
Q 043110          135 HRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHT--SSFLHTNLRWIIFDEADRILELGFGKEIEEILD  212 (316)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~--~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~  212 (316)
                      ..-.......+.|..+.+-.  .-.-.|+|+|+-|+.+..++...  ..-..++++++|+||+|.+-.+.-+--++.++.
T Consensus       581 ~~~t~~rg~sl~g~ltqEYs--inp~nCQVLITvPecleslLlspp~~q~~cerIRyiIfDEVH~iG~~ed~l~~Eqll~  658 (1330)
T KOG0949|consen  581 DTKTFLRGVSLLGDLTQEYS--INPWNCQVLITVPECLESLLLSPPHHQKFCERIRYIIFDEVHLIGNEEDGLLWEQLLL  658 (1330)
T ss_pred             ccCccccchhhHhhhhHHhc--CCchhceEEEEchHHHHHHhcCchhhhhhhhcceEEEechhhhccccccchHHHHHHH
Confidence            32211111122222221111  11224899999999999888763  223557899999999999876654445555555


Q ss_pred             HhccCcccccCCCCccccccceEEEEeeecchh
Q 043110          213 ILGSRNIASIGEGNEVSNVKRQNLLLSATLNEK  245 (316)
Q Consensus       213 ~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~  245 (316)
                      ..                 .+.++.+|||+.+.
T Consensus       659 li-----------------~CP~L~LSATigN~  674 (1330)
T KOG0949|consen  659 LI-----------------PCPFLVLSATIGNP  674 (1330)
T ss_pred             hc-----------------CCCeeEEecccCCH
Confidence            54                 78999999999654

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=99.33  E-value=2.5e-11  Score=108.27  Aligned_cols=76  Identities=28%  Similarity=0.331  Sum_probs=59.7

Q ss_pred             cCCCCCcHHHHH----HHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHH
Q 043110           54 LGFEAPTKVQAQ----AIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI  129 (316)
Q Consensus        54 ~g~~~p~~~Q~~----~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~  129 (316)
                      |.|. |+|.|.+    +...+.+|+++++.||||+|||++|++|++..+......   ..+.+++|+++|..+.+|....
T Consensus         5 FPy~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~---~~~~kvi~~t~T~~~~~q~i~~   80 (289)
T smart00489        5 FPYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER---IQKIKLIYLSRTVSEIEKRLEE   80 (289)
T ss_pred             CCCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc---ccccceeEEeccHHHHHHHHHH
Confidence            6776 7999999    445566889999999999999999999999876653221   0234699999999998888776


Q ss_pred             HHHH
Q 043110          130 LQKL  133 (316)
Q Consensus       130 ~~~~  133 (316)
                      ++++
T Consensus        81 l~~~   84 (289)
T smart00489       81 LRKL   84 (289)
T ss_pred             HHhc
Confidence            6654

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=99.33  E-value=2.5e-11  Score=108.27  Aligned_cols=76  Identities=28%  Similarity=0.331  Sum_probs=59.7

Q ss_pred             cCCCCCcHHHHH----HHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHH
Q 043110           54 LGFEAPTKVQAQ----AIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI  129 (316)
Q Consensus        54 ~g~~~p~~~Q~~----~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~  129 (316)
                      |.|. |+|.|.+    +...+.+|+++++.||||+|||++|++|++..+......   ..+.+++|+++|..+.+|....
T Consensus         5 FPy~-~r~~Q~~~m~~v~~~~~~~~~~~~eapTGtGKTl~~L~~al~~~~~~~~~---~~~~kvi~~t~T~~~~~q~i~~   80 (289)
T smart00488        5 FPYE-PYPIQYEFMEELKRVLDRGKIGILESPTGTGKTLSLLCLTLTWLRSFPER---IQKIKLIYLSRTVSEIEKRLEE   80 (289)
T ss_pred             CCCC-CCHHHHHHHHHHHHHHHcCCcEEEECCCCcchhHHHHHHHHHHHHhCccc---ccccceeEEeccHHHHHHHHHH
Confidence            6776 7999999    445566889999999999999999999999876653221   0234699999999998888776


Q ss_pred             HHHH
Q 043110          130 LQKL  133 (316)
Q Consensus       130 ~~~~  133 (316)
                      ++++
T Consensus        81 l~~~   84 (289)
T smart00488       81 LRKL   84 (289)
T ss_pred             HHhc
Confidence            6654

>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=99.29  E-value=1.4e-11  Score=119.07  Aligned_cols=139  Identities=24%  Similarity=0.267  Sum_probs=98.7

Q ss_pred             CCCcHHHHHHHHHHh----CCCc-EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH
Q 043110           57 EAPTKVQAQAIPVIL----SGRD-VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ  131 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il----~g~d-~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~  131 (316)
                      ..|+.+|..||..+.    .|++ +++++.||+|||.++ +.++.+|.+.      +.-.++|+|+-+++|+.|.+..+.
T Consensus       164 i~~RyyQ~~AI~rv~Eaf~~g~~raLlvMATGTGKTrTA-iaii~rL~r~------~~~KRVLFLaDR~~Lv~QA~~af~  236 (875)
T COG4096         164 IGPRYYQIIAIRRVIEAFSKGQNRALLVMATGTGKTRTA-IAIIDRLIKS------GWVKRVLFLADRNALVDQAYGAFE  236 (875)
T ss_pred             ccchHHHHHHHHHHHHHHhcCCceEEEEEecCCCcceeH-HHHHHHHHhc------chhheeeEEechHHHHHHHHHHHH
Confidence            358899999986654    5654 999999999999986 5577777653      224569999999999999998877


Q ss_pred             HHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcC----CccccCceeEEEEecchhhhcCCcHHHH
Q 043110          132 KLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHT----SSFLHTNLRWIIFDEADRILELGFGKEI  207 (316)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~----~~~~~~~l~~lViDEad~l~~~~~~~~i  207 (316)
                      .+.-.   ........+...       ...++|.|+|...+...+...    ..+....++++|+||||+    |.....
T Consensus       237 ~~~P~---~~~~n~i~~~~~-------~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~FDlIvIDEaHR----gi~~~~  302 (875)
T COG4096         237 DFLPF---GTKMNKIEDKKG-------DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFFDLIVIDEAHR----GIYSEW  302 (875)
T ss_pred             HhCCC---ccceeeeecccC-------CcceeEEEeehHHHHhhhhccccccccCCCCceeEEEechhhh----hHHhhh
Confidence            76532   222222211111       114789999999998877653    123445689999999999    455566


Q ss_pred             HHHHHHhcc
Q 043110          208 EEILDILGS  216 (316)
Q Consensus       208 ~~i~~~l~~  216 (316)
                      ..|+.++..
T Consensus       303 ~~I~dYFdA  311 (875)
T COG4096         303 SSILDYFDA  311 (875)
T ss_pred             HHHHHHHHH
Confidence            688888864

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=99.27  E-value=2.5e-11  Score=118.73  Aligned_cols=159  Identities=25%  Similarity=0.252  Sum_probs=111.2

Q ss_pred             CCcHHHHHHHHHHhCC----CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSG----RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g----~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .+++-|+.+...+...    +..++.+.||||||.+|+=.+-+.+..         |..+|+|+|-.+|..|+.+.++..
T Consensus       198 ~Ln~~Q~~a~~~i~~~~~~~~~~Ll~GvTGSGKTEvYl~~i~~~L~~---------GkqvLvLVPEI~Ltpq~~~rf~~r  268 (730)
T COG1198         198 ALNQEQQAAVEAILSSLGGFAPFLLDGVTGSGKTEVYLEAIAKVLAQ---------GKQVLVLVPEIALTPQLLARFKAR  268 (730)
T ss_pred             ccCHHHHHHHHHHHHhcccccceeEeCCCCCcHHHHHHHHHHHHHHc---------CCEEEEEeccccchHHHHHHHHHH
Confidence            5688999999998765    469999999999999998777777765         566999999999999999999887


Q ss_pred             HhhcCCceeEEeeCCC---ChHHHHHHHh-cCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhc---CCcHHH
Q 043110          134 LHRFRWIVPGYVMGGG---NRSKEKARLR-KGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE---LGFGKE  206 (316)
Q Consensus       134 ~~~~~~~~~~~~~~~~---~~~~~~~~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~---~~~~~~  206 (316)
                      +.    ..+..++++.   ...+.|.... ....|+|||-..++-        .++++.++||||-|.-.-   .+...+
T Consensus       269 Fg----~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF~--------Pf~~LGLIIvDEEHD~sYKq~~~prYh  336 (730)
T COG1198         269 FG----AKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALFL--------PFKNLGLIIVDEEHDSSYKQEDGPRYH  336 (730)
T ss_pred             hC----CChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhcC--------chhhccEEEEeccccccccCCcCCCcC
Confidence            65    2333334433   3334455544 558999999655443        346899999999996431   122333


Q ss_pred             HHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHH
Q 043110          207 IEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLT  250 (316)
Q Consensus       207 i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~  250 (316)
                      .+.+.-...+..             ++++|+-|||.+=+-...+
T Consensus       337 ARdvA~~Ra~~~-------------~~pvvLgSATPSLES~~~~  367 (730)
T COG1198         337 ARDVAVLRAKKE-------------NAPVVLGSATPSLESYANA  367 (730)
T ss_pred             HHHHHHHHHHHh-------------CCCEEEecCCCCHHHHHhh
Confidence            333332222211             7899999999775544444

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=99.27  E-value=5.1e-11  Score=119.12  Aligned_cols=186  Identities=20%  Similarity=0.169  Sum_probs=123.4

Q ss_pred             CCcHHHHHHHHHHhCC---C-cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSG---R-DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g---~-d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .+++.|..++..+...   . .+++.||||+|||.+.+.++...+...     .....+++++.|++.+++++++.++.+
T Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~vl~aPTG~GKT~asl~~a~~~~~~~-----~~~~~r~i~vlP~~t~ie~~~~r~~~~  269 (733)
T COG1203         195 EGYELQEKALELILRLEKRSLLVVLEAPTGYGKTEASLILALALLDEK-----IKLKSRVIYVLPFRTIIEDMYRRAKEI  269 (733)
T ss_pred             hhhHHHHHHHHHHHhcccccccEEEEeCCCCChHHHHHHHHHHHhhcc-----ccccceEEEEccHHHHHHHHHHHHHhh
Confidence            3488999999888743   3 689999999999999999888877652     113567999999999999999999987


Q ss_pred             HhhcCCceeEEeeCCCChHHHHHH-----H---------hcCCcEEEeCcHHHHHHHhcCCccc-cC--ceeEEEEecch
Q 043110          134 LHRFRWIVPGYVMGGGNRSKEKAR-----L---------RKGISILVATPGHLLDHLKHTSSFL-HT--NLRWIIFDEAD  196 (316)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~-----l---------~~~~~IlV~Tp~~l~~~l~~~~~~~-~~--~l~~lViDEad  196 (316)
                      ......... ..++..........     .         .....+.++||-............. +.  -.+.+|+||+|
T Consensus       270 ~~~~~~~~~-~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~S~vIlDE~h  348 (733)
T COG1203         270 FGLFSVIGK-SLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVKGFKFEFLALLLTSLVILDEVH  348 (733)
T ss_pred             hcccccccc-cccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhccccchHHHHHHHhhchhhccHH
Confidence            765432221 01222211111000     0         0113466666665554222211111 11  23689999999


Q ss_pred             hhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcC
Q 043110          197 RILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD  263 (316)
Q Consensus       197 ~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~  263 (316)
                      .+.+......+..++..+...              ...+|++|||+|+...+.....+.+...+...
T Consensus       349 ~~~~~~~~~~l~~~i~~l~~~--------------g~~ill~SATlP~~~~~~l~~~~~~~~~~~~~  401 (733)
T COG1203         349 LYADETMLAALLALLEALAEA--------------GVPVLLMSATLPPFLKEKLKKALGKGREVVEN  401 (733)
T ss_pred             hhcccchHHHHHHHHHHHHhC--------------CCCEEEEecCCCHHHHHHHHHHHhcccceecc
Confidence            987764555666666666543              67999999999999999888877766655543

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=99.26  E-value=6.2e-11  Score=117.21  Aligned_cols=136  Identities=21%  Similarity=0.198  Sum_probs=100.7

Q ss_pred             HHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           49 QLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        49 ~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      +-.+.+|.. |+++|...--.+..|  -++.+.||+|||+++.+|++.....         |..+.|++|+..||.|-++
T Consensus        74 a~~R~lGm~-~ydVQliGg~~Lh~G--~iaEM~TGEGKTLvA~l~a~l~al~---------G~~VhvvT~ndyLA~RD~e  141 (913)
T PRK13103         74 AGKRVMGMR-HFDVQLIGGMTLHEG--KIAEMRTGEGKTLVGTLAVYLNALS---------GKGVHVVTVNDYLARRDAN  141 (913)
T ss_pred             HHHHHhCCC-cchhHHHhhhHhccC--ccccccCCCCChHHHHHHHHHHHHc---------CCCEEEEeCCHHHHHHHHH
Confidence            333456765 899997665555555  4889999999999999999877665         5559999999999999999


Q ss_pred             HHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcCC-----ccccCceeEEEEecchhhh
Q 043110          129 ILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHTS-----SFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~~-----~~~~~~l~~lViDEad~l~  199 (316)
                      ++..+...++ +.++++.++.... +.+..+. ++|++||..-| +++|+..-     ......+.+.||||+|.++
T Consensus       142 ~m~~l~~~lG-l~v~~i~~~~~~~-err~~Y~-~dI~YGT~~e~gFDYLrD~~~~~~~~~vqr~l~~aIVDEvDsiL  215 (913)
T PRK13103        142 WMRPLYEFLG-LSVGIVTPFQPPE-EKRAAYA-ADITYGTNNEFGFDYLRDNMAFSLDDKFQRELNFAVIDEVDSIL  215 (913)
T ss_pred             HHHHHhcccC-CEEEEECCCCCHH-HHHHHhc-CCEEEEcccccccchhhccceechhhhcccccceeEechhhhee
Confidence            9999998766 5666665555443 3444443 79999999876 44444321     1123678899999999876

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

Probab=99.26  E-value=2.1e-10  Score=100.76  Aligned_cols=152  Identities=21%  Similarity=0.240  Sum_probs=106.9

Q ss_pred             CCcHHHHHHHHHH----hCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVI----LSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        58 ~p~~~Q~~~i~~i----l~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      ++++.|+.+-..+    .+.++.++.|-||+|||... .+.++...+        .|.++.|.+|....|.+++.++++-
T Consensus        97 ~Ls~~Q~~as~~l~q~i~~k~~~lv~AV~GaGKTEMi-f~~i~~al~--------~G~~vciASPRvDVclEl~~Rlk~a  167 (441)
T COG4098          97 TLSPGQKKASNQLVQYIKQKEDTLVWAVTGAGKTEMI-FQGIEQALN--------QGGRVCIASPRVDVCLELYPRLKQA  167 (441)
T ss_pred             ccChhHHHHHHHHHHHHHhcCcEEEEEecCCCchhhh-HHHHHHHHh--------cCCeEEEecCcccchHHHHHHHHHh
Confidence            6899998876554    46789999999999999874 445555444        3677999999999999999988876


Q ss_pred             HhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHH
Q 043110          134 LHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDI  213 (316)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~  213 (316)
                      +.   .....+++|+....-+       .+++|+|...|+..-.        .++++||||+|..--.. ...+....+.
T Consensus       168 F~---~~~I~~Lyg~S~~~fr-------~plvVaTtHQLlrFk~--------aFD~liIDEVDAFP~~~-d~~L~~Av~~  228 (441)
T COG4098         168 FS---NCDIDLLYGDSDSYFR-------APLVVATTHQLLRFKQ--------AFDLLIIDEVDAFPFSD-DQSLQYAVKK  228 (441)
T ss_pred             hc---cCCeeeEecCCchhcc-------ccEEEEehHHHHHHHh--------hccEEEEeccccccccC-CHHHHHHHHH
Confidence            54   3455667766554322       4799999888877554        57899999999854221 1222222222


Q ss_pred             hccCcccccCCCCccccccceEEEEeeecchhHHHHHH
Q 043110          214 LGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK  251 (316)
Q Consensus       214 l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~  251 (316)
                      -.              .+..-+|.+|||.++.++.-+.
T Consensus       229 ar--------------k~~g~~IylTATp~k~l~r~~~  252 (441)
T COG4098         229 AR--------------KKEGATIYLTATPTKKLERKIL  252 (441)
T ss_pred             hh--------------cccCceEEEecCChHHHHHHhh
Confidence            11              2266789999999987765443

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=99.24  E-value=1.7e-10  Score=118.21  Aligned_cols=65  Identities=23%  Similarity=0.320  Sum_probs=53.1

Q ss_pred             CCCCCcHHHHHHHHHH----hCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           55 GFEAPTKVQAQAIPVI----LSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~i----l~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      || ++++-|.+.+..+    .+++++++.||||+|||++|++|++.....        .+.+++|-++|+.|.+|+.+
T Consensus       255 ~~-e~R~~Q~~m~~~v~~~l~~~~~~~iEA~TGtGKTlaYLlpa~~~a~~--------~~~~vvIsT~T~~LQ~Ql~~  323 (928)
T PRK08074        255 KY-EKREGQQEMMKEVYTALRDSEHALIEAGTGTGKSLAYLLPAAYFAKK--------KEEPVVISTYTIQLQQQLLE  323 (928)
T ss_pred             CC-cCCHHHHHHHHHHHHHHhcCCCEEEECCCCCchhHHHHHHHHHHhhc--------cCCeEEEEcCCHHHHHHHHH
Confidence            45 4899998865443    467889999999999999999999876543        24459999999999999876

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=99.22  E-value=3.4e-11  Score=94.14  Aligned_cols=140  Identities=20%  Similarity=0.181  Sum_probs=79.9

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCCh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR  151 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (316)
                      .|+-.++...+|+|||--.+.-++.....        .+.++|||.|||.++..+++.++..    + ..  +.. ....
T Consensus         3 kg~~~~~d~hpGaGKTr~vlp~~~~~~i~--------~~~rvLvL~PTRvva~em~~aL~~~----~-~~--~~t-~~~~   66 (148)
T PF07652_consen    3 KGELTVLDLHPGAGKTRRVLPEIVREAIK--------RRLRVLVLAPTRVVAEEMYEALKGL----P-VR--FHT-NARM   66 (148)
T ss_dssp             TTEEEEEE--TTSSTTTTHHHHHHHHHHH--------TT--EEEEESSHHHHHHHHHHTTTS----S-EE--EES-TTSS
T ss_pred             CCceeEEecCCCCCCcccccHHHHHHHHH--------ccCeEEEecccHHHHHHHHHHHhcC----C-cc--cCc-eeee
Confidence            45557899999999999776555554443        2566999999999998888777542    1 11  111 1110


Q ss_pred             HHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccc
Q 043110          152 SKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNV  231 (316)
Q Consensus       152 ~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~  231 (316)
                      .    ....+.-|-|.|.+.+...+.+  .....+.+++|+||||.. |.. .-.....+..+...             .
T Consensus        67 ~----~~~g~~~i~vMc~at~~~~~~~--p~~~~~yd~II~DEcH~~-Dp~-sIA~rg~l~~~~~~-------------g  125 (148)
T PF07652_consen   67 R----THFGSSIIDVMCHATYGHFLLN--PCRLKNYDVIIMDECHFT-DPT-SIAARGYLRELAES-------------G  125 (148)
T ss_dssp             --------SSSSEEEEEHHHHHHHHHT--SSCTTS-SEEEECTTT---SHH-HHHHHHHHHHHHHT-------------T
T ss_pred             c----cccCCCcccccccHHHHHHhcC--cccccCccEEEEeccccC-CHH-HHhhheeHHHhhhc-------------c
Confidence            0    1123456889999988887765  333468999999999974 321 11122223332221             1


Q ss_pred             cceEEEEeeecchhHHH
Q 043110          232 KRQNLLLSATLNEKVNH  248 (316)
Q Consensus       232 ~~q~i~~SAT~~~~v~~  248 (316)
                      .+.+|++|||.|.....
T Consensus       126 ~~~~i~mTATPPG~~~~  142 (148)
T PF07652_consen  126 EAKVIFMTATPPGSEDE  142 (148)
T ss_dssp             S-EEEEEESS-TT---S
T ss_pred             CeeEEEEeCCCCCCCCC
Confidence            46899999999976643

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 ....

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=99.20  E-value=1.7e-10  Score=113.55  Aligned_cols=139  Identities=22%  Similarity=0.279  Sum_probs=104.6

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH
Q 043110           46 LCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL  125 (316)
Q Consensus        46 l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q  125 (316)
                      +.++..+.+|.. |+++|.-.--.+..|+  ++...||+|||++..+|++.....         |..+-+++|+..||.|
T Consensus        69 vrEa~~R~~g~~-~~dvQlig~l~l~~G~--iaEm~TGEGKTLvA~l~a~l~al~---------G~~v~vvT~neyLA~R  136 (796)
T PRK12906         69 AREGAKRVLGLR-PFDVQIIGGIVLHEGN--IAEMKTGEGKTLTATLPVYLNALT---------GKGVHVVTVNEYLSSR  136 (796)
T ss_pred             HHHHHHHHhCCC-CchhHHHHHHHHhcCC--cccccCCCCCcHHHHHHHHHHHHc---------CCCeEEEeccHHHHHh
Confidence            344555567876 9999988776777776  999999999999999999887766         5559999999999999


Q ss_pred             HHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcC-----CccccCceeEEEEecchhhh
Q 043110          126 VYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHT-----SSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~-----~~~~~~~l~~lViDEad~l~  199 (316)
                      -++.+..+...++ +.++++.++.+.... +..+ .++|+.||...| +++++..     .......+.+.||||+|.++
T Consensus       137 d~e~~~~~~~~LG-l~vg~i~~~~~~~~r-~~~y-~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~r~~~~aIvDEvDSiL  213 (796)
T PRK12906        137 DATEMGELYRWLG-LTVGLNLNSMSPDEK-RAAY-NCDITYSTNSELGFDYLRDNMVVYKEQMVQRPLNYAIVDEVDSIL  213 (796)
T ss_pred             hHHHHHHHHHhcC-CeEEEeCCCCCHHHH-HHHh-cCCCeecCCccccccchhhccccchhhhhccCcceeeeccchhee
Confidence            9999999998876 566666665554433 3333 479999999866 3444331     11123567899999999876

>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=99.20  E-value=6.9e-10  Score=96.92  Aligned_cols=137  Identities=22%  Similarity=0.282  Sum_probs=97.6

Q ss_pred             HHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHH
Q 043110           48 DQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY  127 (316)
Q Consensus        48 ~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~  127 (316)
                      ++..+.+|+. |++.|..++-.+..|+  +++..||-|||++..+|++-....         |..|-|++.+..||..=+
T Consensus        68 ea~~r~~g~~-p~~vQll~~l~L~~G~--laEm~TGEGKTli~~l~a~~~AL~---------G~~V~vvT~NdyLA~RD~  135 (266)
T PF07517_consen   68 EAARRTLGLR-PYDVQLLGALALHKGR--LAEMKTGEGKTLIAALPAALNALQ---------GKGVHVVTSNDYLAKRDA  135 (266)
T ss_dssp             HHHHHHTS-----HHHHHHHHHHHTTS--EEEESTTSHHHHHHHHHHHHHHTT---------SS-EEEEESSHHHHHHHH
T ss_pred             HHHHHHcCCc-ccHHHHhhhhhcccce--eEEecCCCCcHHHHHHHHHHHHHh---------cCCcEEEeccHHHhhccH
Confidence            3444456776 9999999987777776  999999999999998888766655         455999999999999999


Q ss_pred             HHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHH-HHHhcCC----cc-ccCceeEEEEecchhhh
Q 043110          128 EILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLL-DHLKHTS----SF-LHTNLRWIIFDEADRIL  199 (316)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~-~~l~~~~----~~-~~~~l~~lViDEad~l~  199 (316)
                      +.+..+...++ +.+++..++..... .+..+ .++|+.+|...+. ++++..-    .. ....+.++||||+|.++
T Consensus       136 ~~~~~~y~~LG-lsv~~~~~~~~~~~-r~~~Y-~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  136 EEMRPFYEFLG-LSVGIITSDMSSEE-RREAY-AADIVYGTNSEFGFDYLRDNLALSKNEQVQRGFDFAIVDEVDSIL  210 (266)
T ss_dssp             HHHHHHHHHTT---EEEEETTTEHHH-HHHHH-HSSEEEEEHHHHHHHHHHHTT-SSGGG--SSSSSEEEECTHHHHT
T ss_pred             HHHHHHHHHhh-hccccCccccCHHH-HHHHH-hCcccccccchhhHHHHHHHHhhccchhccCCCCEEEEeccceEE
Confidence            99999998876 66666666655433 33333 3589999998774 4444321    11 24678999999999876

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 ....

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=99.19  E-value=2.9e-10  Score=110.07  Aligned_cols=138  Identities=22%  Similarity=0.299  Sum_probs=104.6

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           47 CDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        47 ~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .++..+.+|+. |+++|....-.++.|+  ++.+.||+|||++..+|++.....         |..+.|++|+..||.|-
T Consensus        68 REa~~R~lg~r-~ydvQlig~l~Ll~G~--VaEM~TGEGKTLvA~l~a~l~AL~---------G~~VhvvT~NdyLA~RD  135 (764)
T PRK12326         68 REAAERTLGLR-PFDVQLLGALRLLAGD--VIEMATGEGKTLAGAIAAAGYALQ---------GRRVHVITVNDYLARRD  135 (764)
T ss_pred             HHHHHHHcCCC-cchHHHHHHHHHhCCC--cccccCCCCHHHHHHHHHHHHHHc---------CCCeEEEcCCHHHHHHH
Confidence            33444456876 9999999988888875  789999999999999999877765         55599999999999999


Q ss_pred             HHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcC-----CccccCceeEEEEecchhhh
Q 043110          127 YEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHT-----SSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~-----~~~~~~~l~~lViDEad~l~  199 (316)
                      ++.+..+...++ +.++++.++.+.. +.+..+ .+||+.+|...+ +++++..     .......+.+.|+||+|.++
T Consensus       136 ae~m~~ly~~LG-Lsvg~i~~~~~~~-err~aY-~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R~~~faIVDEvDSiL  211 (764)
T PRK12326        136 AEWMGPLYEALG-LTVGWITEESTPE-ERRAAY-ACDVTYASVNEIGFDVLRDQLVTDVADLVSPNPDVAIIDEADSVL  211 (764)
T ss_pred             HHHHHHHHHhcC-CEEEEECCCCCHH-HHHHHH-cCCCEEcCCcccccccchhhhccChHhhcCCccceeeecchhhhe
Confidence            999999998876 6666666655544 444444 479999999764 3333321     11233567899999999876

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=99.08  E-value=1.8e-09  Score=106.51  Aligned_cols=138  Identities=21%  Similarity=0.237  Sum_probs=101.6

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           47 CDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        47 ~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .++..+.+|.. |+++|-..--.+..|  -++.+.||.|||+++.+|+.-....         |..|-||+++..||..-
T Consensus        75 REa~~R~lG~r-~ydVQliGgl~Lh~G--~IAEM~TGEGKTL~atlpaylnAL~---------GkgVhVVTvNdYLA~RD  142 (939)
T PRK12902         75 REASKRVLGMR-HFDVQLIGGMVLHEG--QIAEMKTGEGKTLVATLPSYLNALT---------GKGVHVVTVNDYLARRD  142 (939)
T ss_pred             HHHHHHHhCCC-cchhHHHhhhhhcCC--ceeeecCCCChhHHHHHHHHHHhhc---------CCCeEEEeCCHHHHHhH
Confidence            33444456776 899997766555555  4899999999999999998876655         44499999999999999


Q ss_pred             HHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-----HHHHhcC-CccccCceeEEEEecchhhh
Q 043110          127 YEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-----LDHLKHT-SSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-----~~~l~~~-~~~~~~~l~~lViDEad~l~  199 (316)
                      ++++..+...++ +.++++.++.+.. +.+..+ .+||+.||+..|     .+.+... .......+.+.||||+|.++
T Consensus       143 ae~m~~vy~~LG-Ltvg~i~~~~~~~-err~aY-~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR~~~faIVDEvDSIL  218 (939)
T PRK12902        143 AEWMGQVHRFLG-LSVGLIQQDMSPE-ERKKNY-ACDITYATNSELGFDYLRDNMATDISEVVQRPFNYCVIDEVDSIL  218 (939)
T ss_pred             HHHHHHHHHHhC-CeEEEECCCCChH-HHHHhc-CCCeEEecCCcccccchhhhhcccccccccCccceEEEeccccee
Confidence            999999998876 5666665555443 333333 589999999876     4444321 22344678899999999876

>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=99.06  E-value=2.3e-09  Score=96.09  Aligned_cols=156  Identities=23%  Similarity=0.251  Sum_probs=85.1

Q ss_pred             HHHHHHHHHh-------------CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           62 VQAQAIPVIL-------------SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        62 ~Q~~~i~~il-------------~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      +|.+++..++             ..+.+++.-.+|.|||+..+.. +..+.......   ....+|||+|. .+..|+.+
T Consensus         1 ~Q~~~v~~m~~~~~~~~~~~~~~~~~g~lL~de~GlGKT~~~i~~-~~~l~~~~~~~---~~~~~LIv~P~-~l~~~W~~   75 (299)
T PF00176_consen    1 HQLEAVRWMLDRELVEEYPNSESPPRGGLLADEMGLGKTITAIAL-ISYLKNEFPQR---GEKKTLIVVPS-SLLSQWKE   75 (299)
T ss_dssp             HHHHHHHHHHHHH----TTSSSTTT-EEEE---TTSSHHHHHHHH-HHHHHHCCTTS---S-S-EEEEE-T-TTHHHHHH
T ss_pred             CHHHHHHHHHHHhhhhcccccccCCCCEEEEECCCCCchhhhhhh-hhhhhhccccc---cccceeEeecc-chhhhhhh
Confidence            4666666553             3346899999999999886543 33443322211   11239999999 88899999


Q ss_pred             HHHHHHhhcCCceeEEeeCCCC-hHHHHHHHhcCCcEEEeCcHHHHHHHhcC--CccccCceeEEEEecchhhhcCCcHH
Q 043110          129 ILQKLLHRFRWIVPGYVMGGGN-RSKEKARLRKGISILVATPGHLLDHLKHT--SSFLHTNLRWIIFDEADRILELGFGK  205 (316)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~--~~~~~~~l~~lViDEad~l~~~~~~~  205 (316)
                      .+.++..... .. ...+.+.. ............+++|+|.+.+.......  ..+...+.+++|+||+|.+-+.  ..
T Consensus        76 E~~~~~~~~~-~~-v~~~~~~~~~~~~~~~~~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~vIvDEaH~~k~~--~s  151 (299)
T PF00176_consen   76 EIEKWFDPDS-LR-VIIYDGDSERRRLSKNQLPKYDVVITTYETLRKARKKKDKEDLKQIKWDRVIVDEAHRLKNK--DS  151 (299)
T ss_dssp             HHHHHSGT-T-S--EEEESSSCHHHHTTSSSCCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEEEEETTGGGGTTT--TS
T ss_pred             hhcccccccc-cc-ccccccccccccccccccccceeeeccccccccccccccccccccccceeEEEecccccccc--cc
Confidence            9988874322 23 33344444 22222222345789999999988110000  0111135889999999998432  22


Q ss_pred             HHHHHHHHhccCcccccCCCCccccccceEEEEeeec
Q 043110          206 EIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATL  242 (316)
Q Consensus       206 ~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~  242 (316)
                      .....+..+.                ....+++|||.
T Consensus       152 ~~~~~l~~l~----------------~~~~~lLSgTP  172 (299)
T PF00176_consen  152 KRYKALRKLR----------------ARYRWLLSGTP  172 (299)
T ss_dssp             HHHHHHHCCC----------------ECEEEEE-SS-
T ss_pred             cccccccccc----------------cceEEeecccc
Confidence            2223333233                45678899995

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.

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=99.06  E-value=4e-09  Score=105.00  Aligned_cols=65  Identities=29%  Similarity=0.358  Sum_probs=52.0

Q ss_pred             CCCCCcHHHHHHHHHHh---C------CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH
Q 043110           55 GFEAPTKVQAQAIPVIL---S------GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL  125 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~il---~------g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q  125 (316)
                      ||+ +++-|.+....+.   .      ++.+++.||||+|||++|++|++......        +.++||-+.|..|-+|
T Consensus        23 ~~e-~R~~Q~~M~~~V~~al~~~~~~~~~~lviEAgTGtGKTlaYLlPai~~A~~~--------~k~vVIST~T~~LQeQ   93 (697)
T PRK11747         23 GFI-PRAGQRQMIAEVAKTLAGEYLKDGRILVIEAGTGVGKTLSYLLAGIPIARAE--------KKKLVISTATVALQEQ   93 (697)
T ss_pred             CCC-cCHHHHHHHHHHHHHHhcccccccceEEEECCCCcchhHHHHHHHHHHHHHc--------CCeEEEEcCCHHHHHH
Confidence            564 8999988655543   3      36799999999999999999998766542        3449999999999999


Q ss_pred             HHH
Q 043110          126 VYE  128 (316)
Q Consensus       126 ~~~  128 (316)
                      +..
T Consensus        94 L~~   96 (697)
T PRK11747         94 LVS   96 (697)
T ss_pred             HHh
Confidence            863

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=99.06  E-value=1.2e-09  Score=107.68  Aligned_cols=138  Identities=21%  Similarity=0.237  Sum_probs=99.8

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           47 CDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        47 ~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .++..+.+|+. |+++|....-.+.  +.-++.+.||.|||+++.+|+.-....         |..|.|++++..||.+-
T Consensus        66 rEa~~R~lG~r-~ydvQlig~l~L~--~G~IaEm~TGEGKTL~a~l~ayl~aL~---------G~~VhVvT~NdyLA~RD  133 (870)
T CHL00122         66 REASFRTLGLR-HFDVQLIGGLVLN--DGKIAEMKTGEGKTLVATLPAYLNALT---------GKGVHIVTVNDYLAKRD  133 (870)
T ss_pred             HHHHHHHhCCC-CCchHhhhhHhhc--CCccccccCCCCchHHHHHHHHHHHhc---------CCceEEEeCCHHHHHHH
Confidence            34454567886 8999977654444  446999999999999999998654443         44499999999999999


Q ss_pred             HHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcC-----CccccCceeEEEEecchhhh
Q 043110          127 YEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHT-----SSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~-----~~~~~~~l~~lViDEad~l~  199 (316)
                      ++++..+...++ +.+++..++.+.. +.+..+ .+||+.+|...+ +++++..     .......+.+.|+||+|.++
T Consensus       134 ~e~m~pvy~~LG-Lsvg~i~~~~~~~-err~aY-~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r~~~faIVDEvDSiL  209 (870)
T CHL00122        134 QEWMGQIYRFLG-LTVGLIQEGMSSE-ERKKNY-LKDITYVTNSELGFDYLRDNMALSLSDVVQRPFNYCIIDEVDSIL  209 (870)
T ss_pred             HHHHHHHHHHcC-CceeeeCCCCChH-HHHHhc-CCCCEecCCccccccchhhccCcChHHhhccccceeeeecchhhe
Confidence            999999998877 6666666655553 333444 369999999754 2333321     11233568899999999876

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=99.03  E-value=1.2e-08  Score=104.11  Aligned_cols=162  Identities=15%  Similarity=0.211  Sum_probs=103.2

Q ss_pred             CCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        58 ~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .++++|...+..+.    +|.+.|+.-..|.|||+..+. ++..+.....     ....+|||||. ++..|+.+.+.++
T Consensus       169 ~Lr~YQleGlnWLi~l~~~g~gGILADEMGLGKTlQaIa-lL~~L~~~~~-----~~gp~LIVvP~-SlL~nW~~Ei~kw  241 (1033)
T PLN03142        169 KMRDYQLAGLNWLIRLYENGINGILADEMGLGKTLQTIS-LLGYLHEYRG-----ITGPHMVVAPK-STLGNWMNEIRRF  241 (1033)
T ss_pred             chHHHHHHHHHHHHHHHhcCCCEEEEeCCCccHHHHHHH-HHHHHHHhcC-----CCCCEEEEeCh-HHHHHHHHHHHHH
Confidence            58999999998775    678899999999999997533 4444433111     12238999996 6678888888887


Q ss_pred             HhhcCCceeEEeeCCCChHHHHH-H--HhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHH
Q 043110          134 LHRFRWIVPGYVMGGGNRSKEKA-R--LRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEI  210 (316)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~-~--l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i  210 (316)
                      +   +...+..++|......... .  .....+|+|+|.+.+......   +.--..++||+||||++-.  ....+...
T Consensus       242 ~---p~l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~~---L~k~~W~~VIvDEAHrIKN--~~Sklska  313 (1033)
T PLN03142        242 C---PVLRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKTA---LKRFSWRYIIIDEAHRIKN--ENSLLSKT  313 (1033)
T ss_pred             C---CCCceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHHH---hccCCCCEEEEcCccccCC--HHHHHHHH
Confidence            5   3344444444332222111 1  123578999999988654332   1112467999999999754  33445555


Q ss_pred             HHHhccCcccccCCCCccccccceEEEEeeecc-hhHHHHH
Q 043110          211 LDILGSRNIASIGEGNEVSNVKRQNLLLSATLN-EKVNHLT  250 (316)
Q Consensus       211 ~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~-~~v~~~~  250 (316)
                      +..+.                ....+++|+|.- .++.++-
T Consensus       314 lr~L~----------------a~~RLLLTGTPlqNnl~ELw  338 (1033)
T PLN03142        314 MRLFS----------------TNYRLLITGTPLQNNLHELW  338 (1033)
T ss_pred             HHHhh----------------cCcEEEEecCCCCCCHHHHH
Confidence            55554                334588899973 3444443

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

Probab=98.99  E-value=1.4e-08  Score=101.08  Aligned_cols=166  Identities=19%  Similarity=0.176  Sum_probs=98.0

Q ss_pred             HHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCc
Q 043110           61 KVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWI  140 (316)
Q Consensus        61 ~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~  140 (316)
                      ....+.+.++.+.+-+++.|+||||||...-.-+++...        ..+..+.+.-|.|--|..+++.+.+-...-...
T Consensus        53 ~~~~~i~~ai~~~~vvii~getGsGKTTqlP~~lle~g~--------~~~g~I~~tQPRRlAArsvA~RvAeel~~~~G~  124 (845)
T COG1643          53 AVRDEILKAIEQNQVVIIVGETGSGKTTQLPQFLLEEGL--------GIAGKIGCTQPRRLAARSVAERVAEELGEKLGE  124 (845)
T ss_pred             HHHHHHHHHHHhCCEEEEeCCCCCChHHHHHHHHHhhhc--------ccCCeEEecCchHHHHHHHHHHHHHHhCCCcCc
Confidence            344555666667788999999999999873222332221        123457777799877766666554443322223


Q ss_pred             eeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCccc
Q 043110          141 VPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIA  220 (316)
Q Consensus       141 ~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~  220 (316)
                      .+++.+...+.      ......|-+.|.|.|+..+.+.  ..++.++++|+||+|.=     .-+..-++..+...   
T Consensus       125 ~VGY~iRfe~~------~s~~Trik~mTdGiLlrei~~D--~~Ls~ys~vIiDEaHER-----Sl~tDilLgllk~~---  188 (845)
T COG1643         125 TVGYSIRFESK------VSPRTRIKVMTDGILLREIQND--PLLSGYSVVIIDEAHER-----SLNTDILLGLLKDL---  188 (845)
T ss_pred             eeeEEEEeecc------CCCCceeEEeccHHHHHHHhhC--cccccCCEEEEcchhhh-----hHHHHHHHHHHHHH---
Confidence            33443322221      1234579999999999999853  34679999999999962     22222222222210   


Q ss_pred             ccCCCCccccccceEEEEeeecchhHHHHHHHhcCCC
Q 043110          221 SIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETP  257 (316)
Q Consensus       221 ~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p  257 (316)
                           .....+...+|+||||+..  +.|...+-.-|
T Consensus       189 -----~~~rr~DLKiIimSATld~--~rfs~~f~~ap  218 (845)
T COG1643         189 -----LARRRDDLKLIIMSATLDA--ERFSAYFGNAP  218 (845)
T ss_pred             -----HhhcCCCceEEEEecccCH--HHHHHHcCCCC
Confidence                 0011114789999999973  44554443333

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=98.98  E-value=7.6e-09  Score=104.93  Aligned_cols=175  Identities=17%  Similarity=0.166  Sum_probs=102.8

Q ss_pred             CCcHHHHHHHHHHhCC--CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           58 APTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g--~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      .|.|+|......++..  ..+++.-.+|.|||.-+.+-+-..+...       ..-++|||||. .|+.|+...+.+.+.
T Consensus       152 ~l~pHQl~~~~~vl~~~~~R~LLADEvGLGKTIeAglil~~l~~~g-------~~~rvLIVvP~-sL~~QW~~El~~kF~  223 (956)
T PRK04914        152 SLIPHQLYIAHEVGRRHAPRVLLADEVGLGKTIEAGMIIHQQLLTG-------RAERVLILVPE-TLQHQWLVEMLRRFN  223 (956)
T ss_pred             CCCHHHHHHHHHHhhccCCCEEEEeCCcCcHHHHHHHHHHHHHHcC-------CCCcEEEEcCH-HHHHHHHHHHHHHhC
Confidence            4899999988776543  3699999999999998866554444331       22359999998 899999888865442


Q ss_pred             hcCCceeEEeeCCCChHHHHH---HHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcC--CcHHHHHHH
Q 043110          136 RFRWIVPGYVMGGGNRSKEKA---RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL--GFGKEIEEI  210 (316)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~---~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~--~~~~~i~~i  210 (316)
                          .... ++++........   ......+++|+|.+.+...-.....+.-...+++|+||||++-..  .-...+ ..
T Consensus       224 ----l~~~-i~~~~~~~~~~~~~~~pf~~~~~vI~S~~~l~~~~~~~~~l~~~~wdlvIvDEAH~lk~~~~~~s~~y-~~  297 (956)
T PRK04914        224 ----LRFS-LFDEERYAEAQHDADNPFETEQLVICSLDFLRRNKQRLEQALAAEWDLLVVDEAHHLVWSEEAPSREY-QV  297 (956)
T ss_pred             ----CCeE-EEcCcchhhhcccccCccccCcEEEEEHHHhhhCHHHHHHHhhcCCCEEEEechhhhccCCCCcCHHH-HH
Confidence                1222 222222111100   111235799999887654111001112236789999999998621  111222 23


Q ss_pred             HHHhccCcccccCCCCccccccceEEEEeeecch-hHH-HHHHHhcCCCEEE
Q 043110          211 LDILGSRNIASIGEGNEVSNVKRQNLLLSATLNE-KVN-HLTKISLETPVLI  260 (316)
Q Consensus       211 ~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~-~v~-~~~~~~l~~p~~i  260 (316)
                      +..+...              ...++++|||.-. ... .+....+-+|...
T Consensus       298 v~~La~~--------------~~~~LLLTATP~q~~~~e~falL~lLdP~~f  335 (956)
T PRK04914        298 VEQLAEV--------------IPGVLLLTATPEQLGQESHFARLRLLDPDRF  335 (956)
T ss_pred             HHHHhhc--------------cCCEEEEEcCcccCCcHHHHHhhhhhCCCcC
Confidence            3333221              3468999999753 233 3444455567654

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

Probab=98.97  E-value=3.1e-08  Score=98.70  Aligned_cols=174  Identities=20%  Similarity=0.196  Sum_probs=111.3

Q ss_pred             CcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcC
Q 043110           59 PTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFR  138 (316)
Q Consensus        59 p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~  138 (316)
                      .++.+...+.++.+.+.+++.|.||+|||.-.---+++......      ....+++--|.|--|..+++++..--....
T Consensus       174 a~~~r~~Il~~i~~~qVvvIsGeTGcGKTTQvpQfiLd~~~~~~------~~~~IicTQPRRIsAIsvAeRVa~ER~~~~  247 (924)
T KOG0920|consen  174 AYKMRDTILDAIEENQVVVISGETGCGKTTQVPQFILDEAIESG------AACNIICTQPRRISAISVAERVAKERGESL  247 (924)
T ss_pred             cHHHHHHHHHHHHhCceEEEeCCCCCCchhhhhHHHHHHHHhcC------CCCeEEecCCchHHHHHHHHHHHHHhcccc
Confidence            45677888899999999999999999999874444555544422      345577778999988888876544221112


Q ss_pred             CceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhh-cCCcHHH-HHHHHHHhcc
Q 043110          139 WIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRIL-ELGFGKE-IEEILDILGS  216 (316)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~-~~~~~~~-i~~i~~~l~~  216 (316)
                      ...+++..+.....      .....++.||.|.|+..+..  ...+..+..+|+||+|.=. +..|.-. +..++..   
T Consensus       248 g~~VGYqvrl~~~~------s~~t~L~fcTtGvLLr~L~~--~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~~---  316 (924)
T KOG0920|consen  248 GEEVGYQVRLESKR------SRETRLLFCTTGVLLRRLQS--DPTLSGVTHIIVDEVHERSINTDFLLILLKDLLPR---  316 (924)
T ss_pred             CCeeeEEEeeeccc------CCceeEEEecHHHHHHHhcc--CcccccCceeeeeeEEEccCCcccHHHHHHHHhhh---
Confidence            23333333222211      12257999999999999986  4455789999999999532 2233322 2222222   


Q ss_pred             CcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          217 RNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       217 ~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                                   ++..++|+||||+.   .+..+.+..+.-.+.+..-
T Consensus       317 -------------~p~LkvILMSAT~d---ae~fs~YF~~~pvi~i~gr  349 (924)
T KOG0920|consen  317 -------------NPDLKVILMSATLD---AELFSDYFGGCPVITIPGR  349 (924)
T ss_pred             -------------CCCceEEEeeeecc---hHHHHHHhCCCceEeecCC
Confidence                         23889999999998   4444445545555555443

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

Probab=98.91  E-value=3.5e-09  Score=106.08  Aligned_cols=156  Identities=20%  Similarity=0.211  Sum_probs=109.4

Q ss_pred             CCcHHHHHHHHHHhCCC-cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhh
Q 043110           58 APTKVQAQAIPVILSGR-DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHR  136 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~-d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~  136 (316)
                      ..+|+|.++++.+.+.. ++++.+|+|||||.|+.++++.          .....++++++|..+.+..+++.+.+-...
T Consensus      1143 ~~n~iqtqVf~~~y~~nd~v~vga~~gsgkt~~ae~a~l~----------~~~~~~~vyi~p~~~i~~~~~~~w~~~f~~ 1212 (1674)
T KOG0951|consen 1143 DFNPIQTQVFTSLYNTNDNVLVGAPNGSGKTACAELALLR----------PDTIGRAVYIAPLEEIADEQYRDWEKKFSK 1212 (1674)
T ss_pred             ccCCceEEEEeeeecccceEEEecCCCCchhHHHHHHhcC----------CccceEEEEecchHHHHHHHHHHHHHhhcc
Confidence            34899999999887654 5999999999999999887765          124567999999999998888776665554


Q ss_pred             cCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHH------HHHHH
Q 043110          137 FRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGK------EIEEI  210 (316)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~------~i~~i  210 (316)
                      .......-+.|......   .+....+|+|+||+++-.+ +     ....+++.|.||+|.+.+.+ +.      -++.|
T Consensus      1213 ~~G~~~~~l~ge~s~~l---kl~~~~~vii~tpe~~d~l-q-----~iQ~v~l~i~d~lh~igg~~-g~v~evi~S~r~i 1282 (1674)
T KOG0951|consen 1213 LLGLRIVKLTGETSLDL---KLLQKGQVIISTPEQWDLL-Q-----SIQQVDLFIVDELHLIGGVY-GAVYEVICSMRYI 1282 (1674)
T ss_pred             ccCceEEecCCccccch---HHhhhcceEEechhHHHHH-h-----hhhhcceEeeehhhhhcccC-CceEEEEeeHHHH
Confidence            44344443333333221   2233458999999997654 2     23578999999999887542 11      15666


Q ss_pred             HHHhccCcccccCCCCccccccceEEEEeeecchhHHHH
Q 043110          211 LDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHL  249 (316)
Q Consensus       211 ~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~  249 (316)
                      -..+-+               +.+++.+|..+.. ...+
T Consensus      1283 a~q~~k---------------~ir~v~ls~~lan-a~d~ 1305 (1674)
T KOG0951|consen 1283 ASQLEK---------------KIRVVALSSSLAN-ARDL 1305 (1674)
T ss_pred             HHHHHh---------------heeEEEeehhhcc-chhh
Confidence            666665               7889999888763 3444

>COG1199 DinG Rad3-related DNA helicases [Transcription / DNA replication, recombination, and repair]

Probab=98.91  E-value=1.7e-08  Score=100.48  Aligned_cols=74  Identities=24%  Similarity=0.274  Sum_probs=59.5

Q ss_pred             HHcCCCCCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHH
Q 043110           52 ERLGFEAPTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY  127 (316)
Q Consensus        52 ~~~g~~~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~  127 (316)
                      ..+...+|++.|.+.+..+.    .|+.+++.||||+|||++|++|++.......        ..++|.++|+.|-.|+.
T Consensus         9 ~~~~~~~~r~~Q~~~~~~v~~a~~~~~~~~iEapTGtGKTl~yL~~al~~~~~~~--------~~viist~t~~lq~q~~   80 (654)
T COG1199           9 VAFPGFEPRPEQREMAEAVAEALKGGEGLLIEAPTGTGKTLAYLLPALAYAREEG--------KKVIISTRTKALQEQLL   80 (654)
T ss_pred             hhCCCCCCCHHHHHHHHHHHHHHcCCCcEEEECCCCccHHHHHHHHHHHHHHHcC--------CcEEEECCCHHHHHHHH
Confidence            34566679999998875543    4556999999999999999999998876532        44999999999999998


Q ss_pred             HHHHHH
Q 043110          128 EILQKL  133 (316)
Q Consensus       128 ~~~~~~  133 (316)
                      +....+
T Consensus        81 ~~~~~~   86 (654)
T COG1199          81 EEDLPI   86 (654)
T ss_pred             Hhhcch
Confidence            776554

>TIGR00604 rad3 DNA repair helicase (rad3)

Probab=98.82  E-value=2.9e-08  Score=99.33  Aligned_cols=76  Identities=21%  Similarity=0.204  Sum_probs=61.6

Q ss_pred             HcCCCCCcHHHHHHHHHH----hCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           53 RLGFEAPTKVQAQAIPVI----LSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        53 ~~g~~~p~~~Q~~~i~~i----l~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      .|.|..++|.|.+.+..+    ..|+++++.+|||+|||++.+.|++.......      ...+++|.+.|..-..|..+
T Consensus         5 ~FPy~~~y~~Q~~~m~~v~~~l~~~~~~llEsPTGtGKTlslL~~aL~~~~~~~------~~~kIiy~sRThsQl~q~i~   78 (705)
T TIGR00604         5 YFPYEKIYPEQRSYMRDLKRSLDRGDEAILEMPSGTGKTISLLSLILAYQQEKP------EVRKIIYASRTHSQLEQATE   78 (705)
T ss_pred             ecCCCCCCHHHHHHHHHHHHHhccCCceEEeCCCCCCccHHHHHHHHHHHHhcc------ccccEEEEcccchHHHHHHH
Confidence            378887899998876554    47889999999999999999999998775422      23569999999998888888


Q ss_pred             HHHHHH
Q 043110          129 ILQKLL  134 (316)
Q Consensus       129 ~~~~~~  134 (316)
                      .+++..
T Consensus        79 Elk~~~   84 (705)
T TIGR00604        79 ELRKLM   84 (705)
T ss_pred             HHHhhh
Confidence            888753

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).

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=98.78  E-value=1.6e-07  Score=94.45  Aligned_cols=145  Identities=21%  Similarity=0.241  Sum_probs=84.8

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH-----HHHhh-cCCc-eeEEee
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ-----KLLHR-FRWI-VPGYVM  146 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~-----~~~~~-~~~~-~~~~~~  146 (316)
                      .++.+.++||+|||.+|+-.++.....       ....+.||+||+.+.-+.+.+.+.     ..+.. ++.. .....+
T Consensus        60 ~n~~~~M~TGtGKT~~~~~~i~~l~~~-------~~~~~fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~  132 (986)
T PRK15483         60 ANIDIKMETGTGKTYVYTRLMYELHQK-------YGLFKFIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVI  132 (986)
T ss_pred             ceEEEEeCCCCCHHHHHHHHHHHHHHH-------cCCcEEEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEE
Confidence            378999999999999998877666544       123569999999999888876654     22211 2222 112222


Q ss_pred             CCC--------ChHHHHHHHhc-------CCcEEEeCcHHHHHHHh-cC---------Cccc---cCce-eEEEEecchh
Q 043110          147 GGG--------NRSKEKARLRK-------GISILVATPGHLLDHLK-HT---------SSFL---HTNL-RWIIFDEADR  197 (316)
Q Consensus       147 ~~~--------~~~~~~~~l~~-------~~~IlV~Tp~~l~~~l~-~~---------~~~~---~~~l-~~lViDEad~  197 (316)
                      .+.        +.....+.+..       ..+|+|.|-+.|..-.. +.         ....   +... -.+|+||.|+
T Consensus       133 ~S~k~~k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niqa~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEPh~  212 (986)
T PRK15483        133 NAGDKKKSGRKNFPAQLSNFVKASRQNSNTIHVLLINAGMLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEPHR  212 (986)
T ss_pred             ecCcccccccccChHHHHHHHhccccCCCceEEEEEehHHhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECCCC
Confidence            211        22333333332       36899999988754211 00         0011   1111 2799999999


Q ss_pred             hhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecch
Q 043110          198 ILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       198 l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                      +-..  ...+..| ..+.                ..-++.+|||.+.
T Consensus       213 ~~~~--~k~~~~i-~~ln----------------pl~~lrysAT~~~  240 (986)
T PRK15483        213 FPRD--NKFYQAI-EALK----------------PQMIIRFGATFPD  240 (986)
T ss_pred             CCcc--hHHHHHH-HhcC----------------cccEEEEeeecCC
Confidence            8542  2233444 3332                1135779999987

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.77  E-value=3.9e-08  Score=96.72  Aligned_cols=142  Identities=15%  Similarity=0.086  Sum_probs=91.8

Q ss_pred             EEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChH---H
Q 043110           77 LVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS---K  153 (316)
Q Consensus        77 li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~  153 (316)
                      +..+-+|||||..|+-.+-..+..         |..+||++|...|+.|+.+.++..+.   ...+..++++.+..   .
T Consensus       164 i~~~~~GSGKTevyl~~i~~~l~~---------Gk~vLvLvPEi~lt~q~~~rl~~~f~---~~~v~~lhS~l~~~~R~~  231 (665)
T PRK14873        164 VWQALPGEDWARRLAAAAAATLRA---------GRGALVVVPDQRDVDRLEAALRALLG---AGDVAVLSAGLGPADRYR  231 (665)
T ss_pred             HhhcCCCCcHHHHHHHHHHHHHHc---------CCeEEEEecchhhHHHHHHHHHHHcC---CCcEEEECCCCCHHHHHH
Confidence            334446999999997766666654         55599999999999999999987653   12334455554443   2


Q ss_pred             HHHHHhcC-CcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhc---CCcHHHHHHHHHHhccCcccccCCCCccc
Q 043110          154 EKARLRKG-ISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE---LGFGKEIEEILDILGSRNIASIGEGNEVS  229 (316)
Q Consensus       154 ~~~~l~~~-~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~---~~~~~~i~~i~~~l~~~~~~~~~~~~~~~  229 (316)
                      .+..+..+ ..|+|||-..++-        .+.++.++|+||-|.-.-   .+...+.+.+.....+..           
T Consensus       232 ~w~~~~~G~~~IViGtRSAvFa--------P~~~LgLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~~-----------  292 (665)
T PRK14873        232 RWLAVLRGQARVVVGTRSAVFA--------PVEDLGLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQH-----------  292 (665)
T ss_pred             HHHHHhCCCCcEEEEcceeEEe--------ccCCCCEEEEEcCCchhhcCCCCCCccHHHHHHHHHHHc-----------
Confidence            33344444 7899999544332        456889999999985431   122223333333222211           


Q ss_pred             cccceEEEEeeecchhHHHHHH
Q 043110          230 NVKRQNLLLSATLNEKVNHLTK  251 (316)
Q Consensus       230 ~~~~q~i~~SAT~~~~v~~~~~  251 (316)
                        +..+|+.|||.+-+....+.
T Consensus       293 --~~~lvLgSaTPSles~~~~~  312 (665)
T PRK14873        293 --GCALLIGGHARTAEAQALVE  312 (665)
T ss_pred             --CCcEEEECCCCCHHHHHHHh
Confidence              78999999998866655544

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=98.76  E-value=1e-07  Score=95.84  Aligned_cols=168  Identities=22%  Similarity=0.184  Sum_probs=101.6

Q ss_pred             CCcHHHHHHHHHHhC--------CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILS--------GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI  129 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~--------g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~  129 (316)
                      .-+.+|-+|+..+..        |-=++--|.||+|||++=.= ++..+..      ...|++..|..-.|.|..|..+.
T Consensus       408 ~rF~WQdkA~d~a~~~r~~~~~~GfF~vNMASTGcGKT~aNAR-ImyaLsd------~~~g~RfsiALGLRTLTLQTGda  480 (1110)
T TIGR02562       408 PRFRWQNKAFNLAQKLRQKSPEQGAFGVNMASTGCGKTLANAR-AMYALRD------DKQGARFAIALGLRSLTLQTGHA  480 (1110)
T ss_pred             CCcchHHHHHHHHHHHHhhcccCCeEEEEecCCCcchHHHHHH-HHHHhCC------CCCCceEEEEccccceeccchHH
Confidence            346799999988763        22367789999999998321 2222322      24577888888888888888888


Q ss_pred             HHHHHhhcCCceeEEeeCCCChHH-------------------------------------------HHHHHhc------
Q 043110          130 LQKLLHRFRWIVPGYVMGGGNRSK-------------------------------------------EKARLRK------  160 (316)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~-------------------------------------------~~~~l~~------  160 (316)
                      +++...- +.-...+++|+.....                                           ....+.+      
T Consensus       481 ~r~rL~L-~~ddLAVlIGs~Av~~L~e~~~~~~~~~~~~GSeS~e~l~~e~~~~~~~~~~g~l~~~~l~~~l~~~~k~~r  559 (1110)
T TIGR02562       481 LKTRLNL-SDDDLAVLIGGTAVQTLFDLSKEKIEQVDEDGSESAPIFLAEGQDCNLPDWDGPLDTIELLGRLSLDDKEKT  559 (1110)
T ss_pred             HHHhcCC-CccceEEEECHHHHHHHHHHHhhhccccccCCCccchhhhcccCcCCeeeccCCccchhhhhhhccChhhhh
Confidence            7765421 1112222222211100                                           0000110      


Q ss_pred             --CCcEEEeCcHHHHHHHhcCC--ccccC--c--eeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCcccccc
Q 043110          161 --GISILVATPGHLLDHLKHTS--SFLHT--N--LRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVK  232 (316)
Q Consensus       161 --~~~IlV~Tp~~l~~~l~~~~--~~~~~--~--l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~  232 (316)
                        ...++|||++.++.......  ...+.  .  =+.|||||+|.. |......+..+++.+...              .
T Consensus       560 ll~apv~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaY-D~~~~~~L~rlL~w~~~l--------------G  624 (1110)
T TIGR02562       560 LLAAPVLVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDY-EPEDLPALLRLVQLAGLL--------------G  624 (1110)
T ss_pred             hhcCCeEEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccC-CHHHHHHHHHHHHHHHHc--------------C
Confidence              15799999999987763211  11111  1  258999999974 333444566666544332              6


Q ss_pred             ceEEEEeeecchhHHH
Q 043110          233 RQNLLLSATLNEKVNH  248 (316)
Q Consensus       233 ~q~i~~SAT~~~~v~~  248 (316)
                      ..++++|||+|+.+..
T Consensus       625 ~~VlLmSATLP~~l~~  640 (1110)
T TIGR02562       625 SRVLLSSATLPPALVK  640 (1110)
T ss_pred             CCEEEEeCCCCHHHHH
Confidence            7899999999998765

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.

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=98.75  E-value=1.3e-07  Score=93.36  Aligned_cols=138  Identities=22%  Similarity=0.259  Sum_probs=99.9

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           47 CDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        47 ~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .++..+.+|.. |+++|...--.+..|+  ++.+.||-|||++..+|+.-....         |..|-|++....||.-=
T Consensus        68 REA~~R~lG~r-~ydVQliGglvLh~G~--IAEMkTGEGKTLvAtLpayLnAL~---------GkgVhVVTvNdYLA~RD  135 (925)
T PRK12903         68 REATKRVLGKR-PYDVQIIGGIILDLGS--VAEMKTGEGKTITSIAPVYLNALT---------GKGVIVSTVNEYLAERD  135 (925)
T ss_pred             HHHHHHHhCCC-cCchHHHHHHHHhcCC--eeeecCCCCccHHHHHHHHHHHhc---------CCceEEEecchhhhhhh
Confidence            34444456875 8999988776666664  799999999999999998765544         34488999999999998


Q ss_pred             HHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcCC-----ccccCceeEEEEecchhhh
Q 043110          127 YEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHTS-----SFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~~-----~~~~~~l~~lViDEad~l~  199 (316)
                      .+++..+...++ +.+++...+.... +.+..+ .+||+.||...| +++++..-     ......+.+.|+||+|.++
T Consensus       136 ae~mg~vy~fLG-LsvG~i~~~~~~~-~rr~aY-~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR~~~faIVDEVDSIL  211 (925)
T PRK12903        136 AEEMGKVFNFLG-LSVGINKANMDPN-LKREAY-ACDITYSVHSELGFDYLRDNMVSSKEEKVQRGLNFCLIDEVDSIL  211 (925)
T ss_pred             HHHHHHHHHHhC-CceeeeCCCCChH-HHHHhc-cCCCeeecCcccchhhhhhcccccHHHhcCcccceeeeccchhee
Confidence            899999888776 5556665554443 333334 479999999865 44554321     1233568899999999876

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=98.68  E-value=1.5e-08  Score=93.13  Aligned_cols=156  Identities=15%  Similarity=0.160  Sum_probs=101.8

Q ss_pred             CCCcHHHHHHHHHHh-CC--CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           57 EAPTKVQAQAIPVIL-SG--RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il-~g--~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      ..++|+|..++..+. +|  +..+|..|-|+|||++-+-++.. +           ...+|++|.+---+.|+..+++.|
T Consensus       301 t~iRpYQEksL~KMFGNgRARSGiIVLPCGAGKtLVGvTAa~t-i-----------kK~clvLcts~VSVeQWkqQfk~w  368 (776)
T KOG1123|consen  301 TQIRPYQEKSLSKMFGNGRARSGIIVLPCGAGKTLVGVTAACT-I-----------KKSCLVLCTSAVSVEQWKQQFKQW  368 (776)
T ss_pred             cccCchHHHHHHHHhCCCcccCceEEEecCCCCceeeeeeeee-e-----------cccEEEEecCccCHHHHHHHHHhh
Confidence            356899999998887 44  47899999999999975433221 1           123999999999999999999988


Q ss_pred             HhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCC-------ccccCceeEEEEecchhhhcCCcHHH
Q 043110          134 LHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTS-------SFLHTNLRWIIFDEADRILELGFGKE  206 (316)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~-------~~~~~~l~~lViDEad~l~~~~~~~~  206 (316)
                      ..--+...+.......      .....++.|+|+|..++..--++..       .+.-.+..++++||+|.+-..-|+.-
T Consensus       369 sti~d~~i~rFTsd~K------e~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~~EWGllllDEVHvvPA~MFRRV  442 (776)
T KOG1123|consen  369 STIQDDQICRFTSDAK------ERFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRGREWGLLLLDEVHVVPAKMFRRV  442 (776)
T ss_pred             cccCccceEEeecccc------ccCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhcCeeeeEEeehhccchHHHHHHH
Confidence            7543333333222111      2234568899999876643221110       01114678999999999876545544


Q ss_pred             HHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHH
Q 043110          207 IEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLT  250 (316)
Q Consensus       207 i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~  250 (316)
                      +..+-...                    .++++||+-.+-.++.
T Consensus       443 lsiv~aHc--------------------KLGLTATLvREDdKI~  466 (776)
T KOG1123|consen  443 LSIVQAHC--------------------KLGLTATLVREDDKIT  466 (776)
T ss_pred             HHHHHHHh--------------------hccceeEEeecccccc
Confidence            44443332                    3688999876655443

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

Probab=98.66  E-value=8.6e-07  Score=84.57  Aligned_cols=149  Identities=19%  Similarity=0.184  Sum_probs=88.3

Q ss_pred             HHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH-HHHhhcCCcee
Q 043110           64 AQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ-KLLHRFRWIVP  142 (316)
Q Consensus        64 ~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~-~~~~~~~~~~~  142 (316)
                      .+.+..+-+.+-+++.|+||||||.-    +-+.+.+...    ....++-+.-|.|--|..++++.. +++..++ ..+
T Consensus        57 ~~il~~ve~nqvlIviGeTGsGKSTQ----ipQyL~eaG~----~~~g~I~~TQPRRVAavslA~RVAeE~~~~lG-~~V  127 (674)
T KOG0922|consen   57 DQILYAVEDNQVLIVIGETGSGKSTQ----IPQYLAEAGF----ASSGKIACTQPRRVAAVSLAKRVAEEMGCQLG-EEV  127 (674)
T ss_pred             HHHHHHHHHCCEEEEEcCCCCCcccc----HhHHHHhccc----ccCCcEEeecCchHHHHHHHHHHHHHhCCCcC-cee
Confidence            45556666778899999999999975    3334433211    112226677799887777665443 3332222 222


Q ss_pred             EEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCccccc
Q 043110          143 GYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASI  222 (316)
Q Consensus       143 ~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~  222 (316)
                      ++.+.=.+.      -.....|...|-|.|+.-+..  .-.++..+++|+||||.=.=  .-+.+-.+++.+-+.     
T Consensus       128 GY~IRFed~------ts~~TrikymTDG~LLRE~l~--Dp~LskYsvIIlDEAHERsl--~TDiLlGlLKki~~~-----  192 (674)
T KOG0922|consen  128 GYTIRFEDS------TSKDTRIKYMTDGMLLREILK--DPLLSKYSVIILDEAHERSL--HTDILLGLLKKILKK-----  192 (674)
T ss_pred             eeEEEeccc------CCCceeEEEecchHHHHHHhc--CCccccccEEEEechhhhhh--HHHHHHHHHHHHHhc-----
Confidence            222211111      012357999999999987764  33557899999999995110  123333344433321     


Q ss_pred             CCCCccccccceEEEEeeecc
Q 043110          223 GEGNEVSNVKRQNLLLSATLN  243 (316)
Q Consensus       223 ~~~~~~~~~~~q~i~~SAT~~  243 (316)
                             .+.-++|++|||+.
T Consensus       193 -------R~~LklIimSATld  206 (674)
T KOG0922|consen  193 -------RPDLKLIIMSATLD  206 (674)
T ss_pred             -------CCCceEEEEeeeec
Confidence                   11568999999997

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=98.59  E-value=1.5e-06  Score=83.98  Aligned_cols=156  Identities=18%  Similarity=0.235  Sum_probs=100.6

Q ss_pred             CCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        58 ~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .++++|.+.+.++.    +|-+.|+.-..|-|||+-. ++++..+.....    ..|| -||++|..-|.    +++..+
T Consensus       167 ~lr~YQveGlnWLi~l~engingILaDEMGLGKTlQt-Is~l~yl~~~~~----~~GP-fLVi~P~StL~----NW~~Ef  236 (971)
T KOG0385|consen  167 ELRDYQLEGLNWLISLYENGINGILADEMGLGKTLQT-ISLLGYLKGRKG----IPGP-FLVIAPKSTLD----NWMNEF  236 (971)
T ss_pred             ccchhhhccHHHHHHHHhcCcccEeehhcccchHHHH-HHHHHHHHHhcC----CCCC-eEEEeeHhhHH----HHHHHH
Confidence            58899999887765    6778999999999999874 344444443222    1233 79999998773    344444


Q ss_pred             HhhcCCceeEEeeCCCChHHHH-HHHh--cCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHH
Q 043110          134 LHRFRWIVPGYVMGGGNRSKEK-ARLR--KGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEI  210 (316)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~-~~l~--~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i  210 (316)
                      ....+.+.+.+.+|........ +.+.  ...+|+|+|.+..+.--   ..+.--..+++||||||++-..  ...+..+
T Consensus       237 ~rf~P~l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~dk---~~lk~~~W~ylvIDEaHRiKN~--~s~L~~~  311 (971)
T KOG0385|consen  237 KRFTPSLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKDK---SFLKKFNWRYLVIDEAHRIKNE--KSKLSKI  311 (971)
T ss_pred             HHhCCCcceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhhH---HHHhcCCceEEEechhhhhcch--hhHHHHH
Confidence            4455667777777765433222 2222  24789999998775421   1121125689999999998653  3445567


Q ss_pred             HHHhccCcccccCCCCccccccceEEEEeeecch
Q 043110          211 LDILGSRNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       211 ~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                      ++.+..                ...++++.|.-.
T Consensus       312 lr~f~~----------------~nrLLlTGTPLQ  329 (971)
T KOG0385|consen  312 LREFKT----------------DNRLLLTGTPLQ  329 (971)
T ss_pred             HHHhcc----------------cceeEeeCCccc
Confidence            777653                345677777543

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=98.50  E-value=6e-07  Score=77.16  Aligned_cols=73  Identities=29%  Similarity=0.335  Sum_probs=50.2

Q ss_pred             CcHHHHHHHHHHhCCCc-EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           59 PTKVQAQAIPVILSGRD-VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        59 p~~~Q~~~i~~il~g~d-~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      +++-|.+|+..++.... .++.||.|+|||.... .++..+...........+.++|+++|+..-+.++.+.+.+
T Consensus         2 ln~~Q~~Ai~~~~~~~~~~~i~GpPGTGKT~~l~-~~i~~~~~~~~~~~~~~~~~il~~~~sN~avd~~~~~l~~   75 (236)
T PF13086_consen    2 LNESQREAIQSALSSNGITLIQGPPGTGKTTTLA-SIIAQLLQRFKSRSADRGKKILVVSPSNAAVDNILERLKK   75 (236)
T ss_dssp             --HHHHHHHHHHCTSSE-EEEE-STTSSHHHHHH-HHHHHH-------HCCCSS-EEEEESSHHHHHHHHHHHHC
T ss_pred             CCHHHHHHHHHHHcCCCCEEEECCCCCChHHHHH-HHHHHhccchhhhhhhccccceeecCCchhHHHHHHHHHh
Confidence            67899999999999998 9999999999996543 3444441100000123456699999999999999888877

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=98.47  E-value=3.2e-06  Score=86.91  Aligned_cols=139  Identities=19%  Similarity=0.129  Sum_probs=91.7

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHH
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSK  153 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (316)
                      +..+|.--||||||++-+..+ +.+...      ...+.+++|+-.++|-.|+.+.+..+........     ...+...
T Consensus       274 ~~G~IWHtqGSGKTlTm~~~A-~~l~~~------~~~~~v~fvvDR~dLd~Q~~~~f~~~~~~~~~~~-----~~~s~~~  341 (962)
T COG0610         274 KGGYIWHTQGSGKTLTMFKLA-RLLLEL------PKNPKVLFVVDRKDLDDQTSDEFQSFGKVAFNDP-----KAESTSE  341 (962)
T ss_pred             CceEEEeecCCchHHHHHHHH-HHHHhc------cCCCeEEEEechHHHHHHHHHHHHHHHHhhhhcc-----cccCHHH
Confidence            458999999999999854433 333332      2356799999999999999999999876532111     3344444


Q ss_pred             HHHHHhcCC-cEEEeCcHHHHHHHhcCCcccc-CceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccc
Q 043110          154 EKARLRKGI-SILVATPGHLLDHLKHTSSFLH-TNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNV  231 (316)
Q Consensus       154 ~~~~l~~~~-~IlV~Tp~~l~~~l~~~~~~~~-~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~  231 (316)
                      -.+.+..+. .|+|+|-..|-........... .+=-.+|+||||+-   .++..-..+...++                
T Consensus       342 Lk~~l~~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivvI~DEaHRS---Q~G~~~~~~~~~~~----------------  402 (962)
T COG0610         342 LKELLEDGKGKIIVTTIQKFNKAVKEDELELLKRKNVVVIIDEAHRS---QYGELAKLLKKALK----------------  402 (962)
T ss_pred             HHHHHhcCCCcEEEEEecccchhhhcccccccCCCcEEEEEechhhc---cccHHHHHHHHHhc----------------
Confidence            445555443 7999999999887765311111 12237899999992   34444444455554                


Q ss_pred             cceEEEEeeecc
Q 043110          232 KRQNLLLSATLN  243 (316)
Q Consensus       232 ~~q~i~~SAT~~  243 (316)
                      +...++||.|.-
T Consensus       403 ~a~~~gFTGTPi  414 (962)
T COG0610         403 KAIFIGFTGTPI  414 (962)
T ss_pred             cceEEEeeCCcc
Confidence            567888888863

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=98.45  E-value=4.7e-06  Score=70.24  Aligned_cols=63  Identities=24%  Similarity=0.333  Sum_probs=44.3

Q ss_pred             CCcHHHHHHHHHHhCCC--cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSGR--DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI  129 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~--d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~  129 (316)
                      ++++-|.+++..++...  -.++.++.|+|||.+. -.+...+..        .+.++++++||...+..+.+.
T Consensus         1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l-~~~~~~~~~--------~g~~v~~~apT~~Aa~~L~~~   65 (196)
T PF13604_consen    1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLL-KALAEALEA--------AGKRVIGLAPTNKAAKELREK   65 (196)
T ss_dssp             -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHH-HHHHHHHHH--------TT--EEEEESSHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHH-HHHHHHHHh--------CCCeEEEECCcHHHHHHHHHh
Confidence            36889999999997544  3788899999999753 335555444        245699999999887665544

>PF02562 PhoH: PhoH-like protein; InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli []

Probab=98.45  E-value=1.6e-06  Score=73.02  Aligned_cols=136  Identities=21%  Similarity=0.218  Sum_probs=68.3

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHH-------HH
Q 043110           57 EAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY-------EI  129 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~-------~~  129 (316)
                      ...++-|..++.++++..-+++.||.|+|||+..+..+++.+...       ..-+.+|+-|..+..+.+.       +.
T Consensus         3 ~p~~~~Q~~~~~al~~~~~v~~~G~AGTGKT~LA~a~Al~~v~~g-------~~~kiii~Rp~v~~~~~lGflpG~~~eK   75 (205)
T PF02562_consen    3 KPKNEEQKFALDALLNNDLVIVNGPAGTGKTFLALAAALELVKEG-------EYDKIIITRPPVEAGEDLGFLPGDLEEK   75 (205)
T ss_dssp             ---SHHHHHHHHHHHH-SEEEEE--TTSSTTHHHHHHHHHHHHTT-------S-SEEEEEE-S--TT----SS-------
T ss_pred             cCCCHHHHHHHHHHHhCCeEEEECCCCCcHHHHHHHHHHHHHHhC-------CCcEEEEEecCCCCccccccCCCCHHHH
Confidence            346889999999999777799999999999999998888888651       2334788878765422211       11


Q ss_pred             HHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHH
Q 043110          130 LQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEE  209 (316)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~  209 (316)
                      +..+...+.. ....+.+...    ...+.....|-+..+..+    +.   ..+. -.++|+|||+.+    -..++..
T Consensus        76 ~~p~~~p~~d-~l~~~~~~~~----~~~~~~~~~Ie~~~~~~i----RG---rt~~-~~~iIvDEaQN~----t~~~~k~  138 (205)
T PF02562_consen   76 MEPYLRPIYD-ALEELFGKEK----LEELIQNGKIEIEPLAFI----RG---RTFD-NAFIIVDEAQNL----TPEELKM  138 (205)
T ss_dssp             --TTTHHHHH-HHTTTS-TTC----HHHHHHTTSEEEEEGGGG----TT-----B--SEEEEE-SGGG------HHHHHH
T ss_pred             HHHHHHHHHH-HHHHHhChHh----HHHHhhcCeEEEEehhhh----cC---cccc-ceEEEEecccCC----CHHHHHH
Confidence            1100000000 0000001111    111222334555554322    21   1222 279999999997    4577888


Q ss_pred             HHHHhcc
Q 043110          210 ILDILGS  216 (316)
Q Consensus       210 i~~~l~~  216 (316)
                      ++.++..
T Consensus       139 ilTR~g~  145 (205)
T PF02562_consen  139 ILTRIGE  145 (205)
T ss_dssp             HHTTB-T
T ss_pred             HHcccCC
Confidence            8888876

; GO: 0005524 ATP binding; PDB: 3B85_A.

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.42  E-value=1e-06  Score=81.92  Aligned_cols=201  Identities=22%  Similarity=0.203  Sum_probs=129.8

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEcCC-CCch--HHHHHHHHHHHhhhcCCCC----------------------CCCCCe
Q 043110           57 EAPTKVQAQAIPVILSGRDVLVNAAT-GTGK--TVAYLAPIINHLQSYSPRI----------------------DRSSGT  111 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il~g~d~li~a~T-GsGK--T~~~~lp~l~~l~~~~~~~----------------------~~~~~~  111 (316)
                      ..+|+.|.+.+..+.+-+|++..-.| +.|+  +-.|++-+++++.+.....                      +.-..+
T Consensus       215 ~pltalQ~~L~~~m~~YrDl~y~~~s~kn~~e~R~lYclH~lNHi~K~r~~IL~Nn~r~~Sqk~g~~~~~~frDQG~tRp  294 (698)
T KOG2340|consen  215 EPLTALQKELFKIMFNYRDLLYPTRSQKNGEEYRSLYCLHALNHILKTRDLILGNNRRLASQKEGENPDESFRDQGFTRP  294 (698)
T ss_pred             CcchHHHHHHHHHHHhhhhhccccccccccchhhhhHHHHHHHHHHHHHHHHhcchHhhhhhhcCCCCchhhhhcCCCCc
Confidence            46799999999999999997654433 3444  4568888888885532110                      011357


Q ss_pred             eEEEEeCChHHHHHHHHHHHHHHhhcCCcee------------------------------EEeeCCCCh--------HH
Q 043110          112 FALVLVPTSELCLLVYEILQKLLHRFRWIVP------------------------------GYVMGGGNR--------SK  153 (316)
Q Consensus       112 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~------------------------------~~~~~~~~~--------~~  153 (316)
                      ++|||||+|+-|-.+.+.+..++.....-..                              ..+.|.++.        ..
T Consensus       295 kVLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~ftk  374 (698)
T KOG2340|consen  295 KVLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAFTK  374 (698)
T ss_pred             eEEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHHHH
Confidence            8999999999999888888777432211000                              001111110        00


Q ss_pred             HHHHHh---cCCcEEEeCcHHHHHHHhcCC-----ccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCccccc---
Q 043110          154 EKARLR---KGISILVATPGHLLDHLKHTS-----SFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASI---  222 (316)
Q Consensus       154 ~~~~l~---~~~~IlV~Tp~~l~~~l~~~~-----~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~---  222 (316)
                      ..-.|.   ...||+||+|--|-..+.+.+     ...++.+.++|||.||.++.. -...+..|+..|........   
T Consensus       375 KtikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~Q-NwEhl~~ifdHLn~~P~k~h~~D  453 (698)
T KOG2340|consen  375 KTIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQ-NWEHLLHIFDHLNLQPSKQHDVD  453 (698)
T ss_pred             HHHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHh-hHHHHHHHHHHhhcCcccccCCC
Confidence            111111   236999999998888776432     225688999999999998875 44667777777764322211   


Q ss_pred             ----CCC--CccccccceEEEEeeecchhHHHHHHHhcCCCE
Q 043110          223 ----GEG--NEVSNVKRQNLLLSATLNEKVNHLTKISLETPV  258 (316)
Q Consensus       223 ----~~~--~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~  258 (316)
                          ..|  +.++.--+|+++||+-..+....+...+++|-.
T Consensus       454 fSRVR~wyL~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N~~  495 (698)
T KOG2340|consen  454 FSRVRMWYLDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQNMA  495 (698)
T ss_pred             hhheehheeccHHHHHHHHHHHHhhccHHHHHHHHHhhhhhc
Confidence                122  234555689999999999888888887776554

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=98.42  E-value=1.8e-06  Score=83.65  Aligned_cols=168  Identities=18%  Similarity=0.274  Sum_probs=107.4

Q ss_pred             CCCCCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHH
Q 043110           55 GFEAPTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEIL  130 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~  130 (316)
                      |+. +-++|.-.+.++.    .+-+.|+.-..|-|||.-. ++.+..+.+...     +|+ -|||||..-|    .+++
T Consensus       397 ~i~-LkdYQlvGvNWL~Llyk~~l~gILADEMGLGKTiQv-IaFlayLkq~g~-----~gp-HLVVvPsSTl----eNWl  464 (941)
T KOG0389|consen  397 GIQ-LKDYQLVGVNWLLLLYKKKLNGILADEMGLGKTIQV-IAFLAYLKQIGN-----PGP-HLVVVPSSTL----ENWL  464 (941)
T ss_pred             CCc-ccchhhhhHHHHHHHHHccccceehhhccCcchhHH-HHHHHHHHHcCC-----CCC-cEEEecchhH----HHHH
Confidence            444 6789988887765    4557899999999999653 445555554322     222 7999999776    5677


Q ss_pred             HHHHhhcCCceeEEeeCCCChHHHHHHHh-c---CCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHH
Q 043110          131 QKLLHRFRWIVPGYVMGGGNRSKEKARLR-K---GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKE  206 (316)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~---~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~  206 (316)
                      +++..+++.+.+...+|......+.+... +   ..+|+|+|.......-...+.+.-.++.++|+||+|.|-... ...
T Consensus       465 rEf~kwCPsl~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~~~~n~viyDEgHmLKN~~-SeR  543 (941)
T KOG0389|consen  465 REFAKWCPSLKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKNQKFNYVIYDEGHMLKNRT-SER  543 (941)
T ss_pred             HHHHHhCCceEEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHhccccEEEecchhhhhccc-hHH
Confidence            77777778788877777765555444332 2   478999998655421111112222468899999999887653 223


Q ss_pred             HHHHHHHhccCcccccCCCCccccccceEEEEeeec-chhHHHHHHH
Q 043110          207 IEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATL-NEKVNHLTKI  252 (316)
Q Consensus       207 i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~-~~~v~~~~~~  252 (316)
                      +..++..-                 ..+.++++.|. -.++.+++.+
T Consensus       544 y~~LM~I~-----------------An~RlLLTGTPLQNNL~ELiSL  573 (941)
T KOG0389|consen  544 YKHLMSIN-----------------ANFRLLLTGTPLQNNLKELISL  573 (941)
T ss_pred             HHHhcccc-----------------ccceEEeeCCcccccHHHHHHH
Confidence            33333221                 34567777775 4556777664

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=98.40  E-value=1.6e-06  Score=86.91  Aligned_cols=128  Identities=22%  Similarity=0.275  Sum_probs=91.7

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      .|+++|.-.--.+..|+  |+.+.||-|||+++.+|+.-....         |..|-||+..-.||.-=.+++..+....
T Consensus       138 ~~ydVQLiGgivLh~G~--IAEM~TGEGKTLvatlp~yLnAL~---------G~gVHvVTvNDYLA~RDaewm~p~y~fl  206 (1025)
T PRK12900        138 VPYDVQLIGGIVLHSGK--ISEMATGEGKTLVSTLPTFLNALT---------GRGVHVVTVNDYLAQRDKEWMNPVFEFH  206 (1025)
T ss_pred             cccchHHhhhHHhhcCC--ccccCCCCCcchHhHHHHHHHHHc---------CCCcEEEeechHhhhhhHHHHHHHHHHh
Confidence            47888866555555554  899999999999999999766665         3338889999999999899999998876


Q ss_pred             CCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcC-----CccccCceeEEEEecchhhh
Q 043110          138 RWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHT-----SSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~-----~~~~~~~l~~lViDEad~l~  199 (316)
                      + +.++++..+.+.. +.+.. -.+||..||..-| +++|+..     .......+.+.||||+|.++
T Consensus       207 G-LtVg~i~~~~~~~-~Rr~a-Y~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~~~faIVDEvDSvL  271 (1025)
T PRK12900        207 G-LSVGVILNTMRPE-ERREQ-YLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRDFYFAIVDEVDSVL  271 (1025)
T ss_pred             C-CeeeeeCCCCCHH-HHHHh-CCCcceecCCCccccccchhccccchhhhhccCCceEEEechhhhh
Confidence            6 5666665544443 33333 3579999999754 3444321     11233567899999999865

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=98.40  E-value=3.7e-06  Score=81.71  Aligned_cols=192  Identities=23%  Similarity=0.264  Sum_probs=102.4

Q ss_pred             CCCCcHHHHH------------HHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCC-CCCCeeEEEEeCChHH
Q 043110           56 FEAPTKVQAQ------------AIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRID-RSSGTFALVLVPTSEL  122 (316)
Q Consensus        56 ~~~p~~~Q~~------------~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~-~~~~~~~lil~Pt~~L  122 (316)
                      .++|..+|..            .+.+|..+--+|++|.||||||.-  +|  +.+..-.-... ...+..+=|--|.|--
T Consensus       242 V~R~~EIQ~sR~~LPI~aeEq~IMEaIn~n~vvIIcGeTGsGKTTQ--vP--QFLYEAGf~s~~~~~~gmIGITqPRRVA  317 (1172)
T KOG0926|consen  242 VSRPAEIQESRLDLPIVAEEQRIMEAINENPVVIICGETGSGKTTQ--VP--QFLYEAGFASEQSSSPGMIGITQPRRVA  317 (1172)
T ss_pred             ecCcHHHHHHHhcCchhHHHHHHHHHhhcCCeEEEecCCCCCcccc--ch--HHHHHcccCCccCCCCCeeeecCchHHH
Confidence            3566777743            233444445589999999999975  23  33322111111 1112234456688877


Q ss_pred             HHHHHHHHHHHHhhcCCceeEEe--eCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          123 CLLVYEILQKLLHRFRWIVPGYV--MGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       123 ~~Q~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                      |..++++...-+..++..+ ++.  +.|+-        .....|...|-|.|+.-+.  ..+.+...+.+|+||||.=.-
T Consensus       318 aiamAkRVa~EL~~~~~eV-sYqIRfd~ti--------~e~T~IkFMTDGVLLrEi~--~DflL~kYSvIIlDEAHERSv  386 (1172)
T KOG0926|consen  318 AIAMAKRVAFELGVLGSEV-SYQIRFDGTI--------GEDTSIKFMTDGVLLREIE--NDFLLTKYSVIILDEAHERSV  386 (1172)
T ss_pred             HHHHHHHHHHHhccCccce-eEEEEecccc--------CCCceeEEecchHHHHHHH--HhHhhhhceeEEechhhhccc
Confidence            7666654333222222222 222  12211        2345799999999998877  467778899999999996221


Q ss_pred             CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHH---HHhcCCCEEEEcCCCCCC
Q 043110          201 LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLT---KISLETPVLIGLDEKKFP  268 (316)
Q Consensus       201 ~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~---~~~l~~p~~i~~~~~~~~  268 (316)
                        +-+.+-.++.++-...  ........-.....+|+||||+-  |.+|.   ++|-.-|=.|.++.-.++
T Consensus       387 --nTDILiGmLSRiV~LR--~k~~ke~~~~kpLKLIIMSATLR--VsDFtenk~LFpi~pPlikVdARQfP  451 (1172)
T KOG0926|consen  387 --NTDILIGMLSRIVPLR--QKYYKEQCQIKPLKLIIMSATLR--VSDFTENKRLFPIPPPLIKVDARQFP  451 (1172)
T ss_pred             --hHHHHHHHHHHHHHHH--HHHhhhhcccCceeEEEEeeeEE--ecccccCceecCCCCceeeeecccCc
Confidence              2333333333332100  00000011223567899999985  44444   234333336666655433

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=98.33  E-value=8.7e-06  Score=75.92  Aligned_cols=149  Identities=17%  Similarity=0.173  Sum_probs=98.7

Q ss_pred             CCeeEEEEeCChHHHHHHHHHHHHHHhhcCCce----eEEeeC--------------CCChHHHHHHHhc----------
Q 043110          109 SGTFALVLVPTSELCLLVYEILQKLLHRFRWIV----PGYVMG--------------GGNRSKEKARLRK----------  160 (316)
Q Consensus       109 ~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~----~~~~~~--------------~~~~~~~~~~l~~----------  160 (316)
                      ..|++|||+|+|..|.++.+.+..++.......    ..--+|              ......+...+..          
T Consensus        36 tRPkVLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~DD~FrlG  115 (442)
T PF06862_consen   36 TRPKVLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNNDDCFRLG  115 (442)
T ss_pred             CCceEEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCccceEEEe
Confidence            468899999999999999888877764310000    000000              0111122222222          


Q ss_pred             ---------------CCcEEEeCcHHHHHHHhc-----CCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCccc
Q 043110          161 ---------------GISILVATPGHLLDHLKH-----TSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIA  220 (316)
Q Consensus       161 ---------------~~~IlV~Tp~~l~~~l~~-----~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~  220 (316)
                                     ++||||++|=-|...+..     .....++++.++|+|.||.|+.. -.+.+..+++.+......
T Consensus       116 ik~trk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQ-NW~Hv~~v~~~lN~~P~~  194 (442)
T PF06862_consen  116 IKFTRKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQ-NWEHVLHVFEHLNLQPKK  194 (442)
T ss_pred             EEEecCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHh-hHHHHHHHHHHhccCCCC
Confidence                           278999999998887764     12347899999999999998765 457777777777653222


Q ss_pred             ccCC-------C--CccccccceEEEEeeecchhHHHHHHHhcCCCE
Q 043110          221 SIGE-------G--NEVSNVKRQNLLLSATLNEKVNHLTKISLETPV  258 (316)
Q Consensus       221 ~~~~-------~--~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~  258 (316)
                      ..+.       |  +..+..-+|+|++|+...+++..+.+..+.|..
T Consensus       195 ~~~~DfsRVR~w~Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~  241 (442)
T PF06862_consen  195 SHDTDFSRVRPWYLDGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYA  241 (442)
T ss_pred             CCCCCHHHHHHHHHcCcchheeEeEEecCCCCHHHHHHHHhhCcCcc
Confidence            2111       1  233556689999999999999999998777664

; GO: 0005634 nucleus

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=98.32  E-value=6.4e-06  Score=79.99  Aligned_cols=162  Identities=17%  Similarity=0.195  Sum_probs=96.4

Q ss_pred             CCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHH--HHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYL--APIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ  131 (316)
Q Consensus        58 ~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~--lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~  131 (316)
                      .+.++|+.++..+.    ++.-.|+--..|-|||.-.+  ++.+++-.   ..     ...+|||||. .+..|+.+.+.
T Consensus       205 ~Lf~yQreGV~WL~~L~~q~~GGILgDeMGLGKTIQiisFLaaL~~S~---k~-----~~paLIVCP~-Tii~qW~~E~~  275 (923)
T KOG0387|consen  205 KLFPYQREGVQWLWELYCQRAGGILGDEMGLGKTIQIISFLAALHHSG---KL-----TKPALIVCPA-TIIHQWMKEFQ  275 (923)
T ss_pred             HhhHHHHHHHHHHHHHHhccCCCeecccccCccchhHHHHHHHHhhcc---cc-----cCceEEEccH-HHHHHHHHHHH
Confidence            45889999988876    45568999999999997532  22232221   11     1239999997 56778877777


Q ss_pred             HHHhhcCCceeEEeeCCCCh--------HHHHHH-----HhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhh
Q 043110          132 KLLHRFRWIVPGYVMGGGNR--------SKEKAR-----LRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRI  198 (316)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~--------~~~~~~-----l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l  198 (316)
                      .+..   ...+..+++..+.        ...+..     ...+.+|+|+|.+.+.-.-   ..+.--...++|+||.|++
T Consensus       276 ~w~p---~~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~~---d~l~~~~W~y~ILDEGH~I  349 (923)
T KOG0387|consen  276 TWWP---PFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQG---DDLLGILWDYVILDEGHRI  349 (923)
T ss_pred             HhCc---ceEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhcccC---cccccccccEEEecCcccc
Confidence            7653   3455555544331        111111     1123579999977654321   1222235689999999998


Q ss_pred             hcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeec-chhHHHHHHH
Q 043110          199 LELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATL-NEKVNHLTKI  252 (316)
Q Consensus       199 ~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~-~~~v~~~~~~  252 (316)
                      -..  ..++......++                ..+.|++|.|. -.++.+|-.+
T Consensus       350 rNp--ns~islackki~----------------T~~RiILSGTPiQNnL~ELwsL  386 (923)
T KOG0387|consen  350 RNP--NSKISLACKKIR----------------TVHRIILSGTPIQNNLTELWSL  386 (923)
T ss_pred             cCC--ccHHHHHHHhcc----------------ccceEEeeCccccchHHHHHHH
Confidence            653  234444444554                34567777775 3445554433

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=98.31  E-value=1.8e-06  Score=82.66  Aligned_cols=141  Identities=18%  Similarity=0.224  Sum_probs=85.7

Q ss_pred             CCcHHHHHHHHHHhC-----CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCC-CeeEEEEeCChHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILS-----GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSS-GTFALVLVPTSELCLLVYEILQ  131 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~-----g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~-~~~~lil~Pt~~L~~Q~~~~~~  131 (316)
                      ++.|+|..++.++.-     +.-.|+....|-|||+..+-.++..-.....+.+++. ....|||||- .|..|++..+.
T Consensus       325 ~LmpHQkaal~Wl~wRE~q~~~GGILaddmGLGKTlsmislil~qK~~~~~~~~~~~~a~~TLII~Pa-Sli~qW~~Ev~  403 (901)
T KOG4439|consen  325 ELMPHQKAALRWLLWRESQPPSGGILADDMGLGKTLSMISLILHQKAARKAREKKGESASKTLIICPA-SLIHQWEAEVA  403 (901)
T ss_pred             ecchhhhhhhhhhcccccCCCCCcccccccccccchHHHHHHHHHHHHHHhhcccccccCCeEEeCcH-HHHHHHHHHHH
Confidence            457899999988762     2347889999999999754444443322222211111 1159999996 67889998887


Q ss_pred             HHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHH----HHhcCC-ccccC--ceeEEEEecchhhhcC
Q 043110          132 KLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLD----HLKHTS-SFLHT--NLRWIIFDEADRILEL  201 (316)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~----~l~~~~-~~~~~--~l~~lViDEad~l~~~  201 (316)
                      ......  ...++++.|.+..+........+||||+|..-+..    -....+ ...+.  ....+|+||||.+-+.
T Consensus       404 ~rl~~n--~LsV~~~HG~n~r~i~~~~L~~YDvViTTY~lva~~~~~e~~~~~~~spL~~I~W~RVILDEAH~IrN~  478 (901)
T KOG4439|consen  404 RRLEQN--ALSVYLYHGPNKREISAKELRKYDVVITTYNLVANKPDDELEEGKNSSPLARIAWSRVILDEAHNIRNS  478 (901)
T ss_pred             HHHhhc--ceEEEEecCCccccCCHHHHhhcceEEEeeeccccCCchhhhcccCccHHHHhhHHHhhhhhhhhhccc
Confidence            776542  33345555555433333444568999999865544    010101 11111  2357999999988664

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=98.30  E-value=2.3e-06  Score=86.04  Aligned_cols=129  Identities=20%  Similarity=0.227  Sum_probs=89.9

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      .|+++|...=-.+..|  -++.+.||-|||++..+|+.-....         |..|-||+..-.||.-=.+++..+...+
T Consensus       169 ~~yDVQliGgivLh~G--~IAEM~TGEGKTLvAtlp~yLnAL~---------GkgVHvVTVNDYLA~RDaewmgply~fL  237 (1112)
T PRK12901        169 VHYDVQLIGGVVLHQG--KIAEMATGEGKTLVATLPVYLNALT---------GNGVHVVTVNDYLAKRDSEWMGPLYEFH  237 (1112)
T ss_pred             cccchHHhhhhhhcCC--ceeeecCCCCchhHHHHHHHHHHHc---------CCCcEEEEechhhhhccHHHHHHHHHHh
Confidence            4677775554444444  5899999999999999998776665         3338889999999998888999888876


Q ss_pred             CCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcC-----CccccCceeEEEEecchhhh
Q 043110          138 RWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHT-----SSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~-----~~~~~~~l~~lViDEad~l~  199 (316)
                      + +.++++........+.+..+ .+||..+|..-| +++|+..     .......+.|.||||+|.++
T Consensus       238 G-Lsvg~i~~~~~~~~~rr~aY-~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR~~~fAIVDEvDSIL  303 (1112)
T PRK12901        238 G-LSVDCIDKHQPNSEARRKAY-NADITYGTNNEFGFDYLRDNMAHSPEDLVQRKHNYAIVDEVDSVL  303 (1112)
T ss_pred             C-CceeecCCCCCCHHHHHHhC-CCcceecCCCccccccchhccccchHhhhCcCCceeEeechhhhh
Confidence            6 55555544233333444433 579999999755 3444321     11233567899999999876

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=98.29  E-value=2.1e-05  Score=77.55  Aligned_cols=183  Identities=18%  Similarity=0.172  Sum_probs=113.4

Q ss_pred             CCcHHHHHHHHHHh---CCC-------cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHH
Q 043110           58 APTKVQAQAIPVIL---SGR-------DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY  127 (316)
Q Consensus        58 ~p~~~Q~~~i~~il---~g~-------d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~  127 (316)
                      .++|+|++.+.-+.   .|.       -+|+.-..|+|||+.. ++.++.+.++.+..++ .-.++|||+|. .|+.-++
T Consensus       238 ~LrPHQ~EG~~FL~knl~g~~~~~~~~GCImAd~~GlGKTlq~-IsflwtlLrq~P~~~~-~~~k~lVV~P~-sLv~nWk  314 (776)
T KOG0390|consen  238 ILRPHQREGFEFLYKNLAGLIRPKNSGGCIMADEPGLGKTLQC-ISFIWTLLRQFPQAKP-LINKPLVVAPS-SLVNNWK  314 (776)
T ss_pred             hcCchHHHHHHHHHhhhhcccccCCCCceEeeCCCCcchHHHH-HHHHHHHHHhCcCccc-cccccEEEccH-HHHHHHH
Confidence            46899999987765   232       2788888999999976 5566666665443111 12469999997 7788888


Q ss_pred             HHHHHHHhhcCCceeEEeeCCCCh--HHHHHHHhc-----CCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          128 EILQKLLHRFRWIVPGYVMGGGNR--SKEKARLRK-----GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~l~~-----~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                      +.+.+|... ..+....++++...  ......+.-     ..-|++.+.+.+.+++..   +....+++||+||.|++-.
T Consensus       315 kEF~KWl~~-~~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~---il~~~~glLVcDEGHrlkN  390 (776)
T KOG0390|consen  315 KEFGKWLGN-HRINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRK---ILLIRPGLLVCDEGHRLKN  390 (776)
T ss_pred             HHHHHhccc-cccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH---HhcCCCCeEEECCCCCccc
Confidence            888887653 22444444444442  111111111     135778888887765543   3335789999999999754


Q ss_pred             CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecc-hhHHHHHH-HhcCCCEEEEcCCC
Q 043110          201 LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLN-EKVNHLTK-ISLETPVLIGLDEK  265 (316)
Q Consensus       201 ~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~-~~v~~~~~-~~l~~p~~i~~~~~  265 (316)
                      .  ...+...+..+.                -.+.|++|.|+= .++.++.. ..+.+|-.++...+
T Consensus       391 ~--~s~~~kaL~~l~----------------t~rRVLLSGTp~QNdl~EyFnlL~fvrP~~Lgs~~s  439 (776)
T KOG0390|consen  391 S--DSLTLKALSSLK----------------TPRRVLLTGTPIQNDLKEYFNLLDFVRPGFLGSISS  439 (776)
T ss_pred             h--hhHHHHHHHhcC----------------CCceEEeeCCcccccHHHHHHHHhhcChhhccchHH
Confidence            2  223333344443                456788899974 45666554 45668877765443

>COG4889 Predicted helicase [General function prediction only]

Probab=98.26  E-value=5.7e-06  Score=81.19  Aligned_cols=149  Identities=22%  Similarity=0.161  Sum_probs=87.2

Q ss_pred             CcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCC----cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCe
Q 043110           36 CFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGR----DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT  111 (316)
Q Consensus        36 ~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~----d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~  111 (316)
                      .|+.+.- .++...+ --..-.+|+|+|+.|+....+|-    ..=+.+.-|+|||+..+ -+.+.+..          .
T Consensus       141 DW~~f~p-~e~~~nl-~l~~~kk~R~hQq~Aid~a~~~F~~n~RGkLIMAcGTGKTfTsL-kisEala~----------~  207 (1518)
T COG4889         141 DWDIFDP-TELQDNL-PLKKPKKPRPHQQTAIDAAKEGFSDNDRGKLIMACGTGKTFTSL-KISEALAA----------A  207 (1518)
T ss_pred             ChhhcCc-ccccccc-ccCCCCCCChhHHHHHHHHHhhcccccCCcEEEecCCCccchHH-HHHHHHhh----------h
Confidence            4444432 3334444 22345679999999999988652    13344556999999864 34444433          4


Q ss_pred             eEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCC--------------------ChH---HHHH--HHhcCCcEEE
Q 043110          112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGG--------------------NRS---KEKA--RLRKGISILV  166 (316)
Q Consensus       112 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~--------------------~~~---~~~~--~l~~~~~IlV  166 (316)
                      ++|+|+|+.+|..|..+....-..  ..+....++...                    +..   ..+.  .-..+--|+.
T Consensus       208 ~iL~LvPSIsLLsQTlrew~~~~~--l~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvF  285 (1518)
T COG4889         208 RILFLVPSISLLSQTLREWTAQKE--LDFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVF  285 (1518)
T ss_pred             heEeecchHHHHHHHHHHHhhccC--ccceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEE
Confidence            499999999999887765543221  112222222111                    011   1111  1122345889


Q ss_pred             eCcHHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          167 ATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       167 ~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                      +|...+...-.. ....+..++++|.||||+-..
T Consensus       286 sTYQSl~~i~eA-Qe~G~~~fDliicDEAHRTtG  318 (1518)
T COG4889         286 STYQSLPRIKEA-QEAGLDEFDLIICDEAHRTTG  318 (1518)
T ss_pred             EcccchHHHHHH-HHcCCCCccEEEecchhcccc
Confidence            998877654332 333456899999999998654

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

Probab=98.22  E-value=2.5e-05  Score=74.87  Aligned_cols=167  Identities=19%  Similarity=0.157  Sum_probs=91.8

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH-HHhh
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK-LLHR  136 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~-~~~~  136 (316)
                      .-..++.+.+..+-.++-+++.+.||||||.-    +.+.+.... ..  .+| .+-+--|.|.-|..+++.+.. +...
T Consensus       356 Pvf~~R~~ll~~ir~n~vvvivgETGSGKTTQ----l~QyL~edG-Y~--~~G-mIGcTQPRRvAAiSVAkrVa~EM~~~  427 (1042)
T KOG0924|consen  356 PVFACRDQLLSVIRENQVVVIVGETGSGKTTQ----LAQYLYEDG-YA--DNG-MIGCTQPRRVAAISVAKRVAEEMGVT  427 (1042)
T ss_pred             chHHHHHHHHHHHhhCcEEEEEecCCCCchhh----hHHHHHhcc-cc--cCC-eeeecCchHHHHHHHHHHHHHHhCCc
Confidence            34567777777777788899999999999986    334443311 10  111 233445888888777765433 3222


Q ss_pred             cCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          137 FRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      ++ ..+++.+.=.+.-      .....|=..|-|.|+.-.-  ..-.+...+.+|+||||.=.-  -.+.+-.+++....
T Consensus       428 lG-~~VGYsIRFEdvT------~~~T~IkymTDGiLLrEsL--~d~~L~kYSviImDEAHERsl--NtDilfGllk~~la  496 (1042)
T KOG0924|consen  428 LG-DTVGYSIRFEDVT------SEDTKIKYMTDGILLRESL--KDRDLDKYSVIIMDEAHERSL--NTDILFGLLKKVLA  496 (1042)
T ss_pred             cc-cccceEEEeeecC------CCceeEEEeccchHHHHHh--hhhhhhheeEEEechhhhccc--chHHHHHHHHHHHH
Confidence            12 1122211100000      1234588999998876433  223455788999999996221  11222223322221


Q ss_pred             CcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCC
Q 043110          217 RNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETP  257 (316)
Q Consensus       217 ~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p  257 (316)
                      .            .....+|..||||..  ++|..-|-.-|
T Consensus       497 r------------RrdlKliVtSATm~a--~kf~nfFgn~p  523 (1042)
T KOG0924|consen  497 R------------RRDLKLIVTSATMDA--QKFSNFFGNCP  523 (1042)
T ss_pred             h------------hccceEEEeeccccH--HHHHHHhCCCc
Confidence            0            116789999999973  55555444333

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=98.22  E-value=1.9e-05  Score=77.80  Aligned_cols=155  Identities=16%  Similarity=0.152  Sum_probs=96.1

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE  154 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (316)
                      -.++.||.|||||.+..-++-+.+..        .+.++|+|+-.++|+.++...++...-  ...+...-.++....  
T Consensus        51 V~vVRSpMGTGKTtaLi~wLk~~l~~--------~~~~VLvVShRrSL~~sL~~rf~~~~l--~gFv~Y~d~~~~~i~--  118 (824)
T PF02399_consen   51 VLVVRSPMGTGKTTALIRWLKDALKN--------PDKSVLVVSHRRSLTKSLAERFKKAGL--SGFVNYLDSDDYIID--  118 (824)
T ss_pred             eEEEECCCCCCcHHHHHHHHHHhccC--------CCCeEEEEEhHHHHHHHHHHHHhhcCC--Ccceeeecccccccc--
Confidence            37999999999998864444333322        345599999999999999888875421  111111111111000  


Q ss_pred             HHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHH-------HHHHHhccCcccccCCCCc
Q 043110          155 KARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIE-------EILDILGSRNIASIGEGNE  227 (316)
Q Consensus       155 ~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~-------~i~~~l~~~~~~~~~~~~~  227 (316)
                          ....+-+++..+.|....    ...+.+.++|||||+...+..-|.+.++       .+...+..           
T Consensus       119 ----~~~~~rLivqIdSL~R~~----~~~l~~yDvVIIDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~-----------  179 (824)
T PF02399_consen  119 ----GRPYDRLIVQIDSLHRLD----GSLLDRYDVVIIDEVMSVLNQLFSPTMRQREEVDNLLKELIRN-----------  179 (824)
T ss_pred             ----ccccCeEEEEehhhhhcc----cccccccCEEEEehHHHHHHHHhHHHHhhHHHHHHHHHHHHHh-----------
Confidence                012456667766665433    2234568999999999888764433322       23333333           


Q ss_pred             cccccceEEEEeeecchhHHHHHHHhc-CCCEEEEcCC
Q 043110          228 VSNVKRQNLLLSATLNEKVNHLTKISL-ETPVLIGLDE  264 (316)
Q Consensus       228 ~~~~~~q~i~~SAT~~~~v~~~~~~~l-~~p~~i~~~~  264 (316)
                          ...+|++-|++.+...++..... ..++.+.+.+
T Consensus       180 ----ak~VI~~DA~ln~~tvdFl~~~Rp~~~i~vI~n~  213 (824)
T PF02399_consen  180 ----AKTVIVMDADLNDQTVDFLASCRPDENIHVIVNT  213 (824)
T ss_pred             ----CCeEEEecCCCCHHHHHHHHHhCCCCcEEEEEee
Confidence                56899999999999999888754 3555555444

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

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

Probab=98.14  E-value=7.8e-05  Score=69.06  Aligned_cols=179  Identities=17%  Similarity=0.123  Sum_probs=94.1

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      .+.|...+.++.-.+.|+++-... -...+.+-+..+.+++-+++.+.||||||.-.--.++.......        ..+
T Consensus        24 ~Npf~~~p~s~rY~~ilk~R~~LP-vw~~k~~F~~~l~~nQ~~v~vGetgsGKttQiPq~~~~~~~~~~--------~~v   94 (699)
T KOG0925|consen   24 INPFNGKPYSQRYYDILKKRRELP-VWEQKEEFLKLLLNNQIIVLVGETGSGKTTQIPQFVLEYELSHL--------TGV   94 (699)
T ss_pred             cCCCCCCcCcHHHHHHHHHHhcCc-hHHhHHHHHHHHhcCceEEEEecCCCCccccCcHHHHHHHHhhc--------cce
Confidence            678999999999999996653322 22333444566667788999999999999752111222222211        115


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      ..--|.|--|.+++.+...-..-.-..-+++.+.-.+......      -.-.+|-++|+.-.-+  .-.+.....+|+|
T Consensus        95 ~CTQprrvaamsva~RVadEMDv~lG~EVGysIrfEdC~~~~T------~Lky~tDgmLlrEams--~p~l~~y~viiLD  166 (699)
T KOG0925|consen   95 ACTQPRRVAAMSVAQRVADEMDVTLGEEVGYSIRFEDCTSPNT------LLKYCTDGMLLREAMS--DPLLGRYGVIILD  166 (699)
T ss_pred             eecCchHHHHHHHHHHHHHHhccccchhccccccccccCChhH------HHHHhcchHHHHHHhh--CcccccccEEEec
Confidence            5556888777776654432211000001111110001000000      0124555655543332  2345678999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecc
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLN  243 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~  243 (316)
                      |||.=.=  -.+.+..+++....            ..+...+|.+|||+-
T Consensus       167 eahERtl--ATDiLmGllk~v~~------------~rpdLk~vvmSatl~  202 (699)
T KOG0925|consen  167 EAHERTL--ATDILMGLLKEVVR------------NRPDLKLVVMSATLD  202 (699)
T ss_pred             hhhhhhH--HHHHHHHHHHHHHh------------hCCCceEEEeecccc
Confidence            9995211  11223333333222            112789999999986

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

Probab=98.12  E-value=5e-05  Score=72.69  Aligned_cols=168  Identities=17%  Similarity=0.165  Sum_probs=95.3

Q ss_pred             cHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHH-HHHHHhhcC
Q 043110           60 TKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI-LQKLLHRFR  138 (316)
Q Consensus        60 ~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~-~~~~~~~~~  138 (316)
                      +++-.+.+.++...+-++|.|.||||||.-  +|  +.|....-   ...|.++=+--|.|--|..++.+ .+.++-.++
T Consensus       267 y~ykdell~av~e~QVLiI~GeTGSGKTTQ--iP--QyL~EaGy---tk~gk~IgcTQPRRVAAmSVAaRVA~EMgvkLG  339 (902)
T KOG0923|consen  267 YPYKDELLKAVKEHQVLIIVGETGSGKTTQ--IP--QYLYEAGY---TKGGKKIGCTQPRRVAAMSVAARVAEEMGVKLG  339 (902)
T ss_pred             hhhHHHHHHHHHhCcEEEEEcCCCCCcccc--cc--HHHHhccc---ccCCceEeecCcchHHHHHHHHHHHHHhCcccc
Confidence            455566777888888999999999999976  33  33332111   11233455666888888777654 444443332


Q ss_pred             CceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCc
Q 043110          139 WIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRN  218 (316)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~  218 (316)
                      ..+ ++.+.=.+.-      ....-|=+.|-|+|+.-+.  ....+...+.+||||||.=.-  .-+.+-.++..+.+  
T Consensus       340 ~eV-GYsIRFEdcT------SekTvlKYMTDGmLlREfL--~epdLasYSViiiDEAHERTL--~TDILfgLvKDIar--  406 (902)
T KOG0923|consen  340 HEV-GYSIRFEDCT------SEKTVLKYMTDGMLLREFL--SEPDLASYSVIIVDEAHERTL--HTDILFGLVKDIAR--  406 (902)
T ss_pred             ccc-ceEEEecccc------CcceeeeeecchhHHHHHh--ccccccceeEEEeehhhhhhh--hhhHHHHHHHHHHh--
Confidence            111 1111100100      1123477999999988665  345667899999999995211  11222222222221  


Q ss_pred             ccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEE
Q 043110          219 IASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVL  259 (316)
Q Consensus       219 ~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~  259 (316)
                                -.+...+++.|||+..  .+|..-|-.-|++
T Consensus       407 ----------~RpdLKllIsSAT~DA--ekFS~fFDdapIF  435 (902)
T KOG0923|consen  407 ----------FRPDLKLLISSATMDA--EKFSAFFDDAPIF  435 (902)
T ss_pred             ----------hCCcceEEeeccccCH--HHHHHhccCCcEE
Confidence                      1127789999999973  4444434344444

>PRK10536 hypothetical protein; Provisional

Probab=98.12  E-value=0.00016  Score=62.77  Aligned_cols=139  Identities=18%  Similarity=0.153  Sum_probs=77.0

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH-------H
Q 043110           54 LGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL-------V  126 (316)
Q Consensus        54 ~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q-------~  126 (316)
                      .++..-+..|...+..+.++..+++.|++|+|||+..+..+++.+...       .--+++|.=|+.+..+.       .
T Consensus        55 ~~i~p~n~~Q~~~l~al~~~~lV~i~G~aGTGKT~La~a~a~~~l~~~-------~~~kIiI~RP~v~~ge~LGfLPG~~  127 (262)
T PRK10536         55 SPILARNEAQAHYLKAIESKQLIFATGEAGCGKTWISAAKAAEALIHK-------DVDRIIVTRPVLQADEDLGFLPGDI  127 (262)
T ss_pred             ccccCCCHHHHHHHHHHhcCCeEEEECCCCCCHHHHHHHHHHHHHhcC-------CeeEEEEeCCCCCchhhhCcCCCCH
Confidence            356667889999999888888899999999999998877676665431       12235555566542211       1


Q ss_pred             HHHHHHHHhhcCCceeEEeeCCCChHHHHHHH-h-cCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcH
Q 043110          127 YEILQKLLHRFRWIVPGYVMGGGNRSKEKARL-R-KGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFG  204 (316)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~  204 (316)
                      .+.+..+......... ...+.    .....+ . ..-.|-|..    +.+++. ..+   +-.++|+|||+.+.    .
T Consensus       128 ~eK~~p~~~pi~D~L~-~~~~~----~~~~~~~~~~~~~Iei~~----l~ymRG-rtl---~~~~vIvDEaqn~~----~  190 (262)
T PRK10536        128 AEKFAPYFRPVYDVLV-RRLGA----SFMQYCLRPEIGKVEIAP----FAYMRG-RTF---ENAVVILDEAQNVT----A  190 (262)
T ss_pred             HHHHHHHHHHHHHHHH-HHhCh----HHHHHHHHhccCcEEEec----HHHhcC-Ccc---cCCEEEEechhcCC----H
Confidence            2222222211100000 00111    111111 1 112344444    333443 122   23799999999873    3


Q ss_pred             HHHHHHHHHhcc
Q 043110          205 KEIEEILDILGS  216 (316)
Q Consensus       205 ~~i~~i~~~l~~  216 (316)
                      ..+..++.+++.
T Consensus       191 ~~~k~~ltR~g~  202 (262)
T PRK10536        191 AQMKMFLTRLGE  202 (262)
T ss_pred             HHHHHHHhhcCC
Confidence            778888888876

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=98.10  E-value=4.7e-05  Score=77.25  Aligned_cols=170  Identities=15%  Similarity=0.181  Sum_probs=104.9

Q ss_pred             CcHHHHHHHHHHh--C--CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           59 PTKVQAQAIPVIL--S--GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        59 p~~~Q~~~i~~il--~--g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      ++.+|++.+.++.  +  +-+.|++-..|-|||+-.+--+.................-.|||||. .|+--+...+.+++
T Consensus       976 LRkYQqEGVnWLaFLnky~LHGILcDDMGLGKTLQticilAsd~y~r~s~~~e~~~~PSLIVCPs-TLtGHW~~E~~kf~ 1054 (1549)
T KOG0392|consen  976 LRKYQQEGVNWLAFLNKYKLHGILCDDMGLGKTLQTICILASDHYKRRSESSEFNRLPSLIVCPS-TLTGHWKSEVKKFF 1054 (1549)
T ss_pred             HHHHHHhccHHHHHHHHhcccceeeccccccHHHHHHHHHHHHHHhhcccchhhccCCeEEECCc-hhhhHHHHHHHHhc
Confidence            4779999887653  2  34789999999999997543333333332222222223338999997 67766666666655


Q ss_pred             hhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHh
Q 043110          135 HRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDIL  214 (316)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l  214 (316)
                         +...+....|+...+...+.-.++.+|+|++.+.+..-+..   +.-.+..|+|+||-|.+-.  -...+....+.+
T Consensus      1055 ---pfL~v~~yvg~p~~r~~lR~q~~~~~iiVtSYDv~RnD~d~---l~~~~wNYcVLDEGHVikN--~ktkl~kavkqL 1126 (1549)
T KOG0392|consen 1055 ---PFLKVLQYVGPPAERRELRDQYKNANIIVTSYDVVRNDVDY---LIKIDWNYCVLDEGHVIKN--SKTKLTKAVKQL 1126 (1549)
T ss_pred             ---chhhhhhhcCChHHHHHHHhhccccceEEeeHHHHHHHHHH---HHhcccceEEecCcceecc--hHHHHHHHHHHH
Confidence               33444444455555555555556679999998876532211   1113567999999998754  345555666666


Q ss_pred             ccCcccccCCCCccccccceEEEEeeec-chhHHHHHHHh
Q 043110          215 GSRNIASIGEGNEVSNVKRQNLLLSATL-NEKVNHLTKIS  253 (316)
Q Consensus       215 ~~~~~~~~~~~~~~~~~~~q~i~~SAT~-~~~v~~~~~~~  253 (316)
                      ..               + ..+++|.|. -+++.++-.+|
T Consensus      1127 ~a---------------~-hRLILSGTPIQNnvleLWSLF 1150 (1549)
T KOG0392|consen 1127 RA---------------N-HRLILSGTPIQNNVLELWSLF 1150 (1549)
T ss_pred             hh---------------c-ceEEeeCCCcccCHHHHHHHH
Confidence            53               3 445667775 45566655543

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=98.08  E-value=3.2e-05  Score=71.66  Aligned_cols=151  Identities=20%  Similarity=0.232  Sum_probs=91.9

Q ss_pred             CCCcHHHHHHHHHHh-CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           57 EAPTKVQAQAIPVIL-SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il-~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      +.+.|+|.+.+...+ .|..+++.-..|-|||+-++- +.......-+         .||+||. .+-.-+.+.+..++.
T Consensus       197 s~LlPFQreGv~faL~RgGR~llADeMGLGKTiQAla-IA~yyraEwp---------lliVcPA-svrftWa~al~r~lp  265 (689)
T KOG1000|consen  197 SRLLPFQREGVIFALERGGRILLADEMGLGKTIQALA-IARYYRAEWP---------LLIVCPA-SVRFTWAKALNRFLP  265 (689)
T ss_pred             HhhCchhhhhHHHHHhcCCeEEEecccccchHHHHHH-HHHHHhhcCc---------EEEEecH-HHhHHHHHHHHHhcc
Confidence            346789999887765 677899999999999997643 3333322111         8999997 444556666666654


Q ss_pred             hcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhc
Q 043110          136 RFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILG  215 (316)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~  215 (316)
                      ....  ..++.++.+....   +-....|.|.+.+.+..+-.   .....+.+.+|+||+|.|-+. -....+.++..+.
T Consensus       266 s~~p--i~vv~~~~D~~~~---~~t~~~v~ivSye~ls~l~~---~l~~~~~~vvI~DEsH~Lk~s-ktkr~Ka~~dllk  336 (689)
T KOG1000|consen  266 SIHP--IFVVDKSSDPLPD---VCTSNTVAIVSYEQLSLLHD---ILKKEKYRVVIFDESHMLKDS-KTKRTKAATDLLK  336 (689)
T ss_pred             cccc--eEEEecccCCccc---cccCCeEEEEEHHHHHHHHH---HHhcccceEEEEechhhhhcc-chhhhhhhhhHHH
Confidence            3221  2233333332111   11124588888876654332   222345889999999988765 3333555555554


Q ss_pred             cCcccccCCCCccccccceEEEEeeec
Q 043110          216 SRNIASIGEGNEVSNVKRQNLLLSATL  242 (316)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~q~i~~SAT~  242 (316)
                      .               -.++|++|.|.
T Consensus       337 ~---------------akhvILLSGTP  348 (689)
T KOG1000|consen  337 V---------------AKHVILLSGTP  348 (689)
T ss_pred             H---------------hhheEEecCCc
Confidence            4               45677778774

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length

Probab=98.08  E-value=0.00012  Score=62.36  Aligned_cols=155  Identities=19%  Similarity=0.207  Sum_probs=96.3

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhC---CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCe
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILS---GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT  111 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~---g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~  111 (316)
                      .+|+-...+.+++=.+ + .++- .++.|.+....+.+   |+|.+.+.-+|.|||.+ ++|++..+.....       .
T Consensus         3 ~~w~p~~~P~wLl~E~-e-~~il-iR~~Q~~ia~~mi~~~~~~n~v~QlnMGeGKTsV-I~Pmla~~LAdg~-------~   71 (229)
T PF12340_consen    3 RNWDPMEYPDWLLFEI-E-SNIL-IRPVQVEIAREMISPPSGKNSVMQLNMGEGKTSV-IVPMLALALADGS-------R   71 (229)
T ss_pred             CCCCchhChHHHHHHH-H-cCce-eeHHHHHHHHHHhCCCCCCCeEeeecccCCccch-HHHHHHHHHcCCC-------c
Confidence            5677777777777666 3 3665 79999999888774   67999999999999976 5778777665322       2


Q ss_pred             eEEEEeCChHHHHHHHHHHHHHHhhcCCceeEE--eeCCCCh--H--HHH----HHHhcCCcEEEeCcHHHHHHHhc---
Q 043110          112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGY--VMGGGNR--S--KEK----ARLRKGISILVATPGHLLDHLKH---  178 (316)
Q Consensus       112 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~--~~~~~~~--~--~~~----~~l~~~~~IlV~Tp~~l~~~l~~---  178 (316)
                      .+.+++| ++|..|.++.++......-...+..  +......  .  ...    ......-.|+++||+.++.+.-.   
T Consensus        72 LvrviVp-k~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf~L~~le  150 (229)
T PF12340_consen   72 LVRVIVP-KALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSFKLKGLE  150 (229)
T ss_pred             EEEEEcC-HHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHHHHHHHH
Confidence            3566666 4799999998887765432221111  1111111  1  111    12223447999999987654311   


Q ss_pred             ----CCc----------cccCceeEEEEecchhhhcC
Q 043110          179 ----TSS----------FLHTNLRWIIFDEADRILEL  201 (316)
Q Consensus       179 ----~~~----------~~~~~l~~lViDEad~l~~~  201 (316)
                          ...          ..+.+-..=|+||+|..+..
T Consensus       151 ~l~~~~~~~~~~l~~~q~~l~~~~rdilDEsDe~L~~  187 (229)
T PF12340_consen  151 RLQDGKPEEARELLKIQKWLDEHSRDILDESDEILSV  187 (229)
T ss_pred             HHHhcCHHHHHHHHHHHHHHHhcCCeEeECchhccCc
Confidence                010          01123344688999987764

There are two conserved sequence motifs: LLE and NMG.

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=98.06  E-value=0.00012  Score=71.84  Aligned_cols=148  Identities=21%  Similarity=0.221  Sum_probs=82.7

Q ss_pred             HHHHHHHHHcCCCC-CcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           45 TLCDQLRERLGFEA-PTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        45 ~l~~~l~~~~g~~~-p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      .+.+.|...|+... ..++|+.|+-..+.++-.++.+++|+|||.... .++..+....    .....++++++||..-|
T Consensus       138 ~~~~~l~~lf~~~~~~~d~Qk~Av~~a~~~~~~vItGgpGTGKTt~v~-~ll~~l~~~~----~~~~~~i~l~APTgkAA  212 (615)
T PRK10875        138 LLRQTLDALFGPVTDEVDWQKVAAAVALTRRISVISGGPGTGKTTTVA-KLLAALIQLA----DGERCRIRLAAPTGKAA  212 (615)
T ss_pred             HHHHHHHHhcCcCCCCCHHHHHHHHHHhcCCeEEEEeCCCCCHHHHHH-HHHHHHHHhc----CCCCcEEEEECCcHHHH
Confidence            34445533344331 358999999999998899999999999998742 2333332211    11235688999999888


Q ss_pred             HHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCC-----ccccCceeEEEEecchhh
Q 043110          124 LLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTS-----SFLHTNLRWIIFDEADRI  198 (316)
Q Consensus       124 ~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~-----~~~~~~l~~lViDEad~l  198 (316)
                      ..+.+.+.........          . ...    ......-..|-.+++.......     ....-..+++|||||-++
T Consensus       213 ~rL~e~~~~~~~~~~~----------~-~~~----~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIvDEaSMv  277 (615)
T PRK10875        213 ARLTESLGKALRQLPL----------T-DEQ----KKRIPEEASTLHRLLGAQPGSQRLRYHAGNPLHLDVLVVDEASMV  277 (615)
T ss_pred             HHHHHHHHhhhhcccc----------c-hhh----hhcCCCchHHHHHHhCcCCCccchhhccccCCCCCeEEEChHhcc
Confidence            7777666543322110          0 000    0000111222222222111100     011124689999999865


Q ss_pred             hcCCcHHHHHHHHHHhcc
Q 043110          199 LELGFGKEIEEILDILGS  216 (316)
Q Consensus       199 ~~~~~~~~i~~i~~~l~~  216 (316)
                       |   ...+..+++.++.
T Consensus       278 -d---~~lm~~ll~al~~  291 (615)
T PRK10875        278 -D---LPMMARLIDALPP  291 (615)
T ss_pred             -c---HHHHHHHHHhccc
Confidence             3   3667778888876

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=98.05  E-value=3.1e-05  Score=71.37  Aligned_cols=108  Identities=27%  Similarity=0.308  Sum_probs=64.8

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE  154 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (316)
                      -++|.|..|||||+..+- ++..+..      ...+..++++++..+|...+.+.+.....  .                
T Consensus         3 v~~I~G~aGTGKTvla~~-l~~~l~~------~~~~~~~~~l~~n~~l~~~l~~~l~~~~~--~----------------   57 (352)
T PF09848_consen    3 VILITGGAGTGKTVLALN-LAKELQN------SEEGKKVLYLCGNHPLRNKLREQLAKKYN--P----------------   57 (352)
T ss_pred             EEEEEecCCcCHHHHHHH-HHHHhhc------cccCCceEEEEecchHHHHHHHHHhhhcc--c----------------
Confidence            378999999999998643 3333311      12355599999999999887776655320  0                


Q ss_pred             HHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCC-------cHHHHHHHHHH
Q 043110          155 KARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELG-------FGKEIEEILDI  213 (316)
Q Consensus       155 ~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~-------~~~~i~~i~~~  213 (316)
                           ......+..|..+...+.. ........+++|+||||+|.+.+       ....+..+++.
T Consensus        58 -----~~~~~~~~~~~~~i~~~~~-~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~  117 (352)
T PF09848_consen   58 -----KLKKSDFRKPTSFINNYSE-SDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKR  117 (352)
T ss_pred             -----chhhhhhhhhHHHHhhccc-ccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhc
Confidence                 0011223333333332221 12233578899999999998832       23556666655

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>KOG1803 consensus DNA helicase [Replication, recombination and repair]

Probab=98.05  E-value=1.9e-05  Score=74.89  Aligned_cols=64  Identities=22%  Similarity=0.305  Sum_probs=51.9

Q ss_pred             CCcHHHHHHHHHHhCCCc-EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSGRD-VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEIL  130 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d-~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~  130 (316)
                      .+.+-|++|+....+.++ .++.||+|+|||.+...-+.+.+.+         +.++|+.+||.+-+.-+.+++
T Consensus       185 ~ln~SQk~Av~~~~~~k~l~~I~GPPGTGKT~TlvEiI~qlvk~---------~k~VLVcaPSn~AVdNiverl  249 (649)
T KOG1803|consen  185 NLNSSQKAAVSFAINNKDLLIIHGPPGTGKTRTLVEIISQLVKQ---------KKRVLVCAPSNVAVDNIVERL  249 (649)
T ss_pred             cccHHHHHHHHHHhccCCceEeeCCCCCCceeeHHHHHHHHHHc---------CCeEEEEcCchHHHHHHHHHh
Confidence            467899999999888876 7999999999999876655555544         455999999999988888754

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=97.99  E-value=0.00018  Score=70.33  Aligned_cols=134  Identities=21%  Similarity=0.198  Sum_probs=76.7

Q ss_pred             cHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCC
Q 043110           60 TKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRW  139 (316)
Q Consensus        60 ~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~  139 (316)
                      .++|+.|+..++.++-+++.|+.|+|||... ..++..+....+.   ....++++.+||..-+..+.+.+.........
T Consensus       147 ~~~Qk~A~~~al~~~~~vitGgpGTGKTt~v-~~ll~~l~~~~~~---~~~~~I~l~APTGkAA~rL~e~~~~~~~~l~~  222 (586)
T TIGR01447       147 QNWQKVAVALALKSNFSLITGGPGTGKTTTV-ARLLLALVKQSPK---QGKLRIALAAPTGKAAARLAESLRKAVKNLAA  222 (586)
T ss_pred             cHHHHHHHHHHhhCCeEEEEcCCCCCHHHHH-HHHHHHHHHhccc---cCCCcEEEECCcHHHHHHHHHHHHhhhccccc
Confidence            4799999999999999999999999999864 2233333322111   01246999999988777766655443221110


Q ss_pred             ceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCC-----ccccCceeEEEEecchhhhcCCcHHHHHHHHHHh
Q 043110          140 IVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTS-----SFLHTNLRWIIFDEADRILELGFGKEIEEILDIL  214 (316)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~-----~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l  214 (316)
                                . ...    .....+-..|-.+++.......     ......+++||||||-++ +   ...+..+++.+
T Consensus       223 ----------~-~~~----~~~~~~~a~TiHrlLg~~~~~~~~~~~~~~~l~~dvlIiDEaSMv-d---~~l~~~ll~al  283 (586)
T TIGR01447       223 ----------A-EAL----IAALPSEAVTIHRLLGIKPDTKRFRHHERNPLPLDVLVVDEASMV-D---LPLMAKLLKAL  283 (586)
T ss_pred             ----------c-hhh----hhccccccchhhhhhcccCCcchhhhcccCCCcccEEEEcccccC-C---HHHHHHHHHhc
Confidence                      0 000    0001111233333332211100     011225789999999865 3   35677788887


Q ss_pred             cc
Q 043110          215 GS  216 (316)
Q Consensus       215 ~~  216 (316)
                      +.
T Consensus       284 ~~  285 (586)
T TIGR01447       284 PP  285 (586)
T ss_pred             CC
Confidence            75

This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model.

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=97.98  E-value=6.6e-05  Score=66.30  Aligned_cols=162  Identities=17%  Similarity=0.117  Sum_probs=102.2

Q ss_pred             CcHHHHHHHHHHh----------CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           59 PTKVQAQAIPVIL----------SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        59 p~~~Q~~~i~~il----------~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      ++..|.+++-...          .+.-+++--.||.||--...--+++...+.        ..++|+++.+..|-....+
T Consensus        38 LS~~QLEaV~yA~q~h~~~Lp~~~R~Gf~lGDGtGvGKGR~iAgiI~~n~l~G--------r~r~vwvS~s~dL~~Da~R  109 (303)
T PF13872_consen   38 LSALQLEAVIYACQRHEQILPGGSRAGFFLGDGTGVGKGRQIAGIILENWLRG--------RKRAVWVSVSNDLKYDAER  109 (303)
T ss_pred             ccHHHHHHHHHHHHHHHhhcccccCcEEEeccCCCcCccchhHHHHHHHHHcC--------CCceEEEECChhhhhHHHH
Confidence            5788888876554          233588888999998776555566666552        2349999999999999888


Q ss_pred             HHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcC--Ccccc--------Cce-eEEEEecchh
Q 043110          129 ILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHT--SSFLH--------TNL-RWIIFDEADR  197 (316)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~--~~~~~--------~~l-~~lViDEad~  197 (316)
                      .++.++...  +.+..+.. .... .  ...-.-.|+.+|...|...-...  ....+        .+. .+||+||||.
T Consensus       110 Dl~DIG~~~--i~v~~l~~-~~~~-~--~~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~W~g~dfdgvivfDEcH~  183 (303)
T PF13872_consen  110 DLRDIGADN--IPVHPLNK-FKYG-D--IIRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVDWCGEDFDGVIVFDECHK  183 (303)
T ss_pred             HHHHhCCCc--ccceechh-hccC-c--CCCCCCCccchhHHHHHhHHhccCCccchHHHHHHHHhcCCCceEEeccchh
Confidence            888877542  11111110 0000 0  01112368999988776654221  00000        112 3899999999


Q ss_pred             hhcCCc--------HHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHH
Q 043110          198 ILELGF--------GKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLT  250 (316)
Q Consensus       198 l~~~~~--------~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~  250 (316)
                      .-...-        +..+..+.+.+|                +.+++.+|||-..+..++.
T Consensus       184 akn~~~~~~~~sk~g~avl~LQ~~LP----------------~ARvvY~SATgasep~Nma  228 (303)
T PF13872_consen  184 AKNLSSGSKKPSKTGIAVLELQNRLP----------------NARVVYASATGASEPRNMA  228 (303)
T ss_pred             cCCCCccCccccHHHHHHHHHHHhCC----------------CCcEEEecccccCCCceee
Confidence            765422        245556666676                5679999999988888774

>KOG0952 consensus DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification]

Probab=97.97  E-value=5.5e-06  Score=82.62  Aligned_cols=143  Identities=20%  Similarity=0.166  Sum_probs=93.3

Q ss_pred             CCcHHHHHHHHHHh-CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhh
Q 043110           58 APTKVQAQAIPVIL-SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHR  136 (316)
Q Consensus        58 ~p~~~Q~~~i~~il-~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~  136 (316)
                      ...|+|.+.+-.+. ...++++-+|||+|||++|.+++...+..       .++.+++|++|..+|+..-.+...+....
T Consensus       927 ~fn~~q~~if~~~y~td~~~~~g~ptgsgkt~~ae~a~~~~~~~-------~p~~kvvyIap~kalvker~~Dw~~r~~~  999 (1230)
T KOG0952|consen  927 YFNPIQTQIFHCLYHTDLNFLLGAPTGSGKTVVAELAIFRALSY-------YPGSKVVYIAPDKALVKERSDDWSKRDEL  999 (1230)
T ss_pred             ccCCccceEEEEEeecchhhhhcCCccCcchhHHHHHHHHHhcc-------CCCccEEEEcCCchhhcccccchhhhccc
Confidence            34556655443322 23568999999999999999988877655       34567999999999997766655554322


Q ss_pred             cCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCC-ccccCceeEEEEecchhhhcCCcHHHHHHHHH
Q 043110          137 FRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTS-SFLHTNLRWIIFDEADRILELGFGKEIEEILD  212 (316)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~-~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~  212 (316)
                       +.....-..|.....  .. -...++++|+||++.....+++. .-.+.++..+|+||.|++-+ ++++-++.+..
T Consensus      1000 -~g~k~ie~tgd~~pd--~~-~v~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~iv~de~hllg~-~rgPVle~ivs 1071 (1230)
T KOG0952|consen 1000 -PGIKVIELTGDVTPD--VK-AVREADIVITTPEKWDGISRSWQTRKYVQSVSLIVLDEIHLLGE-DRGPVLEVIVS 1071 (1230)
T ss_pred             -CCceeEeccCccCCC--hh-heecCceEEcccccccCccccccchhhhccccceeecccccccC-CCcceEEEEee
Confidence             223333333333322  11 12346899999999988777543 23456899999999998654 45544444433

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=97.95  E-value=6.2e-05  Score=69.82  Aligned_cols=129  Identities=20%  Similarity=0.279  Sum_probs=85.1

Q ss_pred             CCcHHHHHHHHHHhCCC-----cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSGR-----DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~-----d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      .+-|+|++.+-++....     -.++.-..|.|||.-.+..++..+.          +...||++|+.+|. |+.+.+..
T Consensus       184 ~LL~fQkE~l~Wl~~QE~Ss~~GGiLADEMGMGKTIQtIaLllae~~----------ra~tLVvaP~VAlm-QW~nEI~~  252 (791)
T KOG1002|consen  184 PLLPFQKEGLAWLTSQEESSVAGGILADEMGMGKTIQTIALLLAEVD----------RAPTLVVAPTVALM-QWKNEIER  252 (791)
T ss_pred             cchhhhHHHHHHHHHhhhhhhccceehhhhccchHHHHHHHHHhccc----------cCCeeEEccHHHHH-HHHHHHHH
Confidence            35689999887765433     2577889999999876544444221          23399999999974 77777777


Q ss_pred             HHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcC-Ccc-----------ccC--ceeEEEEecchhh
Q 043110          133 LLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHT-SSF-----------LHT--NLRWIIFDEADRI  198 (316)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~-~~~-----------~~~--~l~~lViDEad~l  198 (316)
                      ...  + ....+++.|.........+. ++|++++|...+..-.+.. .++           .+.  ++--+|+||||.+
T Consensus       253 ~T~--g-slkv~~YhG~~R~~nikel~-~YDvVLTty~vvEs~yRk~~~GfrrKngv~ke~SlLHsi~~~RiIlDEAH~I  328 (791)
T KOG1002|consen  253 HTS--G-SLKVYIYHGAKRDKNIKELM-NYDVVLTTYAVVESVYRKQDYGFRRKNGVDKEKSLLHSIKFYRIILDEAHNI  328 (791)
T ss_pred             hcc--C-ceEEEEEecccccCCHHHhh-cCcEEEEecHHHHHHHHhccccccccCCcccccchhhhceeeeeehhhhccc
Confidence            764  2 33445555554444444443 5899999999887766541 111           112  2346899999998


Q ss_pred             hcC
Q 043110          199 LEL  201 (316)
Q Consensus       199 ~~~  201 (316)
                      -+.
T Consensus       329 K~R  331 (791)
T KOG1002|consen  329 KDR  331 (791)
T ss_pred             ccc
Confidence            764

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=97.92  E-value=5.8e-05  Score=74.16  Aligned_cols=146  Identities=20%  Similarity=0.239  Sum_probs=80.7

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc-----CCcee-EEeeCC
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF-----RWIVP-GYVMGG  148 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~-----~~~~~-~~~~~~  148 (316)
                      ++=|.+.||+|||+||+=.|.+.-..       -.-.+.||+|||.+.-+-++...+.....+     ..... .+.+. 
T Consensus        76 NiDI~METGTGKTy~YlrtmfeLhk~-------YG~~KFIivVPs~AIkeGv~~~s~~~~ehF~k~~Yent~~e~~i~~-  147 (985)
T COG3587          76 NIDILMETGTGKTYTYLRTMFELHKK-------YGLFKFIIVVPSLAIKEGVFLTSKETTEHFFKSEYENTRLESYIYD-  147 (985)
T ss_pred             eeeEEEecCCCceeeHHHHHHHHHHH-------hCceeEEEEeccHHHHhhhHHHHHHHHHHHhhhhccCcceeEEeec-
Confidence            68899999999999997766554332       124569999999998776555554444433     11111 22222 


Q ss_pred             CChHHHHHHHhcCCcEEEeCcHHHHHH------Hhc-----CCcc--------ccCce-eEEEEecchhhhcCCcHHHHH
Q 043110          149 GNRSKEKARLRKGISILVATPGHLLDH------LKH-----TSSF--------LHTNL-RWIIFDEADRILELGFGKEIE  208 (316)
Q Consensus       149 ~~~~~~~~~l~~~~~IlV~Tp~~l~~~------l~~-----~~~~--------~~~~l-~~lViDEad~l~~~~~~~~i~  208 (316)
                      .......-.....+.+++.|-..+-.-      +..     ....        .+..+ -++|+||-|++...  ...+.
T Consensus       148 ~~~~~~~~~~~~~~~vLl~~~~Afnk~~inan~iN~~s~~~~~~~~~~~spvd~la~~rPIvIvDEPh~f~~~--~k~~~  225 (985)
T COG3587         148 EDIEKFKFKSNNKPCVLLIFVSAFNKEEINANMINSESMENTNLFNGATSPVDALASMRPIVIVDEPHRFLGD--DKTYG  225 (985)
T ss_pred             hHHHHHhhccCCCceEEEEehhhhccccccccccchhhhcccCccccccCHHHHHHhcCCEEEecChhhcccc--hHHHH
Confidence            111111112223467777775543211      110     0100        01112 27999999998763  22233


Q ss_pred             HHHHHhccCcccccCCCCccccccce-EEEEeeecchhHHH
Q 043110          209 EILDILGSRNIASIGEGNEVSNVKRQ-NLLLSATLNEKVNH  248 (316)
Q Consensus       209 ~i~~~l~~~~~~~~~~~~~~~~~~~q-~i~~SAT~~~~v~~  248 (316)
                      .|.+.                  ++| ++=++||.++...+
T Consensus       226 ~i~~l------------------~pl~ilRfgATfkd~y~~  248 (985)
T COG3587         226 AIKQL------------------NPLLILRFGATFKDEYNN  248 (985)
T ss_pred             HHHhh------------------CceEEEEecccchhhhcC
Confidence            33332                  334 45599999988773

>KOG1132 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=97.92  E-value=9e-05  Score=73.11  Aligned_cols=81  Identities=20%  Similarity=0.234  Sum_probs=54.5

Q ss_pred             HcCCCCCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHHHHHhhhcC---CC------C--------------
Q 043110           53 RLGFEAPTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPIINHLQSYS---PR------I--------------  105 (316)
Q Consensus        53 ~~g~~~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~---~~------~--------------  105 (316)
                      +|.|+ |++.|..-+..++    .+.+.++.+|||+|||++.+=..+.......   +.      .              
T Consensus        17 ~fP~q-pY~~Q~a~M~rvl~~L~~~q~~llESPTGTGKSLsLLCS~LAW~q~~k~~~~~~~~s~~~~~~~p~~~s~~~g~   95 (945)
T KOG1132|consen   17 EFPFQ-PYPTQLAFMTRVLSCLDRKQNGLLESPTGTGKSLSLLCSTLAWQQHLKSRKPKGKISERKAGFIPTQPSDSGGE   95 (945)
T ss_pred             eccCC-cchHHHHHHHHHHHHHHHhhhhhccCCCCCCccHHHHHHHHHHHHHhhccccccchhhhhccccCCCCccCCCC
Confidence            46676 8999988776655    5578999999999999987654444332221   00      0              


Q ss_pred             ----CC------CCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110          106 ----DR------SSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus       106 ----~~------~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                          ..      -.-+++.|-+-|..-..|+.+.+++..
T Consensus        96 ~s~e~~e~~~~~~~ipkIyyaSRTHsQltQvvrElrrT~  134 (945)
T KOG1132|consen   96 KSEEAGEPIACYTGIPKIYYASRTHSQLTQVVRELRRTG  134 (945)
T ss_pred             chhhhcCccccccCCceEEEecchHHHHHHHHHHHhhcC
Confidence                00      114678888888888888887776653

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=97.90  E-value=8.1e-05  Score=75.61  Aligned_cols=161  Identities=20%  Similarity=0.249  Sum_probs=99.2

Q ss_pred             CCCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHH---HHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHH
Q 043110           57 EAPTKVQAQAIPVIL----SGRDVLVNAATGTGKTVA---YLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI  129 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~---~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~  129 (316)
                      .+++.+|.+.+..++    .+.++|+.-..|-|||+-   |+--+.+....        .|+ .|||+|...+ ..+.+.
T Consensus       369 ~~LRdyQLeGlNWl~~~W~~~~n~ILADEmgLgktvqti~fl~~l~~~~~~--------~gp-flvvvplst~-~~W~~e  438 (1373)
T KOG0384|consen  369 NELRDYQLEGLNWLLYSWYKRNNCILADEMGLGKTVQTITFLSYLFHSLQI--------HGP-FLVVVPLSTI-TAWERE  438 (1373)
T ss_pred             chhhhhhcccchhHHHHHHhcccceehhhcCCCcchHHHHHHHHHHHhhhc--------cCC-eEEEeehhhh-HHHHHH
Confidence            578999999887765    678999999999999974   33333333222        233 6888898664 445566


Q ss_pred             HHHHHhhcCCceeEEeeCCCChHHHHHHHh----c-----CCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          130 LQKLLHRFRWIVPGYVMGGGNRSKEKARLR----K-----GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~----~-----~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                      +..+.    .+.+.+.+|.....+..+...    .     ..+++++|.+.++.--...+.   -...++++||||+|-.
T Consensus       439 f~~w~----~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk~~L~~---i~w~~~~vDeahrLkN  511 (1373)
T KOG0384|consen  439 FETWT----DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDKAELSK---IPWRYLLVDEAHRLKN  511 (1373)
T ss_pred             HHHHh----hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhccHhhhcc---CCcceeeecHHhhcCc
Confidence            66665    244445555555444433321    1     368999999887652222111   2457999999999864


Q ss_pred             CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeec-chhHHHHHHH
Q 043110          201 LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATL-NEKVNHLTKI  252 (316)
Q Consensus       201 ~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~-~~~v~~~~~~  252 (316)
                      .  ...+...+..+..                ...++++.|. -.++.+|..+
T Consensus       512 ~--~~~l~~~l~~f~~----------------~~rllitgTPlQNsikEL~sL  546 (1373)
T KOG0384|consen  512 D--ESKLYESLNQFKM----------------NHRLLITGTPLQNSLKELWSL  546 (1373)
T ss_pred             h--HHHHHHHHHHhcc----------------cceeeecCCCccccHHHHHHH
Confidence            2  2333334444442                3446667775 4456666643

>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]

Probab=97.89  E-value=0.00013  Score=69.93  Aligned_cols=75  Identities=20%  Similarity=0.170  Sum_probs=60.2

Q ss_pred             HHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH
Q 043110           52 ERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ  131 (316)
Q Consensus        52 ~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~  131 (316)
                      ...++.+++.-|..|+.+++...=.++++|.|+|||.+-.--+++.+..        .+..+|+++|+.--+.|+++.+.
T Consensus       404 s~~~lpkLN~SQ~~AV~~VL~rplsLIQGPPGTGKTvtsa~IVyhl~~~--------~~~~VLvcApSNiAVDqLaeKIh  475 (935)
T KOG1802|consen  404 SVPNLPKLNASQSNAVKHVLQRPLSLIQGPPGTGKTVTSATIVYHLARQ--------HAGPVLVCAPSNIAVDQLAEKIH  475 (935)
T ss_pred             cCCCchhhchHHHHHHHHHHcCCceeeecCCCCCceehhHHHHHHHHHh--------cCCceEEEcccchhHHHHHHHHH
Confidence            3457788999999999999999999999999999998864434443333        23449999999999999998887


Q ss_pred             HHH
Q 043110          132 KLL  134 (316)
Q Consensus       132 ~~~  134 (316)
                      +-+
T Consensus       476 ~tg  478 (935)
T KOG1802|consen  476 KTG  478 (935)
T ss_pred             hcC
Confidence            754

>TIGR01448 recD_rel helicase, putative, RecD/TraA family

Probab=97.84  E-value=0.00044  Score=69.46  Aligned_cols=67  Identities=21%  Similarity=0.220  Sum_probs=48.3

Q ss_pred             HHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           52 ERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        52 ~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      ...++ .+++-|++|+..+..++-+++.++.|+|||... -.++..+....      ....+++++||-.-+..+
T Consensus       318 ~~~~~-~l~~~Q~~Ai~~~~~~~~~iitGgpGTGKTt~l-~~i~~~~~~~~------~~~~v~l~ApTg~AA~~L  384 (720)
T TIGR01448       318 KKLRK-GLSEEQKQALDTAIQHKVVILTGGPGTGKTTIT-RAIIELAEELG------GLLPVGLAAPTGRAAKRL  384 (720)
T ss_pred             HhcCC-CCCHHHHHHHHHHHhCCeEEEECCCCCCHHHHH-HHHHHHHHHcC------CCceEEEEeCchHHHHHH
Confidence            44565 489999999999998889999999999999753 23444443311      014488899998776543

This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.

>PF13245 AAA_19: Part of AAA domain

Probab=97.79  E-value=0.00012  Score=51.57  Aligned_cols=60  Identities=33%  Similarity=0.396  Sum_probs=39.2

Q ss_pred             HHHHHhCCCc-EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHH
Q 043110           66 AIPVILSGRD-VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEIL  130 (316)
Q Consensus        66 ~i~~il~g~d-~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~  130 (316)
                      ++...+.+.. +++.+|.|||||...+-.+...+....    .. +.++++++|++..+.++.+.+
T Consensus         2 av~~al~~~~~~vv~g~pGtGKT~~~~~~i~~l~~~~~----~~-~~~vlv~a~t~~aa~~l~~rl   62 (76)
T PF13245_consen    2 AVRRALAGSPLFVVQGPPGTGKTTTLAARIAELLAARA----DP-GKRVLVLAPTRAAADELRERL   62 (76)
T ss_pred             HHHHHHhhCCeEEEECCCCCCHHHHHHHHHHHHHHHhc----CC-CCeEEEECCCHHHHHHHHHHH
Confidence            3443334444 566999999999775444444442211    11 445999999999999888777

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=97.75  E-value=0.00029  Score=68.13  Aligned_cols=156  Identities=19%  Similarity=0.230  Sum_probs=100.5

Q ss_pred             CcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           59 PTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        59 p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      +..+|.+.+.++.    .|-+.|+.-..|-|||.-. +.++.++.....-    .|| .|||+|..-|    .++...+.
T Consensus       568 LKEYQlkGLnWLvnlYdqGiNGILADeMGLGKTVQs-isvlAhLaE~~nI----wGP-FLVVtpaStL----~NWaqEis  637 (1185)
T KOG0388|consen  568 LKEYQLKGLNWLVNLYDQGINGILADEMGLGKTVQS-ISVLAHLAETHNI----WGP-FLVVTPASTL----HNWAQEIS  637 (1185)
T ss_pred             hHHHhhccHHHHHHHHHccccceehhhhccchhHHH-HHHHHHHHHhccC----CCc-eEEeehHHHH----hHHHHHHH
Confidence            4567887776655    6788999999999999875 5566777653321    233 6888998766    44555555


Q ss_pred             hhcCCceeEEeeCCCChHHHHHHH---------hcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHH
Q 043110          135 HRFRWIVPGYVMGGGNRSKEKARL---------RKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGK  205 (316)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~l---------~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~  205 (316)
                      ..++...+.-..|+.+.....+.+         ..+.||+|++...+..--   +.+.--...+.|+|||+.+-.+ ...
T Consensus       638 rFlP~~k~lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtDe---ky~qkvKWQYMILDEAQAIKSS-sS~  713 (1185)
T KOG0388|consen  638 RFLPSFKVLPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTDE---KYLQKVKWQYMILDEAQAIKSS-SSS  713 (1185)
T ss_pred             HhCccceeecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeechH---HHHHhhhhhheehhHHHHhhhh-hhh
Confidence            555666666666776665555442         234789999987653211   1111124579999999987654 344


Q ss_pred             HHHHHHHHhccCcccccCCCCccccccceEEEEeeecchh
Q 043110          206 EIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEK  245 (316)
Q Consensus       206 ~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~  245 (316)
                      .+..++..-                 .+..++++.|.-.+
T Consensus       714 RWKtLLsF~-----------------cRNRLLLTGTPIQN  736 (1185)
T KOG0388|consen  714 RWKTLLSFK-----------------CRNRLLLTGTPIQN  736 (1185)
T ss_pred             HHHHHhhhh-----------------ccceeeecCCccch
Confidence            455555442                 34567888886543

>PF00580 UvrD-helicase: UvrD/REP helicase N-terminal domain; InterPro: IPR000212 Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA

Probab=97.71  E-value=0.00017  Score=64.78  Aligned_cols=124  Identities=23%  Similarity=0.198  Sum_probs=73.9

Q ss_pred             CcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcC
Q 043110           59 PTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFR  138 (316)
Q Consensus        59 p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~  138 (316)
                      +++-|.+++..  ..++++|.|+.|||||.+.+--++..+....     ...-++|++++|+..+.++.+++...+....
T Consensus         1 l~~eQ~~~i~~--~~~~~lV~a~AGSGKT~~l~~ri~~ll~~~~-----~~~~~Il~lTft~~aa~e~~~ri~~~l~~~~   73 (315)
T PF00580_consen    1 LTDEQRRIIRS--TEGPLLVNAGAGSGKTTTLLERIAYLLYEGG-----VPPERILVLTFTNAAAQEMRERIRELLEEEQ   73 (315)
T ss_dssp             S-HHHHHHHHS---SSEEEEEE-TTSSHHHHHHHHHHHHHHTSS-----STGGGEEEEESSHHHHHHHHHHHHHHHHHCC
T ss_pred             CCHHHHHHHhC--CCCCEEEEeCCCCCchHHHHHHHHHhhcccc-----CChHHheecccCHHHHHHHHHHHHHhcCccc
Confidence            47889999977  6778999999999999987665665555432     1233499999999999999999988765432


Q ss_pred             CceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCcccc-CceeEEEEecch
Q 043110          139 WIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLH-TNLRWIIFDEAD  196 (316)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~-~~l~~lViDEad  196 (316)
                      ...       ...............+-|+|-..+...+-....... -.-.+-++|+.+
T Consensus        74 ~~~-------~~~~~~~~~~~~~~~~~i~T~hsf~~~ll~~~~~~~~~~~~~~i~~~~~  125 (315)
T PF00580_consen   74 QES-------SDNERLRRQLSNIDRIYISTFHSFCYRLLREYGYEIGIDPNFEILDEEE  125 (315)
T ss_dssp             HCC-------TT-HHHHHHHHHCTTSEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHH
T ss_pred             ccc-------cccccccccccccchheeehhhhhhhhhhhhhhhhhhccccceeecchh
Confidence            100       000011112222346788887766554422111110 112355667666

THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains []. The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding; PDB: 1UAA_B 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A 1QHG_A 1PJR_A ....

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=97.67  E-value=0.00034  Score=69.56  Aligned_cols=132  Identities=23%  Similarity=0.266  Sum_probs=90.9

Q ss_pred             HcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           53 RLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        53 ~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      -+|.. |..+|...-  +.....-++.+.||-|||++..+|+.-....         |-.+.+++....||.--.+++..
T Consensus        76 vlg~~-~~dVQliG~--i~lh~g~iaEM~TGEGKTL~atlp~ylnaL~---------gkgVhvVTvNdYLA~RDae~m~~  143 (822)
T COG0653          76 VLGMR-HFDVQLLGG--IVLHLGDIAEMRTGEGKTLVATLPAYLNALA---------GKGVHVVTVNDYLARRDAEWMGP  143 (822)
T ss_pred             hcCCC-hhhHHHhhh--hhhcCCceeeeecCCchHHHHHHHHHHHhcC---------CCCcEEeeehHHhhhhCHHHHHH
Confidence            35665 666775544  3344456899999999999999998655444         23388999999999988999999


Q ss_pred             HHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcC-----CccccCceeEEEEecchhhh
Q 043110          133 LLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHT-----SSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~-----~~~~~~~l~~lViDEad~l~  199 (316)
                      +...++ +.+++...+..........  .+||..+|...| +++++-.     .......+.+-|+||+|.++
T Consensus       144 l~~~LG-lsvG~~~~~m~~~ek~~aY--~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~~~faIvDEvDSIL  213 (822)
T COG0653         144 LYEFLG-LSVGVILAGMSPEEKRAAY--ACDITYGTNNELGFDYLRDNMVTSQEEKVQRGLNFAIVDEVDSIL  213 (822)
T ss_pred             HHHHcC-CceeeccCCCChHHHHHHH--hcCceeccccccCcchhhhhhhccHHHhhhccCCeEEEcchhhee
Confidence            988766 5566666666544443333  479999999865 2333211     11123467899999999765

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

Probab=97.65  E-value=5.6e-05  Score=71.24  Aligned_cols=200  Identities=10%  Similarity=-0.035  Sum_probs=129.0

Q ss_pred             HHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHH
Q 043110           48 DQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY  127 (316)
Q Consensus        48 ~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~  127 (316)
                      ..+.+.+.-+....+|.+++..+.+|++.++...|.+||.++|.+.....+...       .....+++.|+.+++....
T Consensus       276 ~~~~~~~~~E~~~~~~~~~~~~~~~G~~~~~~~~~~~GK~~~~~~~s~~~~~~~-------~~s~~~~~~~~~~~~~~~~  348 (1034)
T KOG4150|consen  276 RSLLNKNTGESGIAISLELLKFASEGRADGGNEARQAGKGTCPTSGSRKFQTLC-------HATNSLLPSEMVEHLRNGS  348 (1034)
T ss_pred             HHHHhcccccchhhhhHHHHhhhhhcccccccchhhcCCccCcccchhhhhhcC-------cccceecchhHHHHhhccC
Confidence            333355566677899999999999999999999999999999988877665441       2233788999999886543


Q ss_pred             HHHHHHHhhcCCce--eEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCC-c--cccCceeEEEEecchhhhcC-
Q 043110          128 EILQKLLHRFRWIV--PGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTS-S--FLHTNLRWIIFDEADRILEL-  201 (316)
Q Consensus       128 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~-~--~~~~~l~~lViDEad~l~~~-  201 (316)
                      +...-.....+...  ..-.+.+.+...+..-.+.+.+++.+.|..+....--.. .  ..+=++.+.+.||+|..+.. 
T Consensus       349 ~~~~V~~~~I~~~K~A~V~~~D~~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~~~~~~~~~~~~~~~~~~~~~~~Y~~~~  428 (1034)
T KOG4150|consen  349 KGQVVHVEVIKARKSAYVEMSDKLSETTKSALKRIGLNTLYSHQAEAISAALAKSLCYNVPVFEELCKDTNSCALYLFPT  428 (1034)
T ss_pred             CceEEEEEehhhhhcceeecccCCCchhHHHHHhcCcceeecCHHHHHHHHhhhccccccHHHHHHHhcccceeeeecch
Confidence            32211111111111  112234555555666667788999999998765443211 1  12224568899999976643 


Q ss_pred             --CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCE-EEEcCC
Q 043110          202 --GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPV-LIGLDE  264 (316)
Q Consensus       202 --~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~-~i~~~~  264 (316)
                        .....++.+++.+.-.          ..+.+.|++-.|||+...++.....+--+-+ .|..+.
T Consensus       429 ~~~~~~~~R~L~~L~~~F----------~~~~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~~DG  484 (1034)
T KOG4150|consen  429 KALAQDQLRALSDLIKGF----------EASINMGVYDGDTPYKDRTRLRSELANLSELELVTIDG  484 (1034)
T ss_pred             hhHHHHHHHHHHHHHHHH----------HhhcCcceEeCCCCcCCHHHHHHHhcCCcceEEEEecC
Confidence              1334555555554321          1233789999999999999988887755554 444433

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=97.64  E-value=0.0004  Score=70.47  Aligned_cols=141  Identities=18%  Similarity=0.229  Sum_probs=89.1

Q ss_pred             CcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           59 PTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        59 p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      ++.+|...++++.    +.-|.|+.-..|-|||.-. +.++.++......     ..--|||+||.-+ ..+.-.+++|+
T Consensus       616 LReYQkiGLdWLatLYeknlNGILADEmGLGKTIQt-ISllAhLACeegn-----WGPHLIVVpTsvi-LnWEMElKRwc  688 (1958)
T KOG0391|consen  616 LREYQKIGLDWLATLYEKNLNGILADEMGLGKTIQT-ISLLAHLACEEGN-----WGPHLIVVPTSVI-LNWEMELKRWC  688 (1958)
T ss_pred             HHHHHHhhHHHHHHHHHhcccceehhhhcccchhHH-HHHHHHHHhcccC-----CCCceEEeechhh-hhhhHHHhhhC
Confidence            4678888887765    3457899999999999864 5677777664332     2226899999654 33455566665


Q ss_pred             hhcCCceeEEeeCCCChHHHHHHHhc---CCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHH
Q 043110          135 HRFRWIVPGYVMGGGNRSKEKARLRK---GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEIL  211 (316)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~l~~---~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~  211 (316)
                         ..+.+...+|......+.+.-..   ..||-|++...++.-+.   .+.-...+|+|+||||.+-.+ -...+..++
T Consensus       689 ---PglKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~~---AFkrkrWqyLvLDEaqnIKnf-ksqrWQAll  761 (1958)
T KOG0391|consen  689 ---PGLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDLT---AFKRKRWQYLVLDEAQNIKNF-KSQRWQALL  761 (1958)
T ss_pred             ---CcceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHHH---HHHhhccceeehhhhhhhcch-hHHHHHHHh
Confidence               44555555555444333332222   25788888777665443   233357889999999998764 233455555


Q ss_pred             HH
Q 043110          212 DI  213 (316)
Q Consensus       212 ~~  213 (316)
                      +.
T Consensus       762 nf  763 (1958)
T KOG0391|consen  762 NF  763 (1958)
T ss_pred             cc
Confidence            44

>COG1875 NYN ribonuclease and ATPase of PhoH family domains [General function prediction only]

Probab=97.59  E-value=0.00055  Score=61.68  Aligned_cols=67  Identities=25%  Similarity=0.272  Sum_probs=49.3

Q ss_pred             HHcCCCCCcHHHHHHHHHHhCCC-c-EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHH
Q 043110           52 ERLGFEAPTKVQAQAIPVILSGR-D-VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCL  124 (316)
Q Consensus        52 ~~~g~~~p~~~Q~~~i~~il~g~-d-~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~  124 (316)
                      +-+|+..-+..|..|+..++... + +.+.++.|||||+.++.+.+......+.      .-++||-=|+..+.+
T Consensus       222 ~vwGi~prn~eQ~~ALdlLld~dI~lV~L~G~AGtGKTlLALaAgleqv~e~~~------y~KiiVtRp~vpvG~  290 (436)
T COG1875         222 EVWGIRPRNAEQRVALDLLLDDDIDLVSLGGKAGTGKTLLALAAGLEQVLERKR------YRKIIVTRPTVPVGE  290 (436)
T ss_pred             hhhccCcccHHHHHHHHHhcCCCCCeEEeeccCCccHhHHHHHHHHHHHHHHhh------hceEEEecCCcCccc
Confidence            44688877888899999888654 2 7889999999999998888877665322      233666667766553

>PRK13889 conjugal transfer relaxase TraA; Provisional

Probab=97.55  E-value=0.0014  Score=67.59  Aligned_cols=62  Identities=23%  Similarity=0.219  Sum_probs=46.0

Q ss_pred             CCCCCcHHHHHHHHHHhCCCc-EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           55 GFEAPTKVQAQAIPVILSGRD-VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~il~g~d-~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      |+ .+++-|.+++..++.+++ +++.++.|+|||.+ +-++...+..        .|..++.++||---+..+
T Consensus       344 g~-~Ls~eQr~Av~~il~s~~v~vv~G~AGTGKTT~-l~~~~~~~e~--------~G~~V~~~ApTGkAA~~L  406 (988)
T PRK13889        344 GL-VLSGEQADALAHVTDGRDLGVVVGYAGTGKSAM-LGVAREAWEA--------AGYEVRGAALSGIAAENL  406 (988)
T ss_pred             CC-CCCHHHHHHHHHHhcCCCeEEEEeCCCCCHHHH-HHHHHHHHHH--------cCCeEEEecCcHHHHHHH
Confidence            54 489999999999998765 79999999999976 3334444332        255699999997655433

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=97.50  E-value=0.00072  Score=52.58  Aligned_cols=20  Identities=30%  Similarity=0.451  Sum_probs=13.3

Q ss_pred             CCCcEEEEcCCCCchHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~   91 (316)
                      +++-+++.|++|+|||...-
T Consensus         3 ~~~~~~i~G~~G~GKT~~~~   22 (131)
T PF13401_consen    3 SQRILVISGPPGSGKTTLIK   22 (131)
T ss_dssp             ----EEEEE-TTSSHHHHHH
T ss_pred             CCcccEEEcCCCCCHHHHHH
Confidence            34568999999999998753

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

Probab=97.48  E-value=0.00022  Score=67.01  Aligned_cols=65  Identities=25%  Similarity=0.397  Sum_probs=50.0

Q ss_pred             CcHHHHHHHHHHhCC-----CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           59 PTKVQAQAIPVILSG-----RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        59 p~~~Q~~~i~~il~g-----~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      |..-|-+||..+..|     +.-.+-+.||||||+..    .+.+.+....        +||++|.+.||.|++..++.+
T Consensus        13 PaGDQP~AI~~Lv~gi~~g~~~QtLLGvTGSGKTfT~----AnVI~~~~rP--------tLV~AhNKTLAaQLy~Efk~f   80 (663)
T COG0556          13 PAGDQPEAIAELVEGIENGLKHQTLLGVTGSGKTFTM----ANVIAKVQRP--------TLVLAHNKTLAAQLYSEFKEF   80 (663)
T ss_pred             CCCCcHHHHHHHHHHHhcCceeeEEeeeccCCchhHH----HHHHHHhCCC--------eEEEecchhHHHHHHHHHHHh
Confidence            777888888777644     45788999999999873    3333332222        999999999999999999998


Q ss_pred             Hh
Q 043110          134 LH  135 (316)
Q Consensus       134 ~~  135 (316)
                      +-
T Consensus        81 FP   82 (663)
T COG0556          81 FP   82 (663)
T ss_pred             Cc
Confidence            74

>KOG1805 consensus DNA replication helicase [Replication, recombination and repair]

Probab=97.34  E-value=0.00096  Score=66.72  Aligned_cols=141  Identities=20%  Similarity=0.135  Sum_probs=85.4

Q ss_pred             CCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCc-EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCC
Q 043110           41 GLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRD-VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPT  119 (316)
Q Consensus        41 ~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d-~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt  119 (316)
                      .+.+.+.+..     ...++.-|++|+-.++..+| .+|.|=+|+|||..... ++..+..        .|.++|+.+-|
T Consensus       657 ~~~p~~~~~~-----~~~LN~dQr~A~~k~L~aedy~LI~GMPGTGKTTtI~~-LIkiL~~--------~gkkVLLtsyT  722 (1100)
T KOG1805|consen  657 VLIPKIKKII-----LLRLNNDQRQALLKALAAEDYALILGMPGTGKTTTISL-LIKILVA--------LGKKVLLTSYT  722 (1100)
T ss_pred             ccCchhhHHH-----HhhcCHHHHHHHHHHHhccchheeecCCCCCchhhHHH-HHHHHHH--------cCCeEEEEehh
Confidence            3555555432     22578899999999998887 78999999999987544 3333333        24558988888


Q ss_pred             hHHHHHHHHHHHHHHhhcCCc----------eeEEeeCCC--ChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCce
Q 043110          120 SELCLLVYEILQKLLHRFRWI----------VPGYVMGGG--NRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNL  187 (316)
Q Consensus       120 ~~L~~Q~~~~~~~~~~~~~~~----------~~~~~~~~~--~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l  187 (316)
                      ..-+..+--.++.+...+-.+          .-.+...+.  ........+.+.+.||.||--.+.+.+.     ..+.+
T Consensus       723 hsAVDNILiKL~~~~i~~lRLG~~~kih~~v~e~~~~~~~s~ks~~~l~~~~~~~~IVa~TClgi~~plf-----~~R~F  797 (1100)
T KOG1805|consen  723 HSAVDNILIKLKGFGIYILRLGSEEKIHPDVEEFTLTNETSEKSYADLKKFLDQTSIVACTCLGINHPLF-----VNRQF  797 (1100)
T ss_pred             hHHHHHHHHHHhccCcceeecCCccccchHHHHHhcccccchhhHHHHHHHhCCCcEEEEEccCCCchhh-----hcccc
Confidence            877766555554443221000          000001111  1122333555678899999544444333     33568


Q ss_pred             eEEEEecchhhhc
Q 043110          188 RWIIFDEADRILE  200 (316)
Q Consensus       188 ~~lViDEad~l~~  200 (316)
                      ++.|||||-.++.
T Consensus       798 D~cIiDEASQI~l  810 (1100)
T KOG1805|consen  798 DYCIIDEASQILL  810 (1100)
T ss_pred             CEEEEcccccccc
Confidence            9999999987654

>TIGR00376 DNA helicase, putative

Probab=97.30  E-value=0.001  Score=65.88  Aligned_cols=66  Identities=26%  Similarity=0.275  Sum_probs=51.2

Q ss_pred             CCcHHHHHHHHHHhCC-CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSG-RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g-~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      .+++.|..|+..++.. ..+++.||+|+|||.+..--+.+.+..         |.++|+++||..-+.++.+.+..
T Consensus       157 ~ln~~Q~~Av~~~l~~~~~~lI~GpPGTGKT~t~~~ii~~~~~~---------g~~VLv~a~sn~Avd~l~e~l~~  223 (637)
T TIGR00376       157 NLNESQKEAVSFALSSKDLFLIHGPPGTGKTRTLVELIRQLVKR---------GLRVLVTAPSNIAVDNLLERLAL  223 (637)
T ss_pred             CCCHHHHHHHHHHhcCCCeEEEEcCCCCCHHHHHHHHHHHHHHc---------CCCEEEEcCcHHHHHHHHHHHHh
Confidence            4689999999998876 568999999999997654333333322         34699999999999888887765

The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases.

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=97.29  E-value=0.0016  Score=57.49  Aligned_cols=46  Identities=15%  Similarity=0.244  Sum_probs=31.4

Q ss_pred             ccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecch
Q 043110          183 LHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       183 ~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                      .....+.+|+||||.|... -+..+.+.++..+.               ..++++....+..
T Consensus       126 ~~~~fKiiIlDEcdsmtsd-aq~aLrr~mE~~s~---------------~trFiLIcnylsr  171 (346)
T KOG0989|consen  126 PCPPFKIIILDECDSMTSD-AQAALRRTMEDFSR---------------TTRFILICNYLSR  171 (346)
T ss_pred             CCCcceEEEEechhhhhHH-HHHHHHHHHhcccc---------------ceEEEEEcCChhh
Confidence            4456789999999998653 45566666666554               5677776655543

>PF05970 PIF1: PIF1-like helicase; InterPro: IPR010285 This entry represents PIF1 helicase and related proteins

Probab=97.28  E-value=0.0019  Score=59.82  Aligned_cols=59  Identities=27%  Similarity=0.381  Sum_probs=42.0

Q ss_pred             CcHHHHHHHHHH------hCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           59 PTKVQAQAIPVI------LSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        59 p~~~Q~~~i~~i------l~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      +++-|+.++..+      ..+..+++.|+-|+|||..+- .+.+.+..        .+..+++++||-.-|..+
T Consensus         2 Ln~eQ~~~~~~v~~~~~~~~~~~~fv~G~~GtGKs~l~~-~i~~~~~~--------~~~~~~~~a~tg~AA~~i   66 (364)
T PF05970_consen    2 LNEEQRRVFDTVIEAIENEEGLNFFVTGPAGTGKSFLIK-AIIDYLRS--------RGKKVLVTAPTGIAAFNI   66 (364)
T ss_pred             CCHHHHHHHHHHHHHHHccCCcEEEEEcCCCCChhHHHH-HHHHHhcc--------ccceEEEecchHHHHHhc
Confidence            678899998888      678889999999999997642 22333322        244589999997665444

The PIF1 helicase inhibits telomerase activity and is cell cycle regulated [, ].

>PRK04296 thymidine kinase; Provisional

Probab=97.25  E-value=0.00097  Score=55.86  Aligned_cols=37  Identities=22%  Similarity=0.332  Sum_probs=23.8

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeC
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVP  118 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~P  118 (316)
                      |.=.++.+|+|+|||...+- ++.++..        .+.+++++-|
T Consensus         2 g~i~litG~~GsGKTT~~l~-~~~~~~~--------~g~~v~i~k~   38 (190)
T PRK04296          2 AKLEFIYGAMNSGKSTELLQ-RAYNYEE--------RGMKVLVFKP   38 (190)
T ss_pred             cEEEEEECCCCCHHHHHHHH-HHHHHHH--------cCCeEEEEec
Confidence            33468899999999976543 3333322        2445888866

>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA

Probab=97.23  E-value=0.0062  Score=61.60  Aligned_cols=60  Identities=13%  Similarity=0.109  Sum_probs=43.8

Q ss_pred             CCcHHHHHHHHHHhCC-CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           58 APTKVQAQAIPVILSG-RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g-~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .+++-|+.|+..++.+ +-+++.++.|+|||... -.+...+..        .|..++.++||---+..+
T Consensus       352 ~Ls~~Q~~Av~~i~~s~~~~il~G~aGTGKTtll-~~i~~~~~~--------~g~~V~~~ApTg~Aa~~L  412 (744)
T TIGR02768       352 RLSEEQYEAVRHVTGSGDIAVVVGRAGTGKSTML-KAAREAWEA--------AGYRVIGAALSGKAAEGL  412 (744)
T ss_pred             CCCHHHHHHHHHHhcCCCEEEEEecCCCCHHHHH-HHHHHHHHh--------CCCeEEEEeCcHHHHHHH
Confidence            4899999999998875 55899999999999663 223333332        255699999997665443

This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.

>PRK06526 transposase; Provisional

Probab=97.21  E-value=0.0049  Score=54.05  Aligned_cols=22  Identities=27%  Similarity=0.391  Sum_probs=18.2

Q ss_pred             HhCCCcEEEEcCCCCchHHHHH
Q 043110           70 ILSGRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        70 il~g~d~li~a~TGsGKT~~~~   91 (316)
                      +-.+.++++.||+|+|||....
T Consensus        95 i~~~~nlll~Gp~GtGKThLa~  116 (254)
T PRK06526         95 VTGKENVVFLGPPGTGKTHLAI  116 (254)
T ss_pred             hhcCceEEEEeCCCCchHHHHH
Confidence            3367799999999999997654

>PRK13826 Dtr system oriT relaxase; Provisional

Probab=97.18  E-value=0.015  Score=60.62  Aligned_cols=75  Identities=16%  Similarity=0.096  Sum_probs=50.3

Q ss_pred             CCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhC-CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCC
Q 043110           41 GLDSTLCDQLRERLGFEAPTKVQAQAIPVILS-GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPT  119 (316)
Q Consensus        41 ~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~-g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt  119 (316)
                      ++++..+...... ++ .+++-|..++..+.. ++-.++.|+.|+|||.+. -++...+..        .|.+++.++||
T Consensus       366 ~v~~~~l~a~~~~-~~-~Ls~eQ~~Av~~i~~~~r~~~v~G~AGTGKTt~l-~~~~~~~e~--------~G~~V~g~ApT  434 (1102)
T PRK13826        366 GVREAVLAATFAR-HA-RLSDEQKTAIEHVAGPARIAAVVGRAGAGKTTMM-KAAREAWEA--------AGYRVVGGALA  434 (1102)
T ss_pred             CCCHHHHHHHHhc-CC-CCCHHHHHHHHHHhccCCeEEEEeCCCCCHHHHH-HHHHHHHHH--------cCCeEEEEcCc
Confidence            4555555544232 44 489999999998864 345899999999999763 334443332        35569999999


Q ss_pred             hHHHHHH
Q 043110          120 SELCLLV  126 (316)
Q Consensus       120 ~~L~~Q~  126 (316)
                      -.-+..+
T Consensus       435 gkAA~~L  441 (1102)
T PRK13826        435 GKAAEGL  441 (1102)
T ss_pred             HHHHHHH
Confidence            7665443

>PRK08181 transposase; Validated

Probab=97.17  E-value=0.02  Score=50.64  Aligned_cols=20  Identities=25%  Similarity=0.400  Sum_probs=17.2

Q ss_pred             hCCCcEEEEcCCCCchHHHH
Q 043110           71 LSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        71 l~g~d~li~a~TGsGKT~~~   90 (316)
                      -.++++++.||+|+|||-..
T Consensus       104 ~~~~nlll~Gp~GtGKTHLa  123 (269)
T PRK08181        104 AKGANLLLFGPPGGGKSHLA  123 (269)
T ss_pred             hcCceEEEEecCCCcHHHHH
Confidence            36789999999999999654

>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold

Probab=97.15  E-value=0.0079  Score=46.91  Aligned_cols=18  Identities=33%  Similarity=0.527  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      ++.+++.|++|+|||...
T Consensus        19 ~~~v~i~G~~G~GKT~l~   36 (151)
T cd00009          19 PKNLLLYGPPGTGKTTLA   36 (151)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            678999999999999653

The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=97.15  E-value=0.0014  Score=56.87  Aligned_cols=86  Identities=19%  Similarity=0.214  Sum_probs=59.4

Q ss_pred             CCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCC-CChHHHHHHHhc-CCcEEEeCcHHHHHHHhcCCccccC
Q 043110          108 SSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGG-GNRSKEKARLRK-GISILVATPGHLLDHLKHTSSFLHT  185 (316)
Q Consensus       108 ~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~  185 (316)
                      ...|.+|||+.+---|..+.+.++.+...  ...+.-+... ....++...+.+ .++|.||||+|+..++.+ ..+.++
T Consensus       124 ~gsP~~lvvs~SalRa~dl~R~l~~~~~k--~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~-~~L~l~  200 (252)
T PF14617_consen  124 KGSPHVLVVSSSALRAADLIRALRSFKGK--DCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLEN-GALSLS  200 (252)
T ss_pred             CCCCEEEEEcchHHHHHHHHHHHHhhccC--CchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHc-CCCCcc
Confidence            45688999999977777777777765311  0111111222 234555555654 579999999999999976 677789


Q ss_pred             ceeEEEEecch
Q 043110          186 NLRWIIFDEAD  196 (316)
Q Consensus       186 ~l~~lViDEad  196 (316)
                      ++.+||||--|
T Consensus       201 ~l~~ivlD~s~  211 (252)
T PF14617_consen  201 NLKRIVLDWSY  211 (252)
T ss_pred             cCeEEEEcCCc
Confidence            99999999755

>PHA02533 17 large terminase protein; Provisional

Probab=97.14  E-value=0.0072  Score=58.60  Aligned_cols=137  Identities=15%  Similarity=0.121  Sum_probs=81.5

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      .|.|+|...+..+..++-.++..+=..|||.+...-++......       .+..+++++|+++-|..+++.++.+....
T Consensus        59 ~L~p~Q~~i~~~~~~~R~~ii~~aRq~GKStl~a~~al~~a~~~-------~~~~v~i~A~~~~QA~~vF~~ik~~ie~~  131 (534)
T PHA02533         59 QMRDYQKDMLKIMHKNRFNACNLSRQLGKTTVVAIFLLHYVCFN-------KDKNVGILAHKASMAAEVLDRTKQAIELL  131 (534)
T ss_pred             CCcHHHHHHHHHHhcCeEEEEEEcCcCChHHHHHHHHHHHHHhC-------CCCEEEEEeCCHHHHHHHHHHHHHHHHhC
Confidence            47899999998876666678889999999998764444333321       24579999999999999998888776543


Q ss_pred             CCce-eEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhc
Q 043110          138 RWIV-PGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILG  215 (316)
Q Consensus       138 ~~~~-~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~  215 (316)
                      +... ......    ....-.+.++..|.+.|.+.        ....=.+..++++||+|.+-+  +...+..+...+.
T Consensus       132 P~l~~~~i~~~----~~~~I~l~NGS~I~~lss~~--------~t~rG~~~~~liiDE~a~~~~--~~e~~~ai~p~la  196 (534)
T PHA02533        132 PDFLQPGIVEW----NKGSIELENGSKIGAYASSP--------DAVRGNSFAMIYIDECAFIPN--FIDFWLAIQPVIS  196 (534)
T ss_pred             HHHhhcceeec----CccEEEeCCCCEEEEEeCCC--------CccCCCCCceEEEeccccCCC--HHHHHHHHHHHHH
Confidence            3211 000000    00111123445554444221        111112467899999997644  3344444544444

>PRK12723 flagellar biosynthesis regulator FlhF; Provisional

Probab=97.08  E-value=0.013  Score=54.41  Aligned_cols=132  Identities=12%  Similarity=0.072  Sum_probs=67.0

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEe-C-ChHHHHHHHHHHHHHHhhcCCceeEEeeCCCCh
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLV-P-TSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR  151 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~-P-t~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (316)
                      +.+++.+|||+|||.+..--+........     ..+..+.+++ . .|.-+.   ++++.++...+...          
T Consensus       175 ~vi~lvGptGvGKTTT~aKLA~~~~~~~~-----~~g~~V~lit~Dt~R~aa~---eQL~~~a~~lgvpv----------  236 (388)
T PRK12723        175 RVFILVGPTGVGKTTTIAKLAAIYGINSD-----DKSLNIKIITIDNYRIGAK---KQIQTYGDIMGIPV----------  236 (388)
T ss_pred             eEEEEECCCCCCHHHHHHHHHHHHHhhhc-----cCCCeEEEEeccCccHHHH---HHHHHHhhcCCcce----------
Confidence            46899999999999885432222111100     0123344443 3 333332   22455544332111          


Q ss_pred             HHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccc
Q 043110          152 SKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNV  231 (316)
Q Consensus       152 ~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~  231 (316)
                                  ..+-++..+...+..     +.+.++++||++.++..  -...+..+.+.+....           .+
T Consensus       237 ------------~~~~~~~~l~~~L~~-----~~~~DlVLIDTaGr~~~--~~~~l~el~~~l~~~~-----------~~  286 (388)
T PRK12723        237 ------------KAIESFKDLKEEITQ-----SKDFDLVLVDTIGKSPK--DFMKLAEMKELLNACG-----------RD  286 (388)
T ss_pred             ------------EeeCcHHHHHHHHHH-----hCCCCEEEEcCCCCCcc--CHHHHHHHHHHHHhcC-----------CC
Confidence                        112234444444433     24678999999998753  2223445544443210           01


Q ss_pred             cceEEEEeeecc-hhHHHHHHHh
Q 043110          232 KRQNLLLSATLN-EKVNHLTKIS  253 (316)
Q Consensus       232 ~~q~i~~SAT~~-~~v~~~~~~~  253 (316)
                      .-.++.+|||.. .++.+..+.+
T Consensus       287 ~e~~LVlsat~~~~~~~~~~~~~  309 (388)
T PRK12723        287 AEFHLAVSSTTKTSDVKEIFHQF  309 (388)
T ss_pred             CeEEEEEcCCCCHHHHHHHHHHh
Confidence            235677899985 4455666666

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=97.06  E-value=0.029  Score=44.78  Aligned_cols=38  Identities=29%  Similarity=0.352  Sum_probs=23.3

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHH
Q 043110           76 VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSEL  122 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L  122 (316)
                      +++.|++|+|||.....-+... ..        .+..++++......
T Consensus         2 ~~i~G~~G~GKT~l~~~i~~~~-~~--------~~~~v~~~~~e~~~   39 (165)
T cd01120           2 ILVFGPTGSGKTTLALQLALNI-AT--------KGGKVVYVDIEEEI   39 (165)
T ss_pred             eeEeCCCCCCHHHHHHHHHHHH-Hh--------cCCEEEEEECCcch
Confidence            6789999999998654333222 22        13447777655443

This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=97.00  E-value=0.0069  Score=62.37  Aligned_cols=137  Identities=20%  Similarity=0.164  Sum_probs=83.9

Q ss_pred             CCCcHHHHHHHHHHh-----CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH
Q 043110           57 EAPTKVQAQAIPVIL-----SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ  131 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il-----~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~  131 (316)
                      ..+.++|.+.+..+.     .+.+.++....|.|||+..+..+...... ..    .....++|++|+ +++.++.+.+.
T Consensus       337 ~~lr~yq~~g~~wl~~~l~~~~~~~ilaD~mglGKTiq~i~~l~~~~~~-~~----~~~~~~liv~p~-s~~~nw~~e~~  410 (866)
T COG0553         337 AELRPYQLEGVNWLSELLRSNLLGGILADDMGLGKTVQTIALLLSLLES-IK----VYLGPALIVVPA-SLLSNWKREFE  410 (866)
T ss_pred             hhhHHHHHHHHHHHHHHHHhccCCCcccccccchhHHHHHHHHHhhhhc-cc----CCCCCeEEEecH-HHHHHHHHHHh
Confidence            456788988887644     36678888999999998765444331211 11    113349999998 55677777776


Q ss_pred             HHHhhcCCceeEEeeCCCCh----HHHHHHHhcC-----CcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcC
Q 043110          132 KLLHRFRWIVPGYVMGGGNR----SKEKARLRKG-----ISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL  201 (316)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~----~~~~~~l~~~-----~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~  201 (316)
                      ++......  .....|....    ......+...     .+++++|.+.+.........+.-....++|+||+|.+-..
T Consensus       411 k~~~~~~~--~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l~~~~~~~~v~DEa~~ikn~  487 (866)
T COG0553         411 KFAPDLRL--VLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGLKKIEWDRVVLDEAHRIKND  487 (866)
T ss_pred             hhCccccc--eeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHHhhceeeeeehhhHHHHhhh
Confidence            66543321  3334443331    2233333221     6899999988877432212233346789999999996553

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

Probab=96.82  E-value=0.0017  Score=61.46  Aligned_cols=102  Identities=19%  Similarity=0.157  Sum_probs=64.7

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHH
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSK  153 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~  153 (316)
                      +-++-++||.||||.-    +++++..-+         .+++.-|.|-||.++++.+...+..+.     ++.|......
T Consensus       192 kIi~H~GPTNSGKTy~----ALqrl~~ak---------sGvycGPLrLLA~EV~~r~na~gipCd-----L~TGeE~~~~  253 (700)
T KOG0953|consen  192 KIIMHVGPTNSGKTYR----ALQRLKSAK---------SGVYCGPLRLLAHEVYDRLNALGIPCD-----LLTGEERRFV  253 (700)
T ss_pred             eEEEEeCCCCCchhHH----HHHHHhhhc---------cceecchHHHHHHHHHHHhhhcCCCcc-----ccccceeeec
Confidence            3467789999999987    567666522         289999999999999999888664433     2222211111


Q ss_pred             HHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcH
Q 043110          154 EKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFG  204 (316)
Q Consensus       154 ~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~  204 (316)
                      .-.  .+.++.+-||-++..        . -...+..||||++.|-|...+
T Consensus       254 ~~~--~~~a~hvScTVEM~s--------v-~~~yeVAViDEIQmm~Dp~RG  293 (700)
T KOG0953|consen  254 LDN--GNPAQHVSCTVEMVS--------V-NTPYEVAVIDEIQMMRDPSRG  293 (700)
T ss_pred             CCC--CCcccceEEEEEEee--------c-CCceEEEEehhHHhhcCcccc
Confidence            100  112456666654331        1 135678999999988876443

>smart00382 AAA ATPases associated with a variety of cellular activities

Probab=96.78  E-value=0.0042  Score=48.04  Aligned_cols=18  Identities=33%  Similarity=0.556  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      +..+++.+|+|+|||...
T Consensus         2 ~~~~~l~G~~G~GKTtl~   19 (148)
T smart00382        2 GEVILIVGPPGSGKTTLA   19 (148)
T ss_pred             CCEEEEECCCCCcHHHHH
Confidence            467899999999999874

AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=96.77  E-value=0.0024  Score=64.09  Aligned_cols=130  Identities=17%  Similarity=0.234  Sum_probs=77.9

Q ss_pred             CCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        58 ~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      ++.++|...+.++.    +.-+-|+.-.+|-|||..- +.++..+...+..    .|| -||++|+--|.. +...+..+
T Consensus       394 ~Lk~YQl~GLqWmVSLyNNnLNGILADEMGLGKTIQt-IsLitYLmE~K~~----~GP-~LvivPlstL~N-W~~Ef~kW  466 (1157)
T KOG0386|consen  394 ELKEYQLHGLQWMVSLYNNNLNGILADEMGLGKTIQT-ISLITYLMEHKQM----QGP-FLIIVPLSTLVN-WSSEFPKW  466 (1157)
T ss_pred             CCchhhhhhhHHHhhccCCCcccccchhcccchHHHH-HHHHHHHHHHccc----CCC-eEEeccccccCC-chhhcccc
Confidence            67889999887765    3347899999999999874 4455555554332    344 689999988864 23333333


Q ss_pred             HhhcCCceeEEeeCCCChHH--HHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          134 LHRFRWIVPGYVMGGGNRSK--EKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~--~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                      .   +.+......|......  .........+|+++|.+.+..   ....+.--+..++||||.|+|-.
T Consensus       467 a---PSv~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik---dk~lLsKI~W~yMIIDEGHRmKN  529 (1157)
T KOG0386|consen  467 A---PSVQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK---DKALLSKISWKYMIIDEGHRMKN  529 (1157)
T ss_pred             c---cceeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC---CHHHHhccCCcceeecccccccc
Confidence            2   3333333222222111  111222457999999887654   11111112456999999999854

>cd01124 KaiC KaiC is a circadian clock protein primarily found in cyanobacteria KaiC is a RecA-like ATPase, having both Walker A and Walker B motifs

Probab=96.76  E-value=0.024  Score=46.90  Aligned_cols=48  Identities=27%  Similarity=0.236  Sum_probs=31.2

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      +++.|++|+|||...+--+...+..         |..++|++. .+-..++.+.+..+
T Consensus         2 ~li~G~~G~GKT~l~~~~~~~~~~~---------g~~v~~~s~-e~~~~~~~~~~~~~   49 (187)
T cd01124           2 TLLSGGPGTGKTTFALQFLYAGLAR---------GEPGLYVTL-EESPEELIENAESL   49 (187)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHHHHC---------CCcEEEEEC-CCCHHHHHHHHHHc
Confidence            6899999999998754333333322         344888864 45566776666655

A related protein is found in archaea.

>KOG1131 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription; Replication, recombination and repair]

Probab=96.76  E-value=0.019  Score=54.24  Aligned_cols=76  Identities=21%  Similarity=0.207  Sum_probs=46.9

Q ss_pred             cCCCCCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHH
Q 043110           54 LGFEAPTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI  129 (316)
Q Consensus        54 ~g~~~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~  129 (316)
                      |.|..-+|-|.+=.-.+.    .+.+.++.+|+|+|||.+.+--++.......     ....+.++.+-|..-.+.....
T Consensus        12 FPY~~iYPEQ~~YM~elKrsLDakGh~llEMPSGTGKTvsLLSli~aYq~~~p-----~~~~KliYCSRTvpEieK~l~E   86 (755)
T KOG1131|consen   12 FPYDYIYPEQYEYMRELKRSLDAKGHCLLEMPSGTGKTVSLLSLIIAYQLHYP-----DEHRKLIYCSRTVPEIEKALEE   86 (755)
T ss_pred             cCCcccCHHHHHHHHHHHHhhccCCcEEEECCCCCCcchHHHHHHHHHHHhCC-----cccceEEEecCcchHHHHHHHH
Confidence            677778888866554333    5668999999999999986554444433321     1233466666665544444444


Q ss_pred             HHHHH
Q 043110          130 LQKLL  134 (316)
Q Consensus       130 ~~~~~  134 (316)
                      ++.+.
T Consensus        87 l~~l~   91 (755)
T KOG1131|consen   87 LKRLM   91 (755)
T ss_pred             HHHHH
Confidence            44443

>PRK14974 cell division protein FtsY; Provisional

Probab=96.72  E-value=0.052  Score=49.51  Aligned_cols=54  Identities=11%  Similarity=0.127  Sum_probs=35.5

Q ss_pred             ceeEEEEecchhhhc-CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhc
Q 043110          186 NLRWIIFDEADRILE-LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISL  254 (316)
Q Consensus       186 ~l~~lViDEad~l~~-~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l  254 (316)
                      +.++++||.+.++.. ......+..+.+.+..               ..-++.++||...+....++.|.
T Consensus       222 ~~DvVLIDTaGr~~~~~~lm~eL~~i~~~~~p---------------d~~iLVl~a~~g~d~~~~a~~f~  276 (336)
T PRK14974        222 GIDVVLIDTAGRMHTDANLMDELKKIVRVTKP---------------DLVIFVGDALAGNDAVEQAREFN  276 (336)
T ss_pred             CCCEEEEECCCccCCcHHHHHHHHHHHHhhCC---------------ceEEEeeccccchhHHHHHHHHH
Confidence            456899999998752 2345566666555443               55677888888766666555553

>PRK11889 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.72  E-value=0.039  Score=51.15  Aligned_cols=21  Identities=24%  Similarity=0.325  Sum_probs=16.6

Q ss_pred             CcEEEEcCCCCchHHHHHHHH
Q 043110           74 RDVLVNAATGTGKTVAYLAPI   94 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~   94 (316)
                      +.+.+.+|||+|||.....-+
T Consensus       242 ~vI~LVGptGvGKTTTiaKLA  262 (436)
T PRK11889        242 QTIALIGPTGVGKTTTLAKMA  262 (436)
T ss_pred             cEEEEECCCCCcHHHHHHHHH
Confidence            468999999999998764433

>PRK14722 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=96.71  E-value=0.059  Score=49.82  Aligned_cols=128  Identities=17%  Similarity=0.171  Sum_probs=64.7

Q ss_pred             CcccCCCCHHHHHHHHHHcCC----CCC---cHHHHHHHHH----H-------hCCCcEEEEcCCCCchHHHHHHHHHHH
Q 043110           36 CFSSLGLDSTLCDQLRERLGF----EAP---TKVQAQAIPV----I-------LSGRDVLVNAATGTGKTVAYLAPIINH   97 (316)
Q Consensus        36 ~f~~~~l~~~l~~~l~~~~g~----~~p---~~~Q~~~i~~----i-------l~g~d~li~a~TGsGKT~~~~lp~l~~   97 (316)
                      .+.+.|+++.+.+.|.+.+.-    ..+   ..+....+..    +       ..|..+++.+|||+|||....--+...
T Consensus        82 ~L~~~g~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~g~ii~lvGptGvGKTTtiakLA~~~  161 (374)
T PRK14722         82 YLFAAGFSAQLVRMIVDNLPEGEGYDTLDAAADWAQSVLAANLPVLDSEDALMERGGVFALMGPTGVGKTTTTAKLAARC  161 (374)
T ss_pred             HHHHCCCCHHHHHHHHHhhhhhcccCCHHHHHHHHHHHHHhcchhhcCCCccccCCcEEEEECCCCCCHHHHHHHHHHHH
Confidence            355678888888777554421    111   1222222211    1       135679999999999998864433332


Q ss_pred             hhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH
Q 043110           98 LQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL  172 (316)
Q Consensus        98 l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l  172 (316)
                      .....       ..++.+++ +...-.--.+.++.++..++ ........+.........+.+.--|+|=|+|+.
T Consensus       162 ~~~~G-------~~~V~lit-~D~~R~ga~EqL~~~a~~~g-v~~~~~~~~~~l~~~l~~l~~~DlVLIDTaG~~  227 (374)
T PRK14722        162 VMRFG-------ASKVALLT-TDSYRIGGHEQLRIFGKILG-VPVHAVKDGGDLQLALAELRNKHMVLIDTIGMS  227 (374)
T ss_pred             HHhcC-------CCeEEEEe-cccccccHHHHHHHHHHHcC-CceEecCCcccHHHHHHHhcCCCEEEEcCCCCC
Confidence            22211       11233333 22211112345555555544 233333344444444455554445889999855

>PRK06921 hypothetical protein; Provisional

Probab=96.68  E-value=0.047  Score=48.22  Aligned_cols=45  Identities=20%  Similarity=0.112  Sum_probs=27.1

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL  125 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q  125 (316)
                      .+..+++.|++|+|||... .++...+...       .+..++++. ..++..+
T Consensus       116 ~~~~l~l~G~~G~GKThLa-~aia~~l~~~-------~g~~v~y~~-~~~l~~~  160 (266)
T PRK06921        116 RKNSIALLGQPGSGKTHLL-TAAANELMRK-------KGVPVLYFP-FVEGFGD  160 (266)
T ss_pred             CCCeEEEECCCCCcHHHHH-HHHHHHHhhh-------cCceEEEEE-HHHHHHH
Confidence            3567999999999999654 3344444431       133466655 3444433

>PRK08116 hypothetical protein; Validated

Probab=96.67  E-value=0.069  Score=47.24  Aligned_cols=25  Identities=36%  Similarity=0.375  Sum_probs=19.0

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      .+++.|++|+|||.... ++.+.+..
T Consensus       116 gl~l~G~~GtGKThLa~-aia~~l~~  140 (268)
T PRK08116        116 GLLLWGSVGTGKTYLAA-CIANELIE  140 (268)
T ss_pred             eEEEECCCCCCHHHHHH-HHHHHHHH
Confidence            49999999999997653 45666554

>PHA03368 DNA packaging terminase subunit 1; Provisional

Probab=96.57  E-value=0.075  Score=52.19  Aligned_cols=161  Identities=17%  Similarity=0.157  Sum_probs=92.3

Q ss_pred             HHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           44 STLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        44 ~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      ..+-+.|+..|+...++.   .++ .....+-.++..|--.|||.... +++..+...      ..|.+++|.+|.+..+
T Consensus       229 ~r~~~~lk~~Fdi~~~s~---~~~-~~fkqk~tVflVPRR~GKTwivv-~iI~~ll~s------~~Gi~IgytAH~~~ts  297 (738)
T PHA03368        229 ERVERFLRTVFNTPLFSD---AAV-RHFRQRATVFLVPRRHGKTWFLV-PLIALALAT------FRGIKIGYTAHIRKAT  297 (738)
T ss_pred             HHHHHHHHHHcCCccccH---HHH-HHhhccceEEEecccCCchhhHH-HHHHHHHHh------CCCCEEEEEcCcHHHH
Confidence            344455544455544332   222 23366778999999999998655 666655531      2367799999999999


Q ss_pred             HHHHHHHHHHHhhcCCc-eeEEeeCCCChHHHHHHHhcC--CcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          124 LLVYEILQKLLHRFRWI-VPGYVMGGGNRSKEKARLRKG--ISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       124 ~Q~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~l~~~--~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                      +.+++.+.......... ...... |...   .-.+.++  ..|..++       ..+.+...-..++++|+|||+-+-+
T Consensus       298 ~~vF~eI~~~le~~f~~~~v~~vk-Ge~I---~i~f~nG~kstI~FaS-------arntNsiRGqtfDLLIVDEAqFIk~  366 (738)
T PHA03368        298 EPVFEEIGARLRQWFGASRVDHVK-GETI---SFSFPDGSRSTIVFAS-------SHNTNGIRGQDFNLLFVDEANFIRP  366 (738)
T ss_pred             HHHHHHHHHHHhhhcchhheeeec-CcEE---EEEecCCCccEEEEEe-------ccCCCCccCCcccEEEEechhhCCH
Confidence            99999998877642111 111111 1000   0011111  1333332       1222223234789999999998865


Q ss_pred             CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecch
Q 043110          201 LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       201 ~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                          +.+..++-.+...              ++++|++|.|-+.
T Consensus       367 ----~al~~ilp~l~~~--------------n~k~I~ISS~Ns~  392 (738)
T PHA03368        367 ----DAVQTIMGFLNQT--------------NCKIIFVSSTNTG  392 (738)
T ss_pred             ----HHHHHHHHHHhcc--------------CccEEEEecCCCC
Confidence                4455555444432              6778888877443

>PRK08727 hypothetical protein; Validated

Probab=96.54  E-value=0.028  Score=48.64  Aligned_cols=16  Identities=31%  Similarity=0.349  Sum_probs=13.7

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      .+++.|++|+|||-..
T Consensus        43 ~l~l~G~~G~GKThL~   58 (233)
T PRK08727         43 WLYLSGPAGTGKTHLA   58 (233)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            4999999999999543

>PF00448 SRP54: SRP54-type protein, GTPase domain; InterPro: IPR000897 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]

Probab=96.54  E-value=0.11  Score=43.57  Aligned_cols=51  Identities=22%  Similarity=0.308  Sum_probs=28.9

Q ss_pred             ceeEEEEecchhhhc-CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHH
Q 043110          186 NLRWIIFDEADRILE-LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK  251 (316)
Q Consensus       186 ~l~~lViDEad~l~~-~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~  251 (316)
                      +.++++||-+-+... .....++..+++.+..               ..-.+.+|||...+....+.
T Consensus        83 ~~D~vlIDT~Gr~~~d~~~~~el~~~~~~~~~---------------~~~~LVlsa~~~~~~~~~~~  134 (196)
T PF00448_consen   83 GYDLVLIDTAGRSPRDEELLEELKKLLEALNP---------------DEVHLVLSATMGQEDLEQAL  134 (196)
T ss_dssp             TSSEEEEEE-SSSSTHHHHHHHHHHHHHHHSS---------------SEEEEEEEGGGGGHHHHHHH
T ss_pred             CCCEEEEecCCcchhhHHHHHHHHHHhhhcCC---------------ccceEEEecccChHHHHHHH
Confidence            466788887755331 1233456666666543               45567788888766544333

SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins []. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 2OG2_A 3B9Q_A 3DM9_B 3DMD_B 3E70_C 3DM5_B 2XXA_C 2J28_9 1ZU5_B 1ZU4_A ....

>PRK07952 DNA replication protein DnaC; Validated

Probab=96.50  E-value=0.076  Score=46.22  Aligned_cols=26  Identities=27%  Similarity=0.316  Sum_probs=18.8

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      ..+++.+++|+|||.... ++...+..
T Consensus       100 ~~~~l~G~~GtGKThLa~-aia~~l~~  125 (244)
T PRK07952        100 ASFIFSGKPGTGKNHLAA-AICNELLL  125 (244)
T ss_pred             ceEEEECCCCCCHHHHHH-HHHHHHHh
Confidence            469999999999997643 44445543

>TIGR02785 addA_Gpos recombination helicase AddA, Firmicutes type

Probab=96.50  E-value=0.024  Score=60.72  Aligned_cols=124  Identities=20%  Similarity=0.173  Sum_probs=79.1

Q ss_pred             CcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcC
Q 043110           59 PTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFR  138 (316)
Q Consensus        59 p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~  138 (316)
                      .|+-|.++|..  .|+++++.|..|||||.+.+--++..+... .     .--++++|+=|+.-+.++.+++........
T Consensus         2 ~t~~Q~~ai~~--~~~~~lv~A~AGsGKT~~lv~r~~~~~~~~-~-----~~~~il~~tFt~~aa~e~~~ri~~~l~~~~   73 (1232)
T TIGR02785         2 WTDEQWQAIYT--RGQNILVSASAGSGKTAVLVERIIKKILRG-V-----DIDRLLVVTFTNAAAREMKERIEEALQKAL   73 (1232)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCcHHHHHHHHHHHHHhcC-C-----CHhhEEEEeccHHHHHHHHHHHHHHHHHHH
Confidence            58899999973  688999999999999998766666665432 1     112499999999999999888877664321


Q ss_pred             CceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCcccc-CceeEEEEecchh
Q 043110          139 WIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLH-TNLRWIIFDEADR  197 (316)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~-~~l~~lViDEad~  197 (316)
                      ...       .......+.+..-...-|+|-..++..+-+.....+ -+-.+=|.||...
T Consensus        74 ~~~-------p~~~~L~~q~~~~~~~~i~Tihsf~~~~~~~~~~~l~ldP~F~i~de~e~  126 (1232)
T TIGR02785        74 QQE-------PNSKHLRRQLALLNTANISTLHSFCLKVIRKHYYLLDLDPSFRILTDTEQ  126 (1232)
T ss_pred             hcC-------chhHHHHHHHhhccCCeEeeHHHHHHHHHHHhhhhcCCCCCceeCCHHHH
Confidence            110       011111122222245778998888765544222211 0224556888875

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species.

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=96.48  E-value=0.017  Score=55.52  Aligned_cols=72  Identities=18%  Similarity=0.207  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHh-----CC----CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH
Q 043110           61 KVQAQAIPVIL-----SG----RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ  131 (316)
Q Consensus        61 ~~Q~~~i~~il-----~g----~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~  131 (316)
                      |+|+-.+-.++     .|    +.+++..|=|.|||.....-++..+.-.     ...+..+++++++++-|..+++.+.
T Consensus         1 PwQ~fi~~~i~G~~~~~g~rrf~~~~l~v~RkNGKS~l~a~i~ly~l~~~-----g~~~~~i~~~A~~~~QA~~~f~~~~   75 (477)
T PF03354_consen    1 PWQKFILRSIFGWRKDDGRRRFREVYLEVPRKNGKSTLAAAIALYMLFLD-----GEPGAEIYCAANTRDQAKIVFDEAK   75 (477)
T ss_pred             CcHHHHHHHHhceEcCCCCEEEEEEEEEEcCccCccHHHHHHHHHHHhcC-----CccCceEEEEeCCHHHHHHHHHHHH
Confidence            56776666555     22    2589999999999987544444444321     1246679999999999999999999


Q ss_pred             HHHhhc
Q 043110          132 KLLHRF  137 (316)
Q Consensus       132 ~~~~~~  137 (316)
                      .+....
T Consensus        76 ~~i~~~   81 (477)
T PF03354_consen   76 KMIEAS   81 (477)
T ss_pred             HHHHhC
Confidence            988763

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK05642 DNA replication initiation factor; Validated

Probab=96.48  E-value=0.032  Score=48.30  Aligned_cols=31  Identities=13%  Similarity=0.267  Sum_probs=21.0

Q ss_pred             ceeEEEEecchhhhcC-CcHHHHHHHHHHhcc
Q 043110          186 NLRWIIFDEADRILEL-GFGKEIEEILDILGS  216 (316)
Q Consensus       186 ~l~~lViDEad~l~~~-~~~~~i~~i~~~l~~  216 (316)
                      +.++||+|++|.+... .....+-.+++.+..
T Consensus        97 ~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~  128 (234)
T PRK05642         97 QYELVCLDDLDVIAGKADWEEALFHLFNRLRD  128 (234)
T ss_pred             hCCEEEEechhhhcCChHHHHHHHHHHHHHHh
Confidence            4568999999987543 345556677766654

>PRK14712 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.47  E-value=0.07  Score=57.67  Aligned_cols=62  Identities=27%  Similarity=0.261  Sum_probs=44.7

Q ss_pred             CCcHHHHHHHHHHhCC--CcEEEEcCCCCchHHHH--HHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           58 APTKVQAQAIPVILSG--RDVLVNAATGTGKTVAY--LAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g--~d~li~a~TGsGKT~~~--~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .+++-|++|+..++.+  +-+++++..|+|||...  ++.++..+..       ..+..++.++||-.-+..+
T Consensus       835 ~Lt~~Qr~Av~~iLts~dr~~~IqG~AGTGKTT~l~~i~~~~~~l~e-------~~g~~V~glAPTgkAa~~L  900 (1623)
T PRK14712        835 KLTSGQRAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPE-------SERPRVVGLGPTHRAVGEM  900 (1623)
T ss_pred             ccCHHHHHHHHHHHhCCCceEEEEeCCCCCHHHHHHHHHHHHHHHhh-------ccCceEEEEechHHHHHHH
Confidence            5899999999999966  55999999999999873  2223332221       2345688899997766544

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=96.44  E-value=0.038  Score=52.71  Aligned_cols=43  Identities=14%  Similarity=0.150  Sum_probs=25.9

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL  125 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q  125 (316)
                      .+++.||+|+|||... -++.+.+...      ..+..++++. ..++..+
T Consensus       150 ~l~l~G~~G~GKThL~-~ai~~~~~~~------~~~~~v~yi~-~~~~~~~  192 (450)
T PRK00149        150 PLFIYGGVGLGKTHLL-HAIGNYILEK------NPNAKVVYVT-SEKFTND  192 (450)
T ss_pred             eEEEECCCCCCHHHHH-HHHHHHHHHh------CCCCeEEEEE-HHHHHHH
Confidence            4899999999999764 3344444432      1244566664 3444433

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=96.44  E-value=0.04  Score=52.52  Aligned_cols=47  Identities=19%  Similarity=0.185  Sum_probs=27.9

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI  129 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~  129 (316)
                      .+++.|++|+|||-.. -++.+.+...      ..+.+++++.+ .++..++...
T Consensus       143 pl~i~G~~G~GKTHLl-~Ai~~~l~~~------~~~~~v~yv~~-~~f~~~~~~~  189 (450)
T PRK14087        143 PLFIYGESGMGKTHLL-KAAKNYIESN------FSDLKVSYMSG-DEFARKAVDI  189 (450)
T ss_pred             ceEEECCCCCcHHHHH-HHHHHHHHHh------CCCCeEEEEEH-HHHHHHHHHH
Confidence            4899999999999543 3444444331      12445776665 4555444433

>PRK06893 DNA replication initiation factor; Validated

Probab=96.44  E-value=0.023  Score=49.05  Aligned_cols=47  Identities=13%  Similarity=0.250  Sum_probs=29.3

Q ss_pred             ceeEEEEecchhhhcC-CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhH
Q 043110          186 NLRWIIFDEADRILEL-GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKV  246 (316)
Q Consensus       186 ~l~~lViDEad~l~~~-~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v  246 (316)
                      +.++|+|||+|.+... .+...+..+++.+...              ..+++++|++.++..
T Consensus        91 ~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~--------------~~~illits~~~p~~  138 (229)
T PRK06893         91 QQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQ--------------GKTLLLISADCSPHA  138 (229)
T ss_pred             cCCEEEEeChhhhcCChHHHHHHHHHHHHHHHc--------------CCcEEEEeCCCChHH
Confidence            5679999999987633 2344455555554321              346677777765443

>PRK10919 ATP-dependent DNA helicase Rep; Provisional

Probab=96.43  E-value=0.011  Score=59.30  Aligned_cols=70  Identities=20%  Similarity=0.143  Sum_probs=52.6

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      .+++-|++++.+  ....++|.|+.|||||.+..--+...+.....     ..-++|+++.|+..|.++.+++..+.
T Consensus         2 ~Ln~~Q~~av~~--~~g~~lV~AgpGSGKT~vL~~Ria~Li~~~~v-----~p~~IL~lTFT~kAA~em~~Rl~~~l   71 (672)
T PRK10919          2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGY-----QARHIAAVTFTNKAAREMKERVAQTL   71 (672)
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCC-----CHHHeeeEechHHHHHHHHHHHHHHh
Confidence            478999999865  35678999999999999865555555533111     12349999999999999998887764

>COG3421 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=96.35  E-value=0.0047  Score=59.05  Aligned_cols=115  Identities=15%  Similarity=0.162  Sum_probs=56.9

Q ss_pred             EEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH-hhcCCceeEEeeCCCChH----
Q 043110           78 VNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL-HRFRWIVPGYVMGGGNRS----  152 (316)
Q Consensus        78 i~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~-~~~~~~~~~~~~~~~~~~----  152 (316)
                      ..+.||||||++....+++...+       +. -..|+.|......+.....+..-. ..+- ..-...+++....    
T Consensus         2 f~matgsgkt~~ma~lil~~y~k-------gy-r~flffvnq~nilekt~~nftd~~s~kyl-f~e~i~~~d~~i~ikkv   72 (812)
T COG3421           2 FEMATGSGKTLVMAGLILECYKK-------GY-RNFLFFVNQANILEKTKLNFTDSVSSKYL-FSENININDENIEIKKV   72 (812)
T ss_pred             cccccCCChhhHHHHHHHHHHHh-------ch-hhEEEEecchhHHHHHHhhcccchhhhHh-hhhhhhcCCceeeeeee
Confidence            45789999999865555554433       11 125666665554433322221110 0000 0000111111100    


Q ss_pred             HHHHHHhcCCcEEEeCcHHHHHHHhcCCc--c---ccCcee-EEEEecchhhhcC
Q 043110          153 KEKARLRKGISILVATPGHLLDHLKHTSS--F---LHTNLR-WIIFDEADRILEL  201 (316)
Q Consensus       153 ~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~--~---~~~~l~-~lViDEad~l~~~  201 (316)
                      .....-..+..|..+|-..|...+.+.+.  +   .+.+.+ +++-||||++...
T Consensus        73 n~fsehnd~iei~fttiq~l~~d~~~~ken~itledl~~~klvfl~deahhln~~  127 (812)
T COG3421          73 NNFSEHNDAIEIYFTTIQGLFSDFTRAKENAITLEDLKDQKLVFLADEAHHLNTE  127 (812)
T ss_pred             cccCccCCceEEEEeehHHHHHHHHhhccccccHhhHhhCceEEEechhhhhhhh
Confidence            00001234568999999999887755432  2   233333 4577999998753

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=96.32  E-value=0.014  Score=58.09  Aligned_cols=66  Identities=23%  Similarity=0.404  Sum_probs=50.3

Q ss_pred             CCcHHHHHHHHHHhCC-----CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSG-----RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g-----~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      .|+..|..+|..+.++     +..++.|-||||||+... .+++.+.           ..+|||+|+..+|.|+++.++.
T Consensus         9 ~~~~~Q~~ai~~l~~~~~~~~~~~~l~Gvtgs~kt~~~a-~~~~~~~-----------~p~Lvi~~n~~~A~ql~~el~~   76 (655)
T TIGR00631         9 QPAGDQPKAIAKLVEGLTDGEKHQTLLGVTGSGKTFTMA-NVIAQVN-----------RPTLVIAHNKTLAAQLYNEFKE   76 (655)
T ss_pred             CCChHHHHHHHHHHHhhhcCCCcEEEECCCCcHHHHHHH-HHHHHhC-----------CCEEEEECCHHHHHHHHHHHHH
Confidence            4899999999887643     256799999999998742 2332221           1299999999999999999998


Q ss_pred             HHh
Q 043110          133 LLH  135 (316)
Q Consensus       133 ~~~  135 (316)
                      +..
T Consensus        77 f~p   79 (655)
T TIGR00631        77 FFP   79 (655)
T ss_pred             hCC
Confidence            863

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

>PRK06835 DNA replication protein DnaC; Validated

Probab=96.31  E-value=0.18  Score=45.90  Aligned_cols=45  Identities=27%  Similarity=0.343  Sum_probs=28.0

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .+.++++.|+||+|||... .++...+..        .|..++++. ..+|..++
T Consensus       182 ~~~~Lll~G~~GtGKThLa-~aIa~~l~~--------~g~~V~y~t-~~~l~~~l  226 (329)
T PRK06835        182 NNENLLFYGNTGTGKTFLS-NCIAKELLD--------RGKSVIYRT-ADELIEIL  226 (329)
T ss_pred             cCCcEEEECCCCCcHHHHH-HHHHHHHHH--------CCCeEEEEE-HHHHHHHH
Confidence            3578999999999999754 344444443        133455554 45555443

>PRK12377 putative replication protein; Provisional

Probab=96.31  E-value=0.09  Score=45.90  Aligned_cols=45  Identities=22%  Similarity=0.272  Sum_probs=27.3

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY  127 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~  127 (316)
                      ..++++.|++|+|||-.. .++.+.+...        +..+ +.++..+|..++.
T Consensus       101 ~~~l~l~G~~GtGKThLa-~AIa~~l~~~--------g~~v-~~i~~~~l~~~l~  145 (248)
T PRK12377        101 CTNFVFSGKPGTGKNHLA-AAIGNRLLAK--------GRSV-IVVTVPDVMSRLH  145 (248)
T ss_pred             CCeEEEECCCCCCHHHHH-HHHHHHHHHc--------CCCe-EEEEHHHHHHHHH
Confidence            357999999999999654 3344444431        2224 4445556665543

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=96.28  E-value=0.076  Score=59.21  Aligned_cols=62  Identities=15%  Similarity=0.178  Sum_probs=45.5

Q ss_pred             CCcHHHHHHHHHHhCCC--cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSGR--DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~--d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      .+++-|++++..++...  -.++.++.|+|||.+. -.+++.+..        .|..++.++||..-+..+.+
T Consensus       429 ~Ls~~Q~~Av~~il~s~~~v~ii~G~aGTGKTt~l-~~l~~~~~~--------~G~~V~~lAPTgrAA~~L~e  492 (1960)
T TIGR02760       429 ALSPSNKDAVSTLFTSTKRFIIINGFGGTGSTEIA-QLLLHLASE--------QGYEIQIITAGSLSAQELRQ  492 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCCeEEEEECCCCCHHHHH-HHHHHHHHh--------cCCeEEEEeCCHHHHHHHHH
Confidence            47899999999988764  4899999999999763 333333332        35669999999876655443

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=96.24  E-value=0.045  Score=46.80  Aligned_cols=20  Identities=20%  Similarity=0.290  Sum_probs=16.5

Q ss_pred             CCCcEEEEcCCCCchHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~   91 (316)
                      .+..+++.|++|+|||....
T Consensus        37 ~~~~lll~G~~G~GKT~la~   56 (226)
T TIGR03420        37 GDRFLYLWGESGSGKSHLLQ   56 (226)
T ss_pred             CCCeEEEECCCCCCHHHHHH
Confidence            45679999999999997653

Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.

>PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional

Probab=96.24  E-value=0.031  Score=52.67  Aligned_cols=33  Identities=15%  Similarity=0.331  Sum_probs=26.7

Q ss_pred             CcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHH
Q 043110           59 PTKVQAQAIPVILSGRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        59 p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~   91 (316)
                      |-......+..+..++++++.+++|+|||..+.
T Consensus       180 ~e~~le~l~~~L~~~~~iil~GppGtGKT~lA~  212 (459)
T PRK11331        180 PETTIETILKRLTIKKNIILQGPPGVGKTFVAR  212 (459)
T ss_pred             CHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHH
Confidence            455566677777789999999999999997753

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=96.21  E-value=0.03  Score=55.94  Aligned_cols=68  Identities=26%  Similarity=0.419  Sum_probs=51.5

Q ss_pred             CCCCCcHHHHHHHHHHhCC-----CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHH
Q 043110           55 GFEAPTKVQAQAIPVILSG-----RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI  129 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~il~g-----~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~  129 (316)
                      +|. |++.|..++..+.++     +..++.+.+|+||++.+. .++...           +..+|||+|+...|.|+++.
T Consensus        10 ~~~-~~~~Q~~ai~~l~~~~~~~~~~~ll~Gl~gs~ka~lia-~l~~~~-----------~r~vLIVt~~~~~A~~l~~d   76 (652)
T PRK05298         10 PYK-PAGDQPQAIEELVEGIEAGEKHQTLLGVTGSGKTFTMA-NVIARL-----------QRPTLVLAHNKTLAAQLYSE   76 (652)
T ss_pred             CCC-CChHHHHHHHHHHHhhhcCCCcEEEEcCCCcHHHHHHH-HHHHHh-----------CCCEEEEECCHHHHHHHHHH
Confidence            454 999999999887633     256799999999998742 222221           11299999999999999999


Q ss_pred             HHHHHh
Q 043110          130 LQKLLH  135 (316)
Q Consensus       130 ~~~~~~  135 (316)
                      ++.+..
T Consensus        77 L~~~~~   82 (652)
T PRK05298         77 FKEFFP   82 (652)
T ss_pred             HHHhcC
Confidence            988863

>TIGR01075 uvrD DNA helicase II

Probab=96.18  E-value=0.016  Score=58.64  Aligned_cols=72  Identities=21%  Similarity=0.177  Sum_probs=53.5

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           57 EAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      ..+++-|++++.+  ....++|.|..|||||.+..--+...+....-     ..-.+|+|+.|+..|.++.+++.++..
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~L~~Ria~Li~~~~v-----~p~~IL~lTFTnkAA~em~~Rl~~~~~   74 (715)
T TIGR01075         3 DGLNDKQREAVAA--PPGNLLVLAGAGSGKTRVLTHRIAWLLSVENA-----SPHSIMAVTFTNKAAAEMRHRIGALLG   74 (715)
T ss_pred             cccCHHHHHHHcC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCC-----CHHHeEeeeccHHHHHHHHHHHHHHhc
Confidence            4589999999865  34679999999999999865444444432111     123499999999999999998888754

Designed to identify uvrD members of the uvrD/rep subfamily.

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=96.18  E-value=0.058  Score=50.69  Aligned_cols=36  Identities=17%  Similarity=0.224  Sum_probs=23.5

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEe
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLV  117 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~  117 (316)
                      .+++.|++|+|||... -.+.+.+...      ..+..++++.
T Consensus       138 ~l~l~G~~G~GKThL~-~ai~~~l~~~------~~~~~v~yi~  173 (405)
T TIGR00362       138 PLFIYGGVGLGKTHLL-HAIGNEILEN------NPNAKVVYVS  173 (405)
T ss_pred             eEEEECCCCCcHHHHH-HHHHHHHHHh------CCCCcEEEEE
Confidence            4799999999999764 3445554432      1234577774

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

>PRK11054 helD DNA helicase IV; Provisional

Probab=96.17  E-value=0.035  Score=55.62  Aligned_cols=73  Identities=22%  Similarity=0.124  Sum_probs=52.7

Q ss_pred             CCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           55 GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      .-..+++-|++|+-.  ...+++|.|..|||||.+.+--+...+....     ..+-++|+++.|+..|..+.+++....
T Consensus       193 e~~~L~~~Q~~av~~--~~~~~lV~agaGSGKT~vl~~r~ayLl~~~~-----~~~~~IL~ltft~~AA~em~eRL~~~l  265 (684)
T PRK11054        193 ESSPLNPSQARAVVN--GEDSLLVLAGAGSGKTSVLVARAGWLLARGQ-----AQPEQILLLAFGRQAAEEMDERIRERL  265 (684)
T ss_pred             cCCCCCHHHHHHHhC--CCCCeEEEEeCCCCHHHHHHHHHHHHHHhCC-----CCHHHeEEEeccHHHHHHHHHHHHHhc
Confidence            335689999998853  3456899999999999986544444443311     123359999999999999998877654

>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=96.17  E-value=0.044  Score=46.95  Aligned_cols=109  Identities=19%  Similarity=0.228  Sum_probs=62.3

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE  154 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (316)
                      -+++.|++|+|||-. +-++.+.+....      ++.+++|+... +........++.                      
T Consensus        36 ~l~l~G~~G~GKTHL-L~Ai~~~~~~~~------~~~~v~y~~~~-~f~~~~~~~~~~----------------------   85 (219)
T PF00308_consen   36 PLFLYGPSGLGKTHL-LQAIANEAQKQH------PGKRVVYLSAE-EFIREFADALRD----------------------   85 (219)
T ss_dssp             EEEEEESTTSSHHHH-HHHHHHHHHHHC------TTS-EEEEEHH-HHHHHHHHHHHT----------------------
T ss_pred             ceEEECCCCCCHHHH-HHHHHHHHHhcc------ccccceeecHH-HHHHHHHHHHHc----------------------
Confidence            389999999999973 445555554422      24457777643 333332222211                      


Q ss_pred             HHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcC-CcHHHHHHHHHHhccCcccccCCCCccccccc
Q 043110          155 KARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL-GFGKEIEEILDILGSRNIASIGEGNEVSNVKR  233 (316)
Q Consensus       155 ~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~-~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~  233 (316)
                                  .....+.+.+        ...++|+||+.|.+.+. .....+-.+++.+...              +.
T Consensus        86 ------------~~~~~~~~~~--------~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~--------------~k  131 (219)
T PF00308_consen   86 ------------GEIEEFKDRL--------RSADLLIIDDIQFLAGKQRTQEELFHLFNRLIES--------------GK  131 (219)
T ss_dssp             ------------TSHHHHHHHH--------CTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHT--------------TS
T ss_pred             ------------ccchhhhhhh--------hcCCEEEEecchhhcCchHHHHHHHHHHHHHHhh--------------CC
Confidence                        0111222222        35789999999998654 2345666666666542              56


Q ss_pred             eEEEEeeecchhHH
Q 043110          234 QNLLLSATLNEKVN  247 (316)
Q Consensus       234 q~i~~SAT~~~~v~  247 (316)
                      ++|+.|...|..+.
T Consensus       132 ~li~ts~~~P~~l~  145 (219)
T PF00308_consen  132 QLILTSDRPPSELS  145 (219)
T ss_dssp             EEEEEESS-TTTTT
T ss_pred             eEEEEeCCCCcccc
Confidence            78887777776654

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.

>PRK13709 conjugal transfer nickase/helicase TraI; Provisional

Probab=96.15  E-value=0.074  Score=58.16  Aligned_cols=64  Identities=22%  Similarity=0.234  Sum_probs=44.5

Q ss_pred             CCcHHHHHHHHHHhCCC--cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           58 APTKVQAQAIPVILSGR--DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~--d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .+++.|++|+..++.+.  -+++++..|+|||... -.++..+...    ....+..++.++||-.-+..+
T Consensus       967 ~Lt~~Q~~Av~~il~s~dr~~~I~G~AGTGKTT~l-~~v~~~~~~l----~~~~~~~V~glAPTgrAAk~L 1032 (1747)
T PRK13709        967 GLTSGQRAATRMILESTDRFTVVQGYAGVGKTTQF-RAVMSAVNTL----PESERPRVVGLGPTHRAVGEM 1032 (1747)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHHH-HHHHHHHHHh----hcccCceEEEECCcHHHHHHH
Confidence            58999999999999764  4899999999999763 2233333211    011245588899997766443

>PHA03333 putative ATPase subunit of terminase; Provisional

Probab=96.15  E-value=0.21  Score=49.41  Aligned_cols=72  Identities=17%  Similarity=0.249  Sum_probs=52.2

Q ss_pred             CCcHHHHHHHHHHh---CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVIL---SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        58 ~p~~~Q~~~i~~il---~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      -|+|.=.+-|..++   ..+-.++.+|-|.|||.+..+.+...+..        .+.+++|.+|...-+.++++.++...
T Consensus       169 ~~~~~~~~~id~~~~~fkq~~tV~taPRqrGKS~iVgi~l~~La~f--------~Gi~IlvTAH~~~ts~evF~rv~~~l  240 (752)
T PHA03333        169 APSPRTLREIDRIFDEYGKCYTAATVPRRCGKTTIMAIILAAMISF--------LEIDIVVQAQRKTMCLTLYNRVETVV  240 (752)
T ss_pred             CCChhhHHHHHHHHHHHhhcceEEEeccCCCcHHHHHHHHHHHHHh--------cCCeEEEECCChhhHHHHHHHHHHHH
Confidence            34666555565554   44568889999999998866555443332        24569999999999999999888887


Q ss_pred             hhc
Q 043110          135 HRF  137 (316)
Q Consensus       135 ~~~  137 (316)
                      ...
T Consensus       241 e~l  243 (752)
T PHA03333        241 HAY  243 (752)
T ss_pred             HHh
Confidence            643

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=96.12  E-value=0.043  Score=49.62  Aligned_cols=31  Identities=19%  Similarity=0.264  Sum_probs=19.8

Q ss_pred             ceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          186 NLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      ..+++||||+|.+........+..+++..+.
T Consensus       100 ~~~vliiDe~d~l~~~~~~~~L~~~le~~~~  130 (316)
T PHA02544        100 GGKVIIIDEFDRLGLADAQRHLRSFMEAYSK  130 (316)
T ss_pred             CCeEEEEECcccccCHHHHHHHHHHHHhcCC
Confidence            4578999999988333344555555555443

>COG3973 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=96.11  E-value=0.037  Score=53.30  Aligned_cols=95  Identities=21%  Similarity=0.241  Sum_probs=60.6

Q ss_pred             ccCCCCHHHHHHHHHHcCCCCCc----HHHHHHHHHHhC--CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCe
Q 043110           38 SSLGLDSTLCDQLRERLGFEAPT----KVQAQAIPVILS--GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT  111 (316)
Q Consensus        38 ~~~~l~~~l~~~l~~~~g~~~p~----~~Q~~~i~~il~--g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~  111 (316)
                      ++.++.++++....++.--.+++    -+|++-=..|-.  ++-++++|..|||||.+++--+...+.......   .+.
T Consensus       185 sd~~~~dEvL~~~Lek~ss~~mrdIV~TIQkEQneIIR~ek~~ilVVQGaAGSGKTtiALHRvAyLlY~~R~~l---~~k  261 (747)
T COG3973         185 SDTGGRDEVLQRVLEKNSSAKMRDIVETIQKEQNEIIRFEKNKILVVQGAAGSGKTTIALHRVAYLLYGYRGPL---QAK  261 (747)
T ss_pred             cCCchHHHHHHHHHHhccchhHHHHHHHhhHhHHHHHhccCCCeEEEecCCCCCchhHHHHHHHHHHhcccccc---ccC
Confidence            45566666555432553333333    245554444444  345899999999999987655554444432221   122


Q ss_pred             eEEEEeCChHHHHHHHHHHHHHHh
Q 043110          112 FALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus       112 ~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      .+||+.|.+-+..-+.+++-.++.
T Consensus       262 ~vlvl~PN~vFleYis~VLPeLGe  285 (747)
T COG3973         262 PVLVLGPNRVFLEYISRVLPELGE  285 (747)
T ss_pred             ceEEEcCcHHHHHHHHHhchhhcc
Confidence            399999999999999999888775

>PRK11773 uvrD DNA-dependent helicase II; Provisional

Probab=96.11  E-value=0.019  Score=58.11  Aligned_cols=71  Identities=21%  Similarity=0.190  Sum_probs=52.9

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      .+++-|++++..  ....++|.|..|||||.+..--+...+....-     ..-.+|+|+-|+..|.++.+++.++..
T Consensus         9 ~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~vl~~Ria~Li~~~~v-----~p~~IL~lTFT~kAA~Em~~Rl~~~~~   79 (721)
T PRK11773          9 SLNDKQREAVAA--PLGNMLVLAGAGSGKTRVLVHRIAWLMQVENA-----SPYSIMAVTFTNKAAAEMRHRIEQLLG   79 (721)
T ss_pred             hcCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHcCCC-----ChhHeEeeeccHHHHHHHHHHHHHHhc
Confidence            589999999864  34679999999999999865444444432111     123499999999999999998888754

>PRK05703 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=96.10  E-value=0.14  Score=48.43  Aligned_cols=19  Identities=37%  Similarity=0.459  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 043110           73 GRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~   91 (316)
                      |+.+++.+|||+|||....
T Consensus       221 ~~~i~~vGptGvGKTTt~~  239 (424)
T PRK05703        221 GGVVALVGPTGVGKTTTLA  239 (424)
T ss_pred             CcEEEEECCCCCCHHHHHH
Confidence            5578999999999998754

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=96.10  E-value=0.16  Score=45.28  Aligned_cols=111  Identities=21%  Similarity=0.303  Sum_probs=57.4

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCC---CCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCC
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYSPRI---DRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGN  150 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~---~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~  150 (316)
                      .++++.|+||.|||..     ++...+.-+..   ....-+.+.+-+|...-....+..+-...   +...     ....
T Consensus        62 p~lLivG~snnGKT~I-----i~rF~~~hp~~~d~~~~~~PVv~vq~P~~p~~~~~Y~~IL~~l---gaP~-----~~~~  128 (302)
T PF05621_consen   62 PNLLIVGDSNNGKTMI-----IERFRRLHPPQSDEDAERIPVVYVQMPPEPDERRFYSAILEAL---GAPY-----RPRD  128 (302)
T ss_pred             CceEEecCCCCcHHHH-----HHHHHHHCCCCCCCCCccccEEEEecCCCCChHHHHHHHHHHh---Cccc-----CCCC
Confidence            4799999999999985     23333222211   11123556666777766655554332222   1111     0111


Q ss_pred             hHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCc--HHHHHHHHHHhcc
Q 043110          151 RSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGF--GKEIEEILDILGS  216 (316)
Q Consensus       151 ~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~--~~~i~~i~~~l~~  216 (316)
                      ......             .....+++.      -.+++|||||.|.++.-..  +..+.+.++.+.+
T Consensus       129 ~~~~~~-------------~~~~~llr~------~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~N  177 (302)
T PF05621_consen  129 RVAKLE-------------QQVLRLLRR------LGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGN  177 (302)
T ss_pred             CHHHHH-------------HHHHHHHHH------cCCcEEEeechHHHhcccHHHHHHHHHHHHHHhh
Confidence            111110             012344443      3688999999999887432  2344445555543

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK05707 DNA polymerase III subunit delta'; Validated

Probab=96.09  E-value=0.063  Score=48.90  Aligned_cols=41  Identities=15%  Similarity=0.080  Sum_probs=29.8

Q ss_pred             CcHHHHHHHHHHhCCC----cEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           59 PTKVQAQAIPVILSGR----DVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        59 p~~~Q~~~i~~il~g~----d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      .+|||...|..+....    -.++.||.|.|||..+.. +...+..
T Consensus         4 ~yPWl~~~~~~~~~~~r~~ha~Lf~G~~G~GK~~~A~~-~A~~llC   48 (328)
T PRK05707          4 IYPWQQSLWQQLAGRGRHPHAYLLHGPAGIGKRALAER-LAAALLC   48 (328)
T ss_pred             CCCCcHHHHHHHHHCCCcceeeeeECCCCCCHHHHHHH-HHHHHcC
Confidence            5789999998877443    378999999999976543 4444443

>PHA03372 DNA packaging terminase subunit 1; Provisional

Probab=96.03  E-value=0.28  Score=47.69  Aligned_cols=144  Identities=17%  Similarity=0.200  Sum_probs=88.1

Q ss_pred             HHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHH
Q 043110           45 TLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCL  124 (316)
Q Consensus        45 ~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~  124 (316)
                      .+.+.|+..||...++.   .++.. ...|-.+.-.|--.|||+ +++|++..+...      -.|.++.|++.-+..++
T Consensus       178 r~~~~lk~~Fdi~~~s~---~~l~~-FKQkaTVFLVPRRHGKTW-f~VpiIsllL~s------~~gI~IGYvAHqKhvs~  246 (668)
T PHA03372        178 RVLEYLLHVFDIEFLSE---SSLNI-FKQKATVFLVPRRHGKTW-FIIPIISFLLKN------IIGISIGYVAHQKHVSQ  246 (668)
T ss_pred             HHHHHHHHHcCCcccCH---HHHHH-hhccceEEEecccCCcee-hHHHHHHHHHHh------hcCceEEEEeeHHHHHH
Confidence            34445544556554433   23333 355667888899999996 678898888762      34788999999999888


Q ss_pred             HHHHHHHHHHhhc-CCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH----HHHHhcCCccccCceeEEEEecchhhh
Q 043110          125 LVYEILQKLLHRF-RWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL----LDHLKHTSSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       125 Q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l----~~~l~~~~~~~~~~l~~lViDEad~l~  199 (316)
                      -+++.+...+... +.... ..             .++-.|.+.-|+.=    .....+.+...-.+..++++||||-+ 
T Consensus       247 ~Vf~EI~~~lrrwF~~~~v-i~-------------~k~~tI~~s~pg~Kst~~fasc~n~NsiRGQ~fnll~VDEA~FI-  311 (668)
T PHA03372        247 FVLKEVEFRCRRMFPRKHT-IE-------------NKDNVISIDHRGAKSTALFASCYNTNSIRGQNFHLLLVDEAHFI-  311 (668)
T ss_pred             HHHHHHHHHHhhhcCccce-ee-------------ecCcEEEEecCCCcceeeehhhccCccccCCCCCEEEEehhhcc-
Confidence            8777665544332 21111 00             01224556655421    11122333444457889999999986 


Q ss_pred             cCCcHHHHHHHHHHhccC
Q 043110          200 ELGFGKEIEEILDILGSR  217 (316)
Q Consensus       200 ~~~~~~~i~~i~~~l~~~  217 (316)
                         -.+.+..|+-.+...
T Consensus       312 ---~~~a~~tilgfm~q~  326 (668)
T PHA03372        312 ---KKDAFNTILGFLAQN  326 (668)
T ss_pred             ---CHHHHHHhhhhhccc
Confidence               345677777777654

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=96.03  E-value=0.11  Score=49.33  Aligned_cols=50  Identities=12%  Similarity=0.212  Sum_probs=30.1

Q ss_pred             ceeEEEEecchhhhcCC-cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHH
Q 043110          186 NLRWIIFDEADRILELG-FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHL  249 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~-~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~  249 (316)
                      ..++|+|||+|.+.+.. ....+..+++.+...              ..++++.|-.-|..+..+
T Consensus       194 ~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~--------------~k~iIitsd~~p~~l~~l  244 (440)
T PRK14088        194 KVDVLLIDDVQFLIGKTGVQTELFHTFNELHDS--------------GKQIVICSDREPQKLSEF  244 (440)
T ss_pred             cCCEEEEechhhhcCcHHHHHHHHHHHHHHHHc--------------CCeEEEECCCCHHHHHHH
Confidence            46789999999887542 334455555554431              346666555556555544

>PTZ00112 origin recognition complex 1 protein; Provisional

Probab=96.01  E-value=0.089  Score=53.43  Aligned_cols=23  Identities=35%  Similarity=0.586  Sum_probs=16.6

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHhh
Q 043110           76 VLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      ++|.|+||+|||++.-. ++..+.
T Consensus       784 LYIyG~PGTGKTATVK~-VLrELq  806 (1164)
T PTZ00112        784 LYISGMPGTGKTATVYS-VIQLLQ  806 (1164)
T ss_pred             EEEECCCCCCHHHHHHH-HHHHHH
Confidence            35999999999998543 444443

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=95.99  E-value=0.12  Score=45.49  Aligned_cols=18  Identities=28%  Similarity=0.388  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 043110           74 RDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~   91 (316)
                      .++++.||+|+|||..+-
T Consensus        43 ~~vll~GppGtGKTtlA~   60 (261)
T TIGR02881        43 LHMIFKGNPGTGKTTVAR   60 (261)
T ss_pred             ceEEEEcCCCCCHHHHHH
Confidence            478999999999998753

Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.

>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI

Probab=95.97  E-value=0.13  Score=57.53  Aligned_cols=61  Identities=33%  Similarity=0.388  Sum_probs=44.0

Q ss_pred             CCcHHHHHHHHHHhCCCc--EEEEcCCCCchHHHHH---HHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           58 APTKVQAQAIPVILSGRD--VLVNAATGTGKTVAYL---APIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d--~li~a~TGsGKT~~~~---lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .+++.|+.|+..++.+.|  +++++..|+|||....   -++.+.+..        .+..++.++||..-+.++
T Consensus      1019 ~Lt~~Q~~Ai~~il~~~~~~~~i~G~AGtGKTt~l~~~~~~i~~~~~~--------~g~~v~glApT~~Aa~~L 1084 (1960)
T TIGR02760      1019 RLTHGQKQAIHLIISTKDRFVAVQGLAGVGKTTMLESRYKPVLQAFES--------EQLQVIGLAPTHEAVGEL 1084 (1960)
T ss_pred             CCCHHHHHHHHHHHhCCCcEEEEEeCCCCCHHHhHHHHHHHHHHHHHh--------cCCeEEEEeChHHHHHHH
Confidence            589999999999987654  7889999999997641   223333222        255688899997765544

This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.

>PF05127 Helicase_RecD: Helicase; InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase

Probab=95.94  E-value=0.0033  Score=51.69  Aligned_cols=124  Identities=21%  Similarity=0.231  Sum_probs=53.3

Q ss_pred             EEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH-H
Q 043110           77 LVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE-K  155 (316)
Q Consensus        77 li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~  155 (316)
                      ++.|+-|-|||.+.-+.+...+..        ...+++|.+|+.+-++.+++.+..-+...+...     ........ .
T Consensus         1 VltA~RGRGKSa~lGl~~a~l~~~--------~~~~I~vtAP~~~~~~~lf~~~~~~l~~~~~~~-----~~~~~~~~~~   67 (177)
T PF05127_consen    1 VLTADRGRGKSAALGLAAAALIQK--------GKIRILVTAPSPENVQTLFEFAEKGLKALGYKE-----EKKKRIGQII   67 (177)
T ss_dssp             -EEE-TTSSHHHHHHHCCCCSSS-------------EEEE-SS--S-HHHHHCC--------------------------
T ss_pred             CccCCCCCCHHHHHHHHHHHHHHh--------cCceEEEecCCHHHHHHHHHHHHhhcccccccc-----cccccccccc
Confidence            578999999998865544333322        124599999999988887776655433221110     00000000 0


Q ss_pred             HHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceE
Q 043110          156 ARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQN  235 (316)
Q Consensus       156 ~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~  235 (316)
                      .....+..|-...|+.+...-        ...+++|||||=.+    -.+.+..+++                   ....
T Consensus        68 ~~~~~~~~i~f~~Pd~l~~~~--------~~~DlliVDEAAaI----p~p~L~~ll~-------------------~~~~  116 (177)
T PF05127_consen   68 KLRFNKQRIEFVAPDELLAEK--------PQADLLIVDEAAAI----PLPLLKQLLR-------------------RFPR  116 (177)
T ss_dssp             -----CCC--B--HHHHCCT------------SCEEECTGGGS-----HHHHHHHHC-------------------CSSE
T ss_pred             ccccccceEEEECCHHHHhCc--------CCCCEEEEechhcC----CHHHHHHHHh-------------------hCCE
Confidence            000113456666665553311        13478999999876    2344444432                   3345


Q ss_pred             EEEeeecch
Q 043110          236 LLLSATLNE  244 (316)
Q Consensus       236 i~~SAT~~~  244 (316)
                      ++||.|+..
T Consensus       117 vv~stTi~G  125 (177)
T PF05127_consen  117 VVFSTTIHG  125 (177)
T ss_dssp             EEEEEEBSS
T ss_pred             EEEEeeccc
Confidence            677888753

This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO and C-terminal to IPR013562 from INTERPRO.; PDB: 2ZPA_B.

>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]

Probab=95.93  E-value=0.4  Score=44.41  Aligned_cols=25  Identities=28%  Similarity=0.567  Sum_probs=18.5

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      |+++.|+||+|||...-. ++..+..
T Consensus        44 n~~iyG~~GTGKT~~~~~-v~~~l~~   68 (366)
T COG1474          44 NIIIYGPTGTGKTATVKF-VMEELEE   68 (366)
T ss_pred             cEEEECCCCCCHhHHHHH-HHHHHHh
Confidence            699999999999987533 4444444

>PRK08084 DNA replication initiation factor; Provisional

Probab=95.90  E-value=0.19  Score=43.51  Aligned_cols=18  Identities=11%  Similarity=0.244  Sum_probs=15.0

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      +..+++.||+|+|||-..
T Consensus        45 ~~~l~l~Gp~G~GKThLl   62 (235)
T PRK08084         45 SGYIYLWSREGAGRSHLL   62 (235)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            357999999999999653

>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases

Probab=95.90  E-value=0.068  Score=47.15  Aligned_cols=55  Identities=18%  Similarity=0.165  Sum_probs=31.8

Q ss_pred             HHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           69 VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        69 ~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      -+..|.-+++.|++|+|||...+--+.+....        .+..+++++-- +-..++...+..
T Consensus        26 G~~~g~~~~i~g~~G~GKT~l~~~~~~~~~~~--------~g~~vl~iS~E-~~~~~~~~r~~~   80 (271)
T cd01122          26 GLRKGELIILTAGTGVGKTTFLREYALDLITQ--------HGVRVGTISLE-EPVVRTARRLLG   80 (271)
T ss_pred             EEcCCcEEEEEcCCCCCHHHHHHHHHHHHHHh--------cCceEEEEEcc-cCHHHHHHHHHH
Confidence            34466779999999999997644333332221        14447777632 234444444433

Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.

>TIGR01074 rep ATP-dependent DNA helicase Rep

Probab=95.88  E-value=0.033  Score=55.85  Aligned_cols=69  Identities=22%  Similarity=0.135  Sum_probs=51.6

Q ss_pred             CcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           59 PTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        59 p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      +++-|++++..  .+.+++|.|+.|||||.+.+--+...+.....     ...++|+|+.|+..+.++.+.+.+..
T Consensus         2 Ln~~Q~~av~~--~~~~~~V~Ag~GSGKT~~L~~ri~~ll~~~~~-----~p~~IL~vTFt~~Aa~em~~Rl~~~l   70 (664)
T TIGR01074         2 LNPQQQEAVEY--VTGPCLVLAGAGSGKTRVITNKIAYLIQNCGY-----KARNIAAVTFTNKAAREMKERVAKTL   70 (664)
T ss_pred             CCHHHHHHHhC--CCCCEEEEecCCCCHHHHHHHHHHHHHHhcCC-----CHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            68899998865  45689999999999999865555555532111     12349999999999999998887654

Designed to identify rep members of the uvrD/rep subfamily.

>PRK08769 DNA polymerase III subunit delta'; Validated

Probab=95.88  E-value=0.17  Score=45.95  Aligned_cols=44  Identities=27%  Similarity=0.376  Sum_probs=31.8

Q ss_pred             CCCCcHHHHHHHHHHh----CCC---cEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           56 FEAPTKVQAQAIPVIL----SGR---DVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        56 ~~~p~~~Q~~~i~~il----~g~---d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      +..++|||..++..+.    .|+   -.++.||.|.||+..+.. +.+.+..
T Consensus         2 ~~~~yPW~~~~~~~l~~~~~~~rl~HA~Lf~Gp~G~GK~~lA~~-lA~~LlC   52 (319)
T PRK08769          2 TSAFSPWQQRAYDQTVAALDAGRLGHGLLICGPEGLGKRAVALA-LAEHVLA   52 (319)
T ss_pred             CccccccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHH-HHHHHhC
Confidence            3568899999987766    344   389999999999976543 4444444

>COG1444 Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=95.86  E-value=0.12  Score=51.68  Aligned_cols=145  Identities=17%  Similarity=0.191  Sum_probs=84.2

Q ss_pred             CCCCCcHHHHHHHHHHhCCC--cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           55 GFEAPTKVQAQAIPVILSGR--DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~il~g~--d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      ....+..-|.+.+..++.++  -+++.|.-|-|||.+.-+.+.. +.....      ...++|.+|+.+-++.+++.+.+
T Consensus       211 ~~T~dQ~~~l~~~~~l~~~~~~~~vlTAdRGRGKSA~lGi~~~~-~~~~~~------~~~iiVTAP~~~nv~~Lf~fa~~  283 (758)
T COG1444         211 CLTEDQAEALEILERLLDAPKRALVLTADRGRGKSAALGIALAA-AARLAG------SVRIIVTAPTPANVQTLFEFAGK  283 (758)
T ss_pred             hcChhHHHHHHHHHHHHcCCCceEEEEcCCCCcHhHHHhHHHHH-HHHhcC------CceEEEeCCCHHHHHHHHHHHHH
Confidence            44445555555666666544  4899999999999987766632 222111      34599999999998888877766


Q ss_pred             HHhhcCCceeEEeeC-CCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHH
Q 043110          133 LLHRFRWIVPGYVMG-GGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEIL  211 (316)
Q Consensus       133 ~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~  211 (316)
                      -+...+......... |.....    -.....|=...|....           ..-+++|||||=.+    -.+.+..++
T Consensus       284 ~l~~lg~~~~v~~d~~g~~~~~----~~~~~~i~y~~P~~a~-----------~~~DllvVDEAAaI----plplL~~l~  344 (758)
T COG1444         284 GLEFLGYKRKVAPDALGEIREV----SGDGFRIEYVPPDDAQ-----------EEADLLVVDEAAAI----PLPLLHKLL  344 (758)
T ss_pred             hHHHhCCccccccccccceeee----cCCceeEEeeCcchhc-----------ccCCEEEEehhhcC----ChHHHHHHH
Confidence            555443211110000 000000    0011224444554322           11578999999876    346666666


Q ss_pred             HHhccCcccccCCCCccccccceEEEEeeecch
Q 043110          212 DILGSRNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       212 ~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                      ...                   +.++||.|+..
T Consensus       345 ~~~-------------------~rv~~sTTIhG  358 (758)
T COG1444         345 RRF-------------------PRVLFSTTIHG  358 (758)
T ss_pred             hhc-------------------CceEEEeeecc
Confidence            544                   45888999864

>PF00004 AAA: ATPase family associated with various cellular activities (AAA); InterPro: IPR003959 AAA ATPases (ATPases Associated with diverse cellular Activities) form a large protein family and play a number of roles in the cell including cell-cycle regulation, protein proteolysis and disaggregation, organelle biogenesis and intracellular transport

Probab=95.78  E-value=0.13  Score=39.45  Aligned_cols=15  Identities=40%  Similarity=0.645  Sum_probs=13.1

Q ss_pred             EEEEcCCCCchHHHH
Q 043110           76 VLVNAATGTGKTVAY   90 (316)
Q Consensus        76 ~li~a~TGsGKT~~~   90 (316)
                      +++.||.|+|||...
T Consensus         1 ill~G~~G~GKT~l~   15 (132)
T PF00004_consen    1 ILLHGPPGTGKTTLA   15 (132)
T ss_dssp             EEEESSTTSSHHHHH
T ss_pred             CEEECcCCCCeeHHH
Confidence            589999999999864

Some of them function as molecular chaperones, subunits of proteolytic complexes or independent proteases (FtsH, Lon). They also act as DNA helicases and transcription factors []. AAA ATPases belong to the AAA+ superfamily of ringshaped P-loop NTPases, which act via the energy-dependent unfolding of macromolecules [, ]. There are six major clades of AAA domains (proteasome subunits, metalloproteases, domains D1 and D2 of ATPases with two AAA domains, the MSP1/katanin/spastin group and BCS1 and it homologues), as well as a number of deeply branching minor clades []. They assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that act upon a target substrate, either translocating or remodelling it []. They are found in all living organisms and share the common feature of the presence of a highly conserved AAA domain called the AAA module. This domain is responsible for ATP binding and hydrolysis. It contains 200-250 residues, among them there are two classical motifs, Walker A (GX4GKT) and Walker B (HyDE) []. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself. More information about these proteins can be found at Protein of the Month: AAA ATPases [].; GO: 0005524 ATP binding; PDB: 3H4M_A 1NSF_A 1D2N_A 1HQY_E 1DO0_E 1DO2_C 1G4B_E 1HT1_F 1G4A_F 1HT2_G ....

>PRK12726 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.77  E-value=0.2  Score=46.33  Aligned_cols=20  Identities=30%  Similarity=0.388  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCCchHHHHHH
Q 043110           73 GRDVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~l   92 (316)
                      ++-+++.+|+|+|||....-
T Consensus       206 ~~ii~lvGptGvGKTTt~ak  225 (407)
T PRK12726        206 HRIISLIGQTGVGKTTTLVK  225 (407)
T ss_pred             CeEEEEECCCCCCHHHHHHH
Confidence            45689999999999987543

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=95.76  E-value=0.34  Score=39.21  Aligned_cols=53  Identities=15%  Similarity=0.243  Sum_probs=38.9

Q ss_pred             CceeEEEEecchhhhcCCcH--HHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHH
Q 043110          185 TNLRWIIFDEADRILELGFG--KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKI  252 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~--~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~  252 (316)
                      ...++||+||+=..+..++-  +.+..+++..|.               ..-+|+.+-..|+.+.+++..
T Consensus        94 ~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~---------------~~evIlTGr~~p~~l~e~AD~  148 (159)
T cd00561          94 GEYDLVILDEINYALGYGLLDVEEVVDLLKAKPE---------------DLELVLTGRNAPKELIEAADL  148 (159)
T ss_pred             CCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCC---------------CCEEEEECCCCCHHHHHhCce
Confidence            46789999999988877643  455556655544               667888888888888877653

This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin (vitamin B12) adenosyltransferase, which is involved in cobalamin (vitamin B12) biosynthesis. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O <= phosphate + diphosphate + adenosylcobalamin.

>PLN03025 replication factor C subunit; Provisional

Probab=95.75  E-value=0.14  Score=46.56  Aligned_cols=29  Identities=21%  Similarity=0.366  Sum_probs=19.2

Q ss_pred             ceeEEEEecchhhhcCCcHHHHHHHHHHhc
Q 043110          186 NLRWIIFDEADRILELGFGKEIEEILDILG  215 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~~~~~i~~i~~~l~  215 (316)
                      ..+++||||+|.|... -...+..+++..+
T Consensus        99 ~~kviiiDE~d~lt~~-aq~aL~~~lE~~~  127 (319)
T PLN03025         99 RHKIVILDEADSMTSG-AQQALRRTMEIYS  127 (319)
T ss_pred             CeEEEEEechhhcCHH-HHHHHHHHHhccc
Confidence            4789999999998653 3344555555433

>PRK13342 recombination factor protein RarA; Reviewed

Probab=95.75  E-value=0.15  Score=48.11  Aligned_cols=17  Identities=29%  Similarity=0.390  Sum_probs=14.8

Q ss_pred             cEEEEcCCCCchHHHHH
Q 043110           75 DVLVNAATGTGKTVAYL   91 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~   91 (316)
                      ++++.||+|+|||....
T Consensus        38 ~ilL~GppGtGKTtLA~   54 (413)
T PRK13342         38 SMILWGPPGTGKTTLAR   54 (413)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            68999999999997753

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=95.73  E-value=0.18  Score=47.94  Aligned_cols=50  Identities=8%  Similarity=0.138  Sum_probs=30.6

Q ss_pred             ceeEEEEecchhhhcC-CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHH
Q 043110          186 NLRWIIFDEADRILEL-GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHL  249 (316)
Q Consensus       186 ~l~~lViDEad~l~~~-~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~  249 (316)
                      ..++|+|||+|.+... .....+-.+++.+...              ..|+++.|-+.|..+..+
T Consensus       202 ~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~--------------~k~IIlts~~~p~~l~~l  252 (445)
T PRK12422        202 NVDALFIEDIEVFSGKGATQEEFFHTFNSLHTE--------------GKLIVISSTCAPQDLKAM  252 (445)
T ss_pred             cCCEEEEcchhhhcCChhhHHHHHHHHHHHHHC--------------CCcEEEecCCCHHHHhhh
Confidence            5679999999998653 2344555555544321              456666665556665443

>COG2805 PilT Tfp pilus assembly protein, pilus retraction ATPase PilT [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=95.72  E-value=0.036  Score=49.07  Aligned_cols=27  Identities=33%  Similarity=0.609  Sum_probs=21.6

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHhhhcCC
Q 043110           76 VLVNAATGTGKTVAYLAPIINHLQSYSP  103 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l~~~~~  103 (316)
                      +++.+|||||||.. +.+++.++.+...
T Consensus       128 ILVTGpTGSGKSTT-lAamId~iN~~~~  154 (353)
T COG2805         128 ILVTGPTGSGKSTT-LAAMIDYINKHKA  154 (353)
T ss_pred             EEEeCCCCCcHHHH-HHHHHHHHhccCC
Confidence            89999999999976 4668888876443

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=95.69  E-value=0.095  Score=44.96  Aligned_cols=19  Identities=16%  Similarity=0.291  Sum_probs=15.5

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .+..+++.|++|+|||...
T Consensus        41 ~~~~~~l~G~~G~GKT~La   59 (227)
T PRK08903         41 ADRFFYLWGEAGSGRSHLL   59 (227)
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            3456999999999999653

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=95.66  E-value=0.05  Score=46.48  Aligned_cols=31  Identities=26%  Similarity=0.465  Sum_probs=24.5

Q ss_pred             CceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          185 TNLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      .+-+.+|+||||.|-+ |-+..+++.++...+
T Consensus       112 grhKIiILDEADSMT~-gAQQAlRRtMEiyS~  142 (333)
T KOG0991|consen  112 GRHKIIILDEADSMTA-GAQQALRRTMEIYSN  142 (333)
T ss_pred             CceeEEEeeccchhhh-HHHHHHHHHHHHHcc
Confidence            4678999999999876 577778877777665

>CHL00181 cbbX CbbX; Provisional

Probab=95.65  E-value=0.12  Score=46.29  Aligned_cols=20  Identities=35%  Similarity=0.493  Sum_probs=16.6

Q ss_pred             CCcEEEEcCCCCchHHHHHH
Q 043110           73 GRDVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~l   92 (316)
                      |.++++.||+|+|||..+-.
T Consensus        59 ~~~ill~G~pGtGKT~lAr~   78 (287)
T CHL00181         59 GLHMSFTGSPGTGKTTVALK   78 (287)
T ss_pred             CceEEEECCCCCCHHHHHHH
Confidence            45689999999999987643

>PRK12727 flagellar biosynthesis regulator FlhF; Provisional

Probab=95.65  E-value=0.62  Score=45.03  Aligned_cols=55  Identities=16%  Similarity=0.288  Sum_probs=31.9

Q ss_pred             cccCCCCHHHHHHHHHHcCCC-CCcHHHHHHHHH------------HhCCCcEEEEcCCCCchHHHHH
Q 043110           37 FSSLGLDSTLCDQLRERLGFE-APTKVQAQAIPV------------ILSGRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        37 f~~~~l~~~l~~~l~~~~g~~-~p~~~Q~~~i~~------------il~g~d~li~a~TGsGKT~~~~   91 (316)
                      ....|+++.+.+.|..++.-. ....-.......            +..|+.+.+.+|||+|||....
T Consensus       301 L~~~Gvs~~la~~L~~~l~~~~~~~~~~~~l~~~L~~~l~v~~~~~l~~G~vIaLVGPtGvGKTTtaa  368 (559)
T PRK12727        301 MDDYGFDAGLTRDVAMQIPADTELHRGRGLMLGLLSKRLPVAPVDPLERGGVIALVGPTGAGKTTTIA  368 (559)
T ss_pred             HHHCCCCHHHHHHHHHhhhcccchhhHHHHHHHHHHHhcCcCccccccCCCEEEEECCCCCCHHHHHH
Confidence            455678888777775554221 111111111111            2246678899999999998753

>KOG1133 consensus Helicase of the DEAD superfamily [Replication, recombination and repair]

Probab=95.60  E-value=0.022  Score=55.47  Aligned_cols=46  Identities=20%  Similarity=0.472  Sum_probs=36.1

Q ss_pred             cCCCCCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           54 LGFEAPTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        54 ~g~~~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      ++| +|+.||...+..+.    .|+-.|..+|||+|||++.+=+++..+..
T Consensus        12 fPy-~PYdIQ~~lM~elyrvLe~GkIgIfESPTGTGKSLSLiCaaltWL~~   61 (821)
T KOG1133|consen   12 FPY-TPYDIQEDLMRELYRVLEEGKIGIFESPTGTGKSLSLICAALTWLRD   61 (821)
T ss_pred             CCC-CchhHHHHHHHHHHHHHhcCCeeeeeCCCCCCchHHHHHHHHHHHHH
Confidence            345 49999988776544    78889999999999999987777766643

>TIGR01547 phage_term_2 phage terminase, large subunit, PBSX family

Probab=95.59  E-value=0.11  Score=48.76  Aligned_cols=146  Identities=15%  Similarity=0.199  Sum_probs=78.5

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH-HHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH
Q 043110           76 VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE-LCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE  154 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~-L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (316)
                      .++.++.|||||.+..+-++..+...      ..+.+++++-|+.. |-.-++..++.....++... ..-......  .
T Consensus         4 ~i~~GgrgSGKS~~~~~~~~~~~~~~------~~~~~~~~~r~~~~sl~~sv~~~l~~~i~~~g~~~-~~~~~~~~~--~   74 (396)
T TIGR01547         4 IIAKGGRRSGKTFAIALKLVEKLAIN------KKQQNILAARKVQNSIRDSVFKDIENLLSIEGINY-EFKKSKSSM--E   74 (396)
T ss_pred             EEEeCCCCcccHHHHHHHHHHHHHhc------CCCcEEEEEehhhhHHHHHHHHHHHHHHHHcCChh-heeecCCcc--E
Confidence            67899999999999887777777663      13456899989877 66666677776655443211 000000000  0


Q ss_pred             HHHHhc-CCcEEEeCc-HHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCcccccc
Q 043110          155 KARLRK-GISILVATP-GHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVK  232 (316)
Q Consensus       155 ~~~l~~-~~~IlV~Tp-~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~  232 (316)
                      . .+.. +..|++..- +.... +.     ....+.++.+|||..+..    ..+..++.++....             .
T Consensus        75 i-~~~~~g~~i~f~g~~d~~~~-ik-----~~~~~~~~~idEa~~~~~----~~~~~l~~rlr~~~-------------~  130 (396)
T TIGR01547        75 I-KILNTGKKFIFKGLNDKPNK-LK-----SGAGIAIIWFEEASQLTF----EDIKELIPRLRETG-------------G  130 (396)
T ss_pred             E-EecCCCeEEEeecccCChhH-hh-----CcceeeeehhhhhhhcCH----HHHHHHHHHhhccC-------------C
Confidence            0 0111 233444332 11111 11     123468999999998743    35555555554210             1


Q ss_pred             ceEEEEeeecchhHHHHHHHhc
Q 043110          233 RQNLLLSATLNEKVNHLTKISL  254 (316)
Q Consensus       233 ~q~i~~SAT~~~~v~~~~~~~l  254 (316)
                      .+.+++|.|.+..-.-+.+.+.
T Consensus       131 ~~~i~~t~NP~~~~~w~~~~f~  152 (396)
T TIGR01547       131 KKFIIFSSNPESPLHWVKKRFI  152 (396)
T ss_pred             ccEEEEEcCcCCCccHHHHHHH
Confidence            2247778876543333344443

This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354.

>PRK00411 cdc6 cell division control protein 6; Reviewed

Probab=95.58  E-value=0.27  Score=45.87  Aligned_cols=24  Identities=33%  Similarity=0.523  Sum_probs=17.8

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHh
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHL   98 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l   98 (316)
                      .++++.||+|+|||...- -++..+
T Consensus        56 ~~~lI~G~~GtGKT~l~~-~v~~~l   79 (394)
T PRK00411         56 LNVLIYGPPGTGKTTTVK-KVFEEL   79 (394)
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHH
Confidence            569999999999998743 344444

>PRK04195 replication factor C large subunit; Provisional

Probab=95.50  E-value=0.16  Score=48.84  Aligned_cols=45  Identities=24%  Similarity=0.271  Sum_probs=28.3

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhC---CCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILS---GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~---g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|+++-.++...+.|..-.             ..+..   .+.+++.||+|+|||...
T Consensus         9 rP~~l~dlvg~~~~~~~l~~~l-------------~~~~~g~~~~~lLL~GppG~GKTtla   56 (482)
T PRK04195          9 RPKTLSDVVGNEKAKEQLREWI-------------ESWLKGKPKKALLLYGPPGVGKTSLA   56 (482)
T ss_pred             CCCCHHHhcCCHHHHHHHHHHH-------------HHHhcCCCCCeEEEECCCCCCHHHHH
Confidence            3455667766666666652211             11112   457999999999999764

>PRK09183 transposase/IS protein; Provisional

Probab=95.50  E-value=0.35  Score=42.57  Aligned_cols=22  Identities=23%  Similarity=0.400  Sum_probs=18.1

Q ss_pred             HhCCCcEEEEcCCCCchHHHHH
Q 043110           70 ILSGRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        70 il~g~d~li~a~TGsGKT~~~~   91 (316)
                      +-.|.++++.||+|+|||....
T Consensus        99 i~~~~~v~l~Gp~GtGKThLa~  120 (259)
T PRK09183         99 IERNENIVLLGPSGVGKTHLAI  120 (259)
T ss_pred             hhcCCeEEEEeCCCCCHHHHHH
Confidence            3467899999999999997653

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=95.46  E-value=0.14  Score=42.62  Aligned_cols=140  Identities=14%  Similarity=0.133  Sum_probs=75.0

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH-HHHHHHHHhhcCCceeEEeeCC--
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV-YEILQKLLHRFRWIVPGYVMGG--  148 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~-~~~~~~~~~~~~~~~~~~~~~~--  148 (316)
                      ....+++..++|.|||.+++--++..+..         |.+++++-=.+--..+- ...++.+    ..+.......+  
T Consensus        21 ~~g~v~v~~g~GkGKtt~a~g~a~ra~g~---------G~~V~ivQFlKg~~~~GE~~~l~~l----~~v~~~~~g~~~~   87 (191)
T PRK05986         21 EKGLLIVHTGNGKGKSTAAFGMALRAVGH---------GKKVGVVQFIKGAWSTGERNLLEFG----GGVEFHVMGTGFT   87 (191)
T ss_pred             cCCeEEEECCCCCChHHHHHHHHHHHHHC---------CCeEEEEEEecCCCccCHHHHHhcC----CCcEEEECCCCCc
Confidence            55689999999999999987766666644         55577764222110000 1122221    11111111111  


Q ss_pred             ---CChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcH--HHHHHHHHHhccCcccccC
Q 043110          149 ---GNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFG--KEIEEILDILGSRNIASIG  223 (316)
Q Consensus       149 ---~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~--~~i~~i~~~l~~~~~~~~~  223 (316)
                         ..........           ...+.....  .+.-...++||+||+-..++.++-  +++..+++..|.       
T Consensus        88 ~~~~~~~e~~~~~-----------~~~~~~a~~--~l~~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~-------  147 (191)
T PRK05986         88 WETQDRERDIAAA-----------REGWEEAKR--MLADESYDLVVLDELTYALKYGYLDVEEVLEALNARPG-------  147 (191)
T ss_pred             ccCCCcHHHHHHH-----------HHHHHHHHH--HHhCCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCC-------
Confidence               1111111111           111222211  111246789999999999988753  455555555443       


Q ss_pred             CCCccccccceEEEEeeecchhHHHHHHH
Q 043110          224 EGNEVSNVKRQNLLLSATLNEKVNHLTKI  252 (316)
Q Consensus       224 ~~~~~~~~~~q~i~~SAT~~~~v~~~~~~  252 (316)
                              ..-+|+.--..|+.+.+.+..
T Consensus       148 --------~~evVlTGR~~p~~Lie~ADl  168 (191)
T PRK05986        148 --------MQHVVITGRGAPRELIEAADL  168 (191)
T ss_pred             --------CCEEEEECCCCCHHHHHhCch
Confidence                    566777777788888877664

>PF06745 KaiC: KaiC; InterPro: IPR014774 This entry represents a domain within bacterial and archaeal proteins, most of which are hypothetical

Probab=95.45  E-value=0.11  Score=44.46  Aligned_cols=53  Identities=26%  Similarity=0.336  Sum_probs=32.9

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .|..+++.+++|+|||...+--+.+.+.+.        |-.+++++- .+-..++.+.++.+
T Consensus        18 ~gs~~li~G~~GsGKT~l~~q~l~~~~~~~--------ge~vlyvs~-ee~~~~l~~~~~s~   70 (226)
T PF06745_consen   18 KGSVVLISGPPGSGKTTLALQFLYNGLKNF--------GEKVLYVSF-EEPPEELIENMKSF   70 (226)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHHH--------T--EEEEES-SS-HHHHHHHHHTT
T ss_pred             CCcEEEEEeCCCCCcHHHHHHHHHHhhhhc--------CCcEEEEEe-cCCHHHHHHHHHHc
Confidence            456799999999999987554444444431        222888874 34456666665554

More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria []. The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC [].; PDB: 2W0M_A 2ZTS_C 4DUG_B 3K0E_B 3K09_B 3S1A_E 3JZM_E 2GBL_B 3DVL_A 1TF7_C ....

>PRK08533 flagellar accessory protein FlaH; Reviewed

Probab=95.41  E-value=0.3  Score=42.10  Aligned_cols=53  Identities=19%  Similarity=0.170  Sum_probs=32.5

Q ss_pred             hCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           71 LSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        71 l~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      ..|.-+++.+++|+|||...+--+...+..         +.++++++ +.+-..+..+.+..+
T Consensus        22 ~~g~~~~i~G~~G~GKTtl~~~~~~~~~~~---------g~~~~yi~-~e~~~~~~~~~~~~~   74 (230)
T PRK08533         22 PAGSLILIEGDESTGKSILSQRLAYGFLQN---------GYSVSYVS-TQLTTTEFIKQMMSL   74 (230)
T ss_pred             CCCcEEEEECCCCCCHHHHHHHHHHHHHhC---------CCcEEEEe-CCCCHHHHHHHHHHh
Confidence            356779999999999998743333332222         34478888 434445555555443

>TIGR01073 pcrA ATP-dependent DNA helicase PcrA

Probab=95.39  E-value=0.055  Score=54.86  Aligned_cols=72  Identities=21%  Similarity=0.181  Sum_probs=53.0

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           57 EAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      ..+++-|++++.+  ....++|.|..|||||.+..--+...+....-     ..-++|+++-|+.-|..+.+++..+..
T Consensus         3 ~~Ln~~Q~~av~~--~~g~~lV~AgaGSGKT~~l~~ria~Li~~~~i-----~P~~IL~lTFT~kAA~em~~Rl~~~~~   74 (726)
T TIGR01073         3 AHLNPEQREAVKT--TEGPLLIMAGAGSGKTRVLTHRIAHLIAEKNV-----APWNILAITFTNKAAREMKERVEKLLG   74 (726)
T ss_pred             cccCHHHHHHHhC--CCCCEEEEeCCCCCHHHHHHHHHHHHHHcCCC-----CHHHeeeeeccHHHHHHHHHHHHHHhc
Confidence            3589999999975  35679999999999999865555554433111     112499999999999998888877653

Designed to identify pcrA members of the uvrD/rep subfamily.

>PRK11823 DNA repair protein RadA; Provisional

Probab=95.28  E-value=0.17  Score=48.12  Aligned_cols=51  Identities=24%  Similarity=0.287  Sum_probs=32.0

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      |.-+++.+++|+|||...+--+. .+..        .+.+++|+.- .+-..|+...+..+
T Consensus        80 Gs~~lI~G~pG~GKTtL~lq~a~-~~a~--------~g~~vlYvs~-Ees~~qi~~ra~rl  130 (446)
T PRK11823         80 GSVVLIGGDPGIGKSTLLLQVAA-RLAA--------AGGKVLYVSG-EESASQIKLRAERL  130 (446)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH-HHHh--------cCCeEEEEEc-cccHHHHHHHHHHc
Confidence            44689999999999986443333 2222        1345888874 44556766665554

>PF13177 DNA_pol3_delta2: DNA polymerase III, delta subunit; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G 1IQP_E 2GNO_A 1SXJ_E 1A5T_A

Probab=95.25  E-value=0.2  Score=40.73  Aligned_cols=30  Identities=27%  Similarity=0.306  Sum_probs=19.3

Q ss_pred             CceeEEEEecchhhhcCCcHHHHHHHHHHhc
Q 043110          185 TNLRWIIFDEADRILELGFGKEIEEILDILG  215 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~~~i~~i~~~l~  215 (316)
                      ...+++||||||.|... ....+.+.++.-+
T Consensus       101 ~~~KviiI~~ad~l~~~-a~NaLLK~LEepp  130 (162)
T PF13177_consen  101 GKYKVIIIDEADKLTEE-AQNALLKTLEEPP  130 (162)
T ss_dssp             SSSEEEEEETGGGS-HH-HHHHHHHHHHSTT
T ss_pred             CCceEEEeehHhhhhHH-HHHHHHHHhcCCC
Confidence            46899999999998653 3344444554443

...

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=95.25  E-value=0.17  Score=41.42  Aligned_cols=53  Identities=17%  Similarity=0.300  Sum_probs=39.3

Q ss_pred             CceeEEEEecchhhhcCCcH--HHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHH
Q 043110          185 TNLRWIIFDEADRILELGFG--KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKI  252 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~--~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~  252 (316)
                      ...++||+||+-..++.++-  +.+..+++..|.               ..-+|+..-..|+.+.+++..
T Consensus        96 ~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~---------------~~evVlTGR~~p~~l~e~AD~  150 (173)
T TIGR00708        96 PELDLVLLDELTYALKYGYLDVEEVVEALQERPG---------------HQHVIITGRGCPQDLLELADL  150 (173)
T ss_pred             CCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCC---------------CCEEEEECCCCCHHHHHhCce
Confidence            46889999999998887743  455566655554               667888888888888877663

Alternate name: corrinoid adenosyltransferase.

>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed

Probab=95.23  E-value=0.24  Score=49.94  Aligned_cols=16  Identities=25%  Similarity=0.457  Sum_probs=14.5

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      ++++.||+|+|||...
T Consensus        54 slLL~GPpGtGKTTLA   69 (725)
T PRK13341         54 SLILYGPPGVGKTTLA   69 (725)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            6999999999999765

>PRK12402 replication factor C small subunit 2; Reviewed

Probab=95.22  E-value=0.24  Score=45.06  Aligned_cols=17  Identities=41%  Similarity=0.604  Sum_probs=14.9

Q ss_pred             cEEEEcCCCCchHHHHH
Q 043110           75 DVLVNAATGTGKTVAYL   91 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~   91 (316)
                      ++++.||+|+|||....
T Consensus        38 ~lll~Gp~GtGKT~la~   54 (337)
T PRK12402         38 HLLVQGPPGSGKTAAVR   54 (337)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            69999999999998753

>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]

Probab=95.20  E-value=0.17  Score=45.61  Aligned_cols=28  Identities=32%  Similarity=0.376  Sum_probs=20.1

Q ss_pred             CCCc-EEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           72 SGRD-VLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        72 ~g~d-~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      +..+ +++.+|.|+|||.++.. +...+..
T Consensus        22 ~~~halL~~Gp~G~Gktt~a~~-lA~~l~~   50 (325)
T COG0470          22 RLPHALLFYGPPGVGKTTAALA-LAKELLC   50 (325)
T ss_pred             CCCceeeeeCCCCCCHHHHHHH-HHHHHhC
Confidence            3456 99999999999988643 4444443

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=95.18  E-value=0.22  Score=48.97  Aligned_cols=48  Identities=13%  Similarity=0.171  Sum_probs=30.0

Q ss_pred             ceeEEEEecchhhhcCC-cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHH
Q 043110          186 NLRWIIFDEADRILELG-FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVN  247 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~-~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~  247 (316)
                      ++++|||||+|.+.... ....+-.+++.+...              +.++|+.|-..|..+.
T Consensus       377 ~~DLLlIDDIq~l~gke~tqeeLF~l~N~l~e~--------------gk~IIITSd~~P~eL~  425 (617)
T PRK14086        377 EMDILLVDDIQFLEDKESTQEEFFHTFNTLHNA--------------NKQIVLSSDRPPKQLV  425 (617)
T ss_pred             cCCEEEEehhccccCCHHHHHHHHHHHHHHHhc--------------CCCEEEecCCChHhhh
Confidence            56899999999886532 344555566655431              4567766655555543

>PRK13833 conjugal transfer protein TrbB; Provisional

Probab=95.18  E-value=0.074  Score=48.25  Aligned_cols=58  Identities=24%  Similarity=0.304  Sum_probs=38.8

Q ss_pred             CcHHHHHHHHHH-hCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           59 PTKVQAQAIPVI-LSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        59 p~~~Q~~~i~~i-l~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      +++.|...+..+ ..+++++++|+||||||... -.++..+....      .+-+++.+-.+.||.
T Consensus       129 ~~~~~~~~L~~~v~~~~nilI~G~tGSGKTTll-~aL~~~i~~~~------~~~rivtiEd~~El~  187 (323)
T PRK13833        129 MTEAQASVIRSAIDSRLNIVISGGTGSGKTTLA-NAVIAEIVASA------PEDRLVILEDTAEIQ  187 (323)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHHhcCC------CCceEEEecCCcccc
Confidence            456777666554 46678999999999999753 44555443211      234578888888874

>PRK13894 conjugal transfer ATPase TrbB; Provisional

Probab=95.14  E-value=0.07  Score=48.40  Aligned_cols=58  Identities=29%  Similarity=0.381  Sum_probs=38.8

Q ss_pred             CcHHHHHHHHH-HhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           59 PTKVQAQAIPV-ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        59 p~~~Q~~~i~~-il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      +++.|.+.+.. +..++++++.|+||||||.. +-.++..+...      ....+++++-.+.||.
T Consensus       133 ~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTl-l~aL~~~~~~~------~~~~rivtIEd~~El~  191 (319)
T PRK13894        133 MTAAQREAIIAAVRAHRNILVIGGTGSGKTTL-VNAIINEMVIQ------DPTERVFIIEDTGEIQ  191 (319)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHH-HHHHHHhhhhc------CCCceEEEEcCCCccc
Confidence            45677777754 45678999999999999954 44455443221      1234588888888873

>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]

Probab=95.13  E-value=0.12  Score=47.73  Aligned_cols=58  Identities=17%  Similarity=0.140  Sum_probs=33.1

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcC
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFR  138 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~  138 (316)
                      ++.+.+.||||.|||....=-+.......      .....+||-+.|--.+.  +++++.++.-++
T Consensus       203 ~~vi~LVGPTGVGKTTTlAKLAar~~~~~------~~~kVaiITtDtYRIGA--~EQLk~Ya~im~  260 (407)
T COG1419         203 KRVIALVGPTGVGKTTTLAKLAARYVMLK------KKKKVAIITTDTYRIGA--VEQLKTYADIMG  260 (407)
T ss_pred             CcEEEEECCCCCcHHHHHHHHHHHHHhhc------cCcceEEEEeccchhhH--HHHHHHHHHHhC
Confidence            67799999999999988432222222111      11233677776644332  455566555443

>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]

Probab=95.12  E-value=0.12  Score=46.77  Aligned_cols=79  Identities=24%  Similarity=0.316  Sum_probs=51.8

Q ss_pred             cccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCC-cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCC
Q 043110           32 FASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGR-DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSG  110 (316)
Q Consensus        32 ~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~-d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~  110 (316)
                      ++-..|..-.+.-.   .|   ..|...++-|...+..+..++ |+++++.||||||...     +.+...-+     ..
T Consensus       137 lsIRKf~k~~ltl~---dl---i~~gt~~~~~a~~L~~av~~r~NILisGGTGSGKTTlL-----Nal~~~i~-----~~  200 (355)
T COG4962         137 LSIRKFPKIKLTLL---DL---IIFGTMIRRAAKFLRRAVGIRCNILISGGTGSGKTTLL-----NALSGFID-----SD  200 (355)
T ss_pred             ccccccccccccHH---HH---HHcCCcCHHHHHHHHHHHhhceeEEEeCCCCCCHHHHH-----HHHHhcCC-----Cc
Confidence            44445554444332   33   467788999999888877766 9999999999999752     22222111     12


Q ss_pred             eeEEEEeCChHHHHHH
Q 043110          111 TFALVLVPTSELCLLV  126 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~  126 (316)
                      -++|.+--|.||--+.
T Consensus       201 eRvItiEDtaELql~~  216 (355)
T COG4962         201 ERVITIEDTAELQLAH  216 (355)
T ss_pred             ccEEEEeehhhhccCC
Confidence            2599999999886443

>TIGR02880 cbbX_cfxQ probable Rubsico expression protein CbbX

Probab=95.11  E-value=0.17  Score=45.15  Aligned_cols=18  Identities=28%  Similarity=0.313  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      +.++++.||+|+|||.++
T Consensus        58 ~~~vll~G~pGTGKT~lA   75 (284)
T TIGR02880        58 TLHMSFTGNPGTGKTTVA   75 (284)
T ss_pred             CceEEEEcCCCCCHHHHH
Confidence            457999999999999875

Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis.

>PRK08939 primosomal protein DnaI; Reviewed

Probab=95.03  E-value=0.64  Score=41.95  Aligned_cols=26  Identities=23%  Similarity=0.330  Sum_probs=18.9

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      ++.+++.|++|+|||.... ++.+.+.
T Consensus       156 ~~gl~L~G~~G~GKThLa~-Aia~~l~  181 (306)
T PRK08939        156 VKGLYLYGDFGVGKSYLLA-AIANELA  181 (306)
T ss_pred             CCeEEEECCCCCCHHHHHH-HHHHHHH
Confidence            4579999999999997643 3444444

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=95.01  E-value=0.12  Score=52.58  Aligned_cols=90  Identities=14%  Similarity=-0.005  Sum_probs=63.8

Q ss_pred             HhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEE
Q 043110          158 LRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLL  237 (316)
Q Consensus       158 l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~  237 (316)
                      ++....|+++||..|..-+-. +.+.++++..+|+||||++.+..-...+..+++.-.+               ..-+.+
T Consensus         4 ly~~ggi~~~T~rIl~~DlL~-~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr~~n~---------------~gfIka   67 (814)
T TIGR00596         4 VYLEGGIFSITSRILVVDLLT-GIIPPELITGILVLRADRIIESSQEAFILRLYRQKNK---------------TGFIKA   67 (814)
T ss_pred             HhhcCCEEEEechhhHhHHhc-CCCCHHHccEEEEeecccccccccHHHHHHHHHHhCC---------------CcceEE
Confidence            344568999999988654543 5677789999999999999887666777777766554               667899


Q ss_pred             Eeeecch------hHHHHHHHhcCCCEEEEcC
Q 043110          238 LSATLNE------KVNHLTKISLETPVLIGLD  263 (316)
Q Consensus       238 ~SAT~~~------~v~~~~~~~l~~p~~i~~~  263 (316)
                      |||....      .+...++...-.-+.+.-.
T Consensus        68 fSdsP~~~~~g~~~l~~vmk~L~i~~v~l~pr   99 (814)
T TIGR00596        68 FSDNPEAFTMGFSPLETKMRNLFLRHVYLWPR   99 (814)
T ss_pred             ecCCCcccccchHHHHHHHHHhCcCeEEEeCC
Confidence            9999764      3555555443344555433

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

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=94.96  E-value=0.075  Score=52.86  Aligned_cols=115  Identities=22%  Similarity=0.204  Sum_probs=66.1

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE  154 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (316)
                      -.|+.-.-|-|||..-+..++.+-...........+...||+||+ ++..|+...+.+.... ....+.+.+|   ...+
T Consensus       154 ggIladd~glgkt~~ti~l~l~~~~~~~~~~~~~~~kttLivcp~-s~~~qW~~elek~~~~-~~l~v~v~~g---r~kd  228 (674)
T KOG1001|consen  154 GGILADDMGLGKTVKTIALILKQKLKSKEEDRQKEFKTTLIVCPT-SLLTQWKTELEKVTEE-DKLSIYVYHG---RTKD  228 (674)
T ss_pred             cceEeeccccchHHHHHHHHHhcccCCcchhhccccCceeEecch-HHHHHHHHHHhccCCc-cceEEEEecc---cccc
Confidence            368888899999998644333221111100011234558899987 5567777777444332 3344444444   1112


Q ss_pred             HHHHhcCCcEEEeCcHHHHH-HHhcCCccccCceeEEEEecchhhhcC
Q 043110          155 KARLRKGISILVATPGHLLD-HLKHTSSFLHTNLRWIIFDEADRILEL  201 (316)
Q Consensus       155 ~~~l~~~~~IlV~Tp~~l~~-~l~~~~~~~~~~l~~lViDEad~l~~~  201 (316)
                      . ....+++||++|++.+.. .+.      .-..-.+|+||||.+-..
T Consensus       229 ~-~el~~~dVVltTy~il~~~~l~------~i~w~Riildea~~ikn~  269 (674)
T KOG1001|consen  229 K-SELNSYDVVLTTYDILKNSPLV------KIKWLRIVLDEAHTIKNK  269 (674)
T ss_pred             c-chhcCCceEEeeHHHhhccccc------ceeEEEEEeccccccCCc
Confidence            2 223457899999988863 221      123457899999987654

>PF13173 AAA_14: AAA domain

Probab=94.95  E-value=0.55  Score=36.30  Aligned_cols=27  Identities=15%  Similarity=0.327  Sum_probs=19.6

Q ss_pred             ceeEEEEecchhhhcCCcHHHHHHHHHHh
Q 043110          186 NLRWIIFDEADRILELGFGKEIEEILDIL  214 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~~~~~i~~i~~~l  214 (316)
                      .-.+++|||+|.+-+  +...+..+...-
T Consensus        61 ~~~~i~iDEiq~~~~--~~~~lk~l~d~~   87 (128)
T PF13173_consen   61 GKKYIFIDEIQYLPD--WEDALKFLVDNG   87 (128)
T ss_pred             CCcEEEEehhhhhcc--HHHHHHHHHHhc
Confidence            456899999999854  666666666643

>TIGR00064 ftsY signal recognition particle-docking protein FtsY

Probab=94.92  E-value=0.79  Score=40.62  Aligned_cols=19  Identities=26%  Similarity=0.364  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCCchHHHHHH
Q 043110           74 RDVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~l   92 (316)
                      +-+++.+++|+|||....-
T Consensus        73 ~vi~l~G~~G~GKTTt~ak   91 (272)
T TIGR00064        73 NVILFVGVNGVGKTTTIAK   91 (272)
T ss_pred             eEEEEECCCCCcHHHHHHH
Confidence            3477889999999987543

There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.

>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA

Probab=94.90  E-value=0.098  Score=51.22  Aligned_cols=126  Identities=18%  Similarity=0.194  Sum_probs=73.6

Q ss_pred             CCcHHHHHHHHHHhCC--CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHH-HHHHHHH
Q 043110           58 APTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY-EILQKLL  134 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g--~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~-~~~~~~~  134 (316)
                      ..+|+|.+.+..+...  +.+++..++-+|||.+.+. ++-......+.       -+|++.||.++|.... ..+..+.
T Consensus        16 ~~~Py~~eimd~~~~~~v~~Vv~~k~aQ~GkT~~~~n-~~g~~i~~~P~-------~~l~v~Pt~~~a~~~~~~rl~Pmi   87 (557)
T PF05876_consen   16 DRTPYLREIMDALSDPSVREVVVMKSAQVGKTELLLN-WIGYSIDQDPG-------PMLYVQPTDDAAKDFSKERLDPMI   87 (557)
T ss_pred             CCChhHHHHHHhcCCcCccEEEEEEcchhhHhHHHHh-hceEEEEeCCC-------CEEEEEEcHHHHHHHHHHHHHHHH
Confidence            4689999998887654  4699999999999995433 33333333322       2999999999999877 4676666


Q ss_pred             hhcCCceeEEeeC----CCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          135 HRFRWIVPGYVMG----GGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       135 ~~~~~~~~~~~~~----~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                      ...+.+.. .+..    ..........+. +..+.++.-+       ....+.-..++++++||.|..-+
T Consensus        88 ~~sp~l~~-~~~~~~~~~~~~t~~~k~f~-gg~l~~~ga~-------S~~~l~s~~~r~~~~DEvD~~p~  148 (557)
T PF05876_consen   88 RASPVLRR-KLSPSKSRDSGNTILYKRFP-GGFLYLVGAN-------SPSNLRSRPARYLLLDEVDRYPD  148 (557)
T ss_pred             HhCHHHHH-HhCchhhcccCCchhheecC-CCEEEEEeCC-------CCcccccCCcCEEEEechhhccc
Confidence            55432221 1111    011111111122 2334333321       11122224688999999999853

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].

>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.89  E-value=0.76  Score=40.64  Aligned_cols=21  Identities=24%  Similarity=0.286  Sum_probs=17.0

Q ss_pred             CCcEEEEcCCCCchHHHHHHH
Q 043110           73 GRDVLVNAATGTGKTVAYLAP   93 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp   93 (316)
                      +..+.+.+++|+|||..+..-
T Consensus        75 ~~~i~~~G~~g~GKTtl~~~l   95 (270)
T PRK06731         75 VQTIALIGPTGVGKTTTLAKM   95 (270)
T ss_pred             CCEEEEECCCCCcHHHHHHHH
Confidence            356899999999999876543

>cd01121 Sms Sms (bacterial radA) DNA repair protein

Probab=94.87  E-value=0.4  Score=44.47  Aligned_cols=51  Identities=22%  Similarity=0.270  Sum_probs=31.3

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      |.-+++.+++|+|||...+- +...+..        .+.+++|+.-. +-..|+...+..+
T Consensus        82 GslvLI~G~pG~GKStLllq-~a~~~a~--------~g~~VlYvs~E-Es~~qi~~Ra~rl  132 (372)
T cd01121          82 GSVILIGGDPGIGKSTLLLQ-VAARLAK--------RGGKVLYVSGE-ESPEQIKLRADRL  132 (372)
T ss_pred             CeEEEEEeCCCCCHHHHHHH-HHHHHHh--------cCCeEEEEECC-cCHHHHHHHHHHc
Confidence            45689999999999986543 2233322        12348888754 3455665555444

This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.

>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif

Probab=94.86  E-value=0.077  Score=43.89  Aligned_cols=46  Identities=28%  Similarity=0.345  Sum_probs=27.2

Q ss_pred             hCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           71 LSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        71 l~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      -+++++++.|++|+|||..+.. +...+...        |..++++ +..+|...+
T Consensus        45 ~~~~~l~l~G~~G~GKThLa~a-i~~~~~~~--------g~~v~f~-~~~~L~~~l   90 (178)
T PF01695_consen   45 ENGENLILYGPPGTGKTHLAVA-IANEAIRK--------GYSVLFI-TASDLLDEL   90 (178)
T ss_dssp             SC--EEEEEESTTSSHHHHHHH-HHHHHHHT--------T--EEEE-EHHHHHHHH
T ss_pred             ccCeEEEEEhhHhHHHHHHHHH-HHHHhccC--------CcceeEe-ecCceeccc
Confidence            3677899999999999987543 44444431        3335554 455665443

They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.

>TIGR03499 FlhF flagellar biosynthetic protein FlhF

Probab=94.85  E-value=0.4  Score=42.73  Aligned_cols=54  Identities=22%  Similarity=0.262  Sum_probs=30.5

Q ss_pred             ccCCCCHHHHHHHHHHcC-CCCCcHHHHHHHHHH---h-----------CCCcEEEEcCCCCchHHHHH
Q 043110           38 SSLGLDSTLCDQLRERLG-FEAPTKVQAQAIPVI---L-----------SGRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        38 ~~~~l~~~l~~~l~~~~g-~~~p~~~Q~~~i~~i---l-----------~g~d~li~a~TGsGKT~~~~   91 (316)
                      .+.++++++.+.|.+.+. ...+...+......+   +           .++.+++.+|||+|||....
T Consensus       144 ~~~gv~~~la~~L~~~l~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~vi~~vGptGvGKTTt~~  212 (282)
T TIGR03499       144 LRAGVSPELARELLEKLPERADAEDAWRWLREALEKMLPVKPEEDEILEQGGVIALVGPTGVGKTTTLA  212 (282)
T ss_pred             HHCCCCHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHhccCCccccccCCCeEEEEECCCCCCHHHHHH
Confidence            345777777777655442 122222222222221   1           23468899999999998754

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

Probab=94.83  E-value=0.14  Score=51.47  Aligned_cols=117  Identities=21%  Similarity=0.203  Sum_probs=71.1

Q ss_pred             HHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH-HHHhhcCCceeEEe
Q 043110           67 IPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ-KLLHRFRWIVPGYV  145 (316)
Q Consensus        67 i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~-~~~~~~~~~~~~~~  145 (316)
                      +.++....-+++.+.||+|||.-+.--+++.+.....-    ...-+.+--|+|-.+.-+.+.+. +.+...... ++  
T Consensus       387 ~q~v~dn~v~~I~getgcgk~tq~aq~iLe~~~~ns~g----~~~na~v~qprrisaisiaerva~er~e~~g~t-vg--  459 (1282)
T KOG0921|consen  387 LQAVAENRVVIIKGETGCGKSTQVAQFLLESFLENSNG----ASFNAVVSQPRRISAISLAERVANERGEEVGET-CG--  459 (1282)
T ss_pred             HHHHhcCceeeEeecccccchhHHHHHHHHHHhhcccc----ccccceeccccccchHHHHHHHHHhhHHhhccc-cc--
Confidence            34444556689999999999998877777777663321    12236777799888877766443 322222111 11  


Q ss_pred             eCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchh
Q 043110          146 MGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADR  197 (316)
Q Consensus       146 ~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~  197 (316)
                         .+..-...--..---|+.||-+-++..+.+.    +..+.++++||.|.
T Consensus       460 ---y~vRf~Sa~prpyg~i~fctvgvllr~~e~g----lrg~sh~i~deihe  504 (1282)
T KOG0921|consen  460 ---YNVRFDSATPRPYGSIMFCTVGVLLRMMENG----LRGISHVIIDEIHE  504 (1282)
T ss_pred             ---ccccccccccccccceeeeccchhhhhhhhc----ccccccccchhhhh
Confidence               1110000000001248999999998888752    24678999999996

>TIGR02688 conserved hypothetical protein TIGR02688

Probab=94.81  E-value=0.34  Score=45.41  Aligned_cols=46  Identities=26%  Similarity=0.506  Sum_probs=31.4

Q ss_pred             HHHHHHHHHcCCCCCcHHHH--------HHHHHHhCCCcEEEEcCCCCchHHHHH
Q 043110           45 TLCDQLRERLGFEAPTKVQA--------QAIPVILSGRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        45 ~l~~~l~~~~g~~~p~~~Q~--------~~i~~il~g~d~li~a~TGsGKT~~~~   91 (316)
                      +.+..|...+||+ |..+-.        .++|.+-.+.|++..+|+|+|||-.|.
T Consensus       174 EWid~LlrSiG~~-P~~~~~r~k~~~L~rl~~fve~~~Nli~lGp~GTGKThla~  227 (449)
T TIGR02688       174 EWIDVLIRSIGYE-PEGFEARQKLLLLARLLPLVEPNYNLIELGPKGTGKSYIYN  227 (449)
T ss_pred             HHHHHHHHhcCCC-cccCChHHHHHHHHhhHHHHhcCCcEEEECCCCCCHHHHHH
Confidence            4456666778887 432211        123556678899999999999996654

Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687.

>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily

Probab=94.78  E-value=0.64  Score=40.74  Aligned_cols=33  Identities=24%  Similarity=0.376  Sum_probs=22.7

Q ss_pred             CcHHHHHHHHHHh----CCC-cEEEEcCCCCchHHHHH
Q 043110           59 PTKVQAQAIPVIL----SGR-DVLVNAATGTGKTVAYL   91 (316)
Q Consensus        59 p~~~Q~~~i~~il----~g~-d~li~a~TGsGKT~~~~   91 (316)
                      +++.+.+++..+.    .+. .+++.|++|+|||....
T Consensus        24 ~~~~~~~~~~~l~~~~~~~~~~~~l~G~~G~GKTtl~~   61 (269)
T TIGR03015        24 PSKGHKRAMAYLEYGLSQREGFILITGEVGAGKTTLIR   61 (269)
T ss_pred             CCHHHHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHHH
Confidence            4556666665543    333 58899999999997643

Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.

>PRK06645 DNA polymerase III subunits gamma and tau; Validated

Probab=94.75  E-value=1.4  Score=42.69  Aligned_cols=18  Identities=28%  Similarity=0.364  Sum_probs=15.7

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      .+++.||.|+|||.++.+
T Consensus        45 a~Lf~Gp~G~GKTT~Ari   62 (507)
T PRK06645         45 GYLLTGIRGVGKTTSARI   62 (507)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            589999999999988654

>TIGR03881 KaiC_arch_4 KaiC domain protein, PAE1156 family

Probab=94.71  E-value=0.51  Score=40.41  Aligned_cols=52  Identities=23%  Similarity=0.223  Sum_probs=31.1

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .|..+++.+++|+|||....--+.+.+..         +-.++++.- .+...++.+.++.+
T Consensus        19 ~G~~~~i~G~~G~GKT~l~~~~~~~~~~~---------g~~~~~is~-e~~~~~i~~~~~~~   70 (229)
T TIGR03881        19 RGFFVAVTGEPGTGKTIFCLHFAYKGLRD---------GDPVIYVTT-EESRESIIRQAAQF   70 (229)
T ss_pred             CCeEEEEECCCCCChHHHHHHHHHHHHhc---------CCeEEEEEc-cCCHHHHHHHHHHh
Confidence            45679999999999997654333333322         223677764 34445555554443

Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain.

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=94.67  E-value=0.4  Score=48.69  Aligned_cols=18  Identities=28%  Similarity=0.394  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      ..++++.||+|+|||...
T Consensus       207 ~~n~LLvGppGvGKT~la  224 (758)
T PRK11034        207 KNNPLLVGESGVGKTAIA  224 (758)
T ss_pred             CCCeEEECCCCCCHHHHH
Confidence            347999999999999875

>PRK14956 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.63  E-value=0.41  Score=45.68  Aligned_cols=17  Identities=24%  Similarity=0.241  Sum_probs=14.9

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      +++.||.|+|||.++.+
T Consensus        43 ~Lf~GP~GtGKTTlAri   59 (484)
T PRK14956         43 YIFFGPRGVGKTTIARI   59 (484)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            79999999999988654

>PRK05563 DNA polymerase III subunits gamma and tau; Validated

Probab=94.61  E-value=1.5  Score=43.07  Aligned_cols=19  Identities=37%  Similarity=0.319  Sum_probs=15.5

Q ss_pred             cEEEEcCCCCchHHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLAP   93 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp   93 (316)
                      -.+++||.|+|||.++-+-
T Consensus        40 ayLf~Gp~GtGKTt~Ak~l   58 (559)
T PRK05563         40 AYLFSGPRGTGKTSAAKIF   58 (559)
T ss_pred             EEEEECCCCCCHHHHHHHH
Confidence            3788999999999886543

>PRK00771 signal recognition particle protein Srp54; Provisional

Probab=94.60  E-value=0.86  Score=43.21  Aligned_cols=18  Identities=22%  Similarity=0.409  Sum_probs=15.0

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      .+++.+++|+|||.+..-
T Consensus        97 vI~lvG~~GsGKTTtaak  114 (437)
T PRK00771         97 TIMLVGLQGSGKTTTAAK  114 (437)
T ss_pred             EEEEECCCCCcHHHHHHH
Confidence            478999999999987643

>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]

Probab=94.56  E-value=0.24  Score=45.67  Aligned_cols=18  Identities=28%  Similarity=0.346  Sum_probs=15.4

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      +.|+.+|.|+|||..+-+
T Consensus        50 SmIl~GPPG~GKTTlA~l   67 (436)
T COG2256          50 SMILWGPPGTGKTTLARL   67 (436)
T ss_pred             eeEEECCCCCCHHHHHHH
Confidence            699999999999987543

>TIGR02928 orc1/cdc6 family replication initiation protein

Probab=94.52  E-value=0.29  Score=45.16  Aligned_cols=25  Identities=32%  Similarity=0.539  Sum_probs=18.4

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      .++++.||+|+|||... -.++..+.
T Consensus        41 ~~i~I~G~~GtGKT~l~-~~~~~~l~   65 (365)
T TIGR02928        41 SNVFIYGKTGTGKTAVT-KYVMKELE   65 (365)
T ss_pred             CcEEEECCCCCCHHHHH-HHHHHHHH
Confidence            57999999999999764 33444443

Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.

>KOG0737 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.51  E-value=0.27  Score=44.80  Aligned_cols=72  Identities=18%  Similarity=0.155  Sum_probs=43.7

Q ss_pred             eEEEEecchhhhcCC--cH-HHHHHHHHHhccCcccccCCCCcc-ccccceEEEEeeec-chhHHHHHHHhcCCCEEEEc
Q 043110          188 RWIIFDEADRILELG--FG-KEIEEILDILGSRNIASIGEGNEV-SNVKRQNLLLSATL-NEKVNHLTKISLETPVLIGL  262 (316)
Q Consensus       188 ~~lViDEad~l~~~~--~~-~~i~~i~~~l~~~~~~~~~~~~~~-~~~~~q~i~~SAT~-~~~v~~~~~~~l~~p~~i~~  262 (316)
                      ..+-|||+|.++..-  .. +....+...+-       ..|... ++...|++++.||= |.+++..+-..|..-.+|.+
T Consensus       188 ~iIFIDEvds~L~~R~s~dHEa~a~mK~eFM-------~~WDGl~s~~~~rVlVlgATNRP~DlDeAiiRR~p~rf~V~l  260 (386)
T KOG0737|consen  188 SIIFIDEVDSFLGQRRSTDHEATAMMKNEFM-------ALWDGLSSKDSERVLVLGATNRPFDLDEAIIRRLPRRFHVGL  260 (386)
T ss_pred             ceeehhhHHHHHhhcccchHHHHHHHHHHHH-------HHhccccCCCCceEEEEeCCCCCccHHHHHHHhCcceeeeCC
Confidence            578899999988531  11 11222222211       123333 34456899999997 77788877777766777777


Q ss_pred             CCCC
Q 043110          263 DEKK  266 (316)
Q Consensus       263 ~~~~  266 (316)
                      ....
T Consensus       261 P~~~  264 (386)
T KOG0737|consen  261 PDAE  264 (386)
T ss_pred             Cchh
Confidence            6643

>PRK06995 flhF flagellar biosynthesis regulator FlhF; Validated

Probab=94.51  E-value=0.48  Score=45.37  Aligned_cols=129  Identities=15%  Similarity=0.122  Sum_probs=61.3

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS  152 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (316)
                      |+-+.+.||||+|||.+...-+........      ....+++-+-+.-..  ..+.++.++...+. ............
T Consensus       256 g~Vi~LvGpnGvGKTTTiaKLA~~~~~~~G------~~kV~LI~~Dt~Rig--A~EQLr~~AeilGV-pv~~~~~~~Dl~  326 (484)
T PRK06995        256 GGVFALMGPTGVGKTTTTAKLAARCVMRHG------ASKVALLTTDSYRIG--GHEQLRIYGKILGV-PVHAVKDAADLR  326 (484)
T ss_pred             CcEEEEECCCCccHHHHHHHHHHHHHHhcC------CCeEEEEeCCccchh--HHHHHHHHHHHhCC-CeeccCCchhHH
Confidence            445889999999999986443322222211      011233333332222  14455555554432 222222233333


Q ss_pred             HHHHHHhcCCcEEEeCcHHHHHH------HhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          153 KEKARLRKGISILVATPGHLLDH------LKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       153 ~~~~~l~~~~~IlV~Tp~~l~~~------l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      .....+...-.++|-|+|+....      +..........=.+||+|..-.      ...+..+...+..
T Consensus       327 ~aL~~L~d~d~VLIDTaGr~~~d~~~~e~~~~l~~~~~p~e~~LVLdAt~~------~~~l~~i~~~f~~  390 (484)
T PRK06995        327 LALSELRNKHIVLIDTIGMSQRDRMVSEQIAMLHGAGAPVKRLLLLNATSH------GDTLNEVVQAYRG  390 (484)
T ss_pred             HHHHhccCCCeEEeCCCCcChhhHHHHHHHHHHhccCCCCeeEEEEeCCCc------HHHHHHHHHHhcc
Confidence            34444444456899999954321      1110111101116788886532      2445556555543

>PRK14958 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.50  E-value=0.4  Score=46.46  Aligned_cols=17  Identities=29%  Similarity=0.346  Sum_probs=14.7

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      .++.||.|+|||.++.+
T Consensus        41 ~Lf~Gp~G~GKTt~A~~   57 (509)
T PRK14958         41 YLFTGTRGVGKTTISRI   57 (509)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            69999999999987654

>PF05729 NACHT: NACHT domain

Probab=94.47  E-value=1.4  Score=35.05  Aligned_cols=24  Identities=17%  Similarity=0.426  Sum_probs=17.2

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           76 VLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      +++.|+.|+|||... --++..+..
T Consensus         3 l~I~G~~G~GKStll-~~~~~~~~~   26 (166)
T PF05729_consen    3 LWISGEPGSGKSTLL-RKLAQQLAE   26 (166)
T ss_pred             EEEECCCCCChHHHH-HHHHHHHHh
Confidence            689999999999864 334444444

>PRK07003 DNA polymerase III subunits gamma and tau; Validated

Probab=94.44  E-value=0.27  Score=49.31  Aligned_cols=17  Identities=29%  Similarity=0.339  Sum_probs=14.5

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      +++.++.|+|||.+..+
T Consensus        41 yLFtGPpGvGKTTlAri   57 (830)
T PRK07003         41 YLFTGTRGVGKTTLSRI   57 (830)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            68999999999987544

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.35  E-value=0.19  Score=47.90  Aligned_cols=56  Identities=27%  Similarity=0.436  Sum_probs=35.1

Q ss_pred             cccCCcccCC---CCHHHHHHHHHHcCCCC--CcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           32 FASCCFSSLG---LDSTLCDQLRERLGFEA--PTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        32 ~~~~~f~~~~---l~~~l~~~l~~~~g~~~--p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      -..++|+++|   |+.+.-+.+++.|-..-  |--+-+--+++   -+-+++.+|+|+|||+.+
T Consensus       213 ~Pdf~Fe~mGIGGLd~EFs~IFRRAFAsRvFpp~vie~lGi~H---VKGiLLyGPPGTGKTLiA  273 (744)
T KOG0741|consen  213 NPDFNFESMGIGGLDKEFSDIFRRAFASRVFPPEVIEQLGIKH---VKGILLYGPPGTGKTLIA  273 (744)
T ss_pred             CCCCChhhcccccchHHHHHHHHHHHHhhcCCHHHHHHcCccc---eeeEEEECCCCCChhHHH
Confidence            3457889985   88888777754432221  22222222222   256899999999999875

>PRK07764 DNA polymerase III subunits gamma and tau; Validated

Probab=94.33  E-value=0.46  Score=48.65  Aligned_cols=19  Identities=26%  Similarity=0.260  Sum_probs=16.0

Q ss_pred             EEEEcCCCCchHHHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLAPI   94 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~   94 (316)
                      +|+.+|.|+|||.+..+-+
T Consensus        40 ~Lf~Gp~G~GKTt~A~~lA   58 (824)
T PRK07764         40 YLFSGPRGCGKTSSARILA   58 (824)
T ss_pred             EEEECCCCCCHHHHHHHHH
Confidence            7999999999999876533

>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB

Probab=94.30  E-value=0.29  Score=43.98  Aligned_cols=58  Identities=22%  Similarity=0.347  Sum_probs=37.5

Q ss_pred             CcHHHHHHHHH-HhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           59 PTKVQAQAIPV-ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        59 p~~~Q~~~i~~-il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      +++-|...+.. +..+++++++++||||||... -.++..+...      ....+++++-.+.|+.
T Consensus       117 ~~~~~~~~L~~~v~~~~~ilI~G~tGSGKTTll-~al~~~i~~~------~~~~ri~tiEd~~El~  175 (299)
T TIGR02782       117 MTAAQRDVLREAVLARKNILVVGGTGSGKTTLA-NALLAEIAKN------DPTDRVVIIEDTRELQ  175 (299)
T ss_pred             CCHHHHHHHHHHHHcCCeEEEECCCCCCHHHHH-HHHHHHhhcc------CCCceEEEECCchhhc
Confidence            44555555544 446679999999999999753 4444444331      1134588888888874

The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA.

>PRK08699 DNA polymerase III subunit delta'; Validated

Probab=94.30  E-value=0.69  Score=42.10  Aligned_cols=39  Identities=21%  Similarity=0.099  Sum_probs=28.0

Q ss_pred             cHHHHHHHHHHhC--CC---cEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           60 TKVQAQAIPVILS--GR---DVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        60 ~~~Q~~~i~~il~--g~---d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      +|||+..|..+..  |+   -.++.||.|.|||..+.. +...+.
T Consensus         3 yPW~~~~w~~l~~~~~r~~hA~Lf~G~~G~GK~~la~~-~a~~ll   46 (325)
T PRK08699          3 YPWHQEQWRQIAEHWERRPNAWLFAGKKGIGKTAFARF-AAQALL   46 (325)
T ss_pred             CCccHHHHHHHHHhcCCcceEEEeECCCCCCHHHHHHH-HHHHHc
Confidence            6888888877763  33   388999999999987644 333443

>TIGR03878 thermo_KaiC_2 KaiC domain protein, AF_0795 family

Probab=94.28  E-value=0.64  Score=40.86  Aligned_cols=38  Identities=13%  Similarity=0.153  Sum_probs=25.2

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeC
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVP  118 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~P  118 (316)
                      .|.-+++.+++|+|||...+--+.+.+..         |-+++|++-
T Consensus        35 ~gs~~lI~G~pGtGKT~l~~qf~~~~a~~---------Ge~vlyis~   72 (259)
T TIGR03878        35 AYSVINITGVSDTGKSLMVEQFAVTQASR---------GNPVLFVTV   72 (259)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhC---------CCcEEEEEe
Confidence            45568999999999998754433333322         334788773

This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles.

>PF14516 AAA_35: AAA-like domain

Probab=94.26  E-value=0.18  Score=46.06  Aligned_cols=39  Identities=23%  Similarity=0.358  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHhC-CCcEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           61 KVQAQAIPVILS-GRDVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        61 ~~Q~~~i~~il~-g~d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      |+.++++..+.+ |.-+.+.||-.+|||.. +.-+++.+..
T Consensus        18 ~~e~~~~~~i~~~G~~~~I~apRq~GKTSl-l~~l~~~l~~   57 (331)
T PF14516_consen   18 PAEQECYQEIVQPGSYIRIKAPRQMGKTSL-LLRLLERLQQ   57 (331)
T ss_pred             HHHHHHHHHHhcCCCEEEEECcccCCHHHH-HHHHHHHHHH
Confidence            489999999887 88999999999999975 4455555544

>PRK13851 type IV secretion system protein VirB11; Provisional

Probab=94.24  E-value=0.087  Score=48.28  Aligned_cols=45  Identities=22%  Similarity=0.327  Sum_probs=30.6

Q ss_pred             HHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           69 VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        69 ~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      .+..++++++.|+||||||... -.++..+..         ..+++.+-.+.||.
T Consensus       158 ~v~~~~nilI~G~tGSGKTTll-~aLl~~i~~---------~~rivtiEd~~El~  202 (344)
T PRK13851        158 CVVGRLTMLLCGPTGSGKTTMS-KTLISAIPP---------QERLITIEDTLELV  202 (344)
T ss_pred             HHHcCCeEEEECCCCccHHHHH-HHHHcccCC---------CCCEEEECCCcccc
Confidence            3447889999999999999753 334433321         23477788888774

>PRK14960 DNA polymerase III subunits gamma and tau; Provisional

Probab=94.23  E-value=0.28  Score=48.55  Aligned_cols=18  Identities=28%  Similarity=0.316  Sum_probs=15.2

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      -+++.||.|+|||.++.+
T Consensus        39 AyLF~GPpGvGKTTlAri   56 (702)
T PRK14960         39 AYLFTGTRGVGKTTIARI   56 (702)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            369999999999987654

>PRK06964 DNA polymerase III subunit delta'; Validated

Probab=94.14  E-value=0.64  Score=42.58  Aligned_cols=41  Identities=17%  Similarity=0.142  Sum_probs=28.6

Q ss_pred             CcHHHHHHHHHHhC--CC---cEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           59 PTKVQAQAIPVILS--GR---DVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        59 p~~~Q~~~i~~il~--g~---d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      .+|||...+..+..  ++   -.++.||.|.||+..+.. +.+.+..
T Consensus         2 ~yPW~~~~~~~l~~~~~rl~ha~Lf~Gp~G~GK~~lA~~-~A~~LlC   47 (342)
T PRK06964          2 LYPWQTDDWNRLQALRARLPHALLLHGQAGIGKLDFAQH-LAQGLLC   47 (342)
T ss_pred             CCcccHHHHHHHHHhcCCcceEEEEECCCCCCHHHHHHH-HHHHHcC
Confidence            36788888877663  33   478999999999987643 4444444

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=94.13  E-value=0.42  Score=48.67  Aligned_cols=122  Identities=12%  Similarity=0.149  Sum_probs=61.9

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCc-ee-EEeeCCCC
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWI-VP-GYVMGGGN  150 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~-~~-~~~~~~~~  150 (316)
                      |--+|+.-..|-|||+-. +..++.++....    ..-.+||||+|..- +..+.+.+.+|...+... .. ....+...
T Consensus       696 GsGcILAHcMGLGKTlQV-vtflhTvL~c~k----lg~ktaLvV~PlNt-~~NW~~EFekWm~~~e~~~~leV~eL~~vk  769 (1567)
T KOG1015|consen  696 GSGCILAHCMGLGKTLQV-VTFLHTVLLCDK----LGFKTALVVCPLNT-ALNWMNEFEKWMEGLEDDEKLEVSELATVK  769 (1567)
T ss_pred             CcchHHHHhhcccceehh-hHHHHHHHHhhc----cCCceEEEEcchHH-HHHHHHHHHHhcccccccccceeehhhhcc
Confidence            345788888999999864 333443332211    12335999999865 455666677766532111 11 11222222


Q ss_pred             h-HHHHHHH---hcCCcEEEeCcHHHHHHHhcCC------------ccccCceeEEEEecchhhhc
Q 043110          151 R-SKEKARL---RKGISILVATPGHLLDHLKHTS------------SFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       151 ~-~~~~~~l---~~~~~IlV~Tp~~l~~~l~~~~------------~~~~~~l~~lViDEad~l~~  200 (316)
                      . ......|   .+.-.|.|.-...+-.+.....            .+.-..-+++|.||+|.|-.
T Consensus       770 r~e~R~~~L~~W~~~ggVmIiGYdmyRnLa~gr~vk~rk~ke~f~k~lvdpGPD~vVCDE~HiLKN  835 (1567)
T KOG1015|consen  770 RPEERSYMLQRWQEDGGVMIIGYDMYRNLAQGRNVKSRKLKEIFNKALVDPGPDFVVCDEGHILKN  835 (1567)
T ss_pred             ChHHHHHHHHHHHhcCCEEEEehHHHHHHhcccchhhhHHHHHHHHhccCCCCCeEEecchhhhcc
Confidence            2 2221122   1222455555554433322111            11112457999999998754

>KOG0738 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.13  E-value=0.91  Score=41.89  Aligned_cols=73  Identities=19%  Similarity=0.220  Sum_probs=40.9

Q ss_pred             eeEEEEecchhhhcC-CcH-------HHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCE
Q 043110          187 LRWIIFDEADRILEL-GFG-------KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPV  258 (316)
Q Consensus       187 l~~lViDEad~l~~~-~~~-------~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~  258 (316)
                      -..|.|||+|.|... |-.       ..=..++-.+..       .....-+.+.-+|+.+-.+|=++.+..+..+..-+
T Consensus       305 PStIFiDEIDslcs~RG~s~EHEaSRRvKsELLvQmDG-------~~~t~e~~k~VmVLAATN~PWdiDEAlrRRlEKRI  377 (491)
T KOG0738|consen  305 PSTIFIDEIDSLCSQRGGSSEHEASRRVKSELLVQMDG-------VQGTLENSKVVMVLAATNFPWDIDEALRRRLEKRI  377 (491)
T ss_pred             CceeehhhHHHHHhcCCCccchhHHHHHHHHHHHHhhc-------cccccccceeEEEEeccCCCcchHHHHHHHHhhhe
Confidence            357899999998754 211       111223333321       11111112333344444478889888888888888


Q ss_pred             EEEcCCCC
Q 043110          259 LIGLDEKK  266 (316)
Q Consensus       259 ~i~~~~~~  266 (316)
                      +|-+.+.+
T Consensus       378 yIPLP~~~  385 (491)
T KOG0738|consen  378 YIPLPDAE  385 (491)
T ss_pred             eeeCCCHH
Confidence            88776654

>PRK06067 flagellar accessory protein FlaH; Validated

Probab=94.13  E-value=1.7  Score=37.41  Aligned_cols=51  Identities=18%  Similarity=0.249  Sum_probs=31.5

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      |.-+++.+++|+|||....--+...+.+         +-+++|+.-.. -..++.+.+..+
T Consensus        25 g~~~~i~G~~GsGKt~l~~~~~~~~~~~---------g~~~~y~~~e~-~~~~~~~~~~~~   75 (234)
T PRK06067         25 PSLILIEGDHGTGKSVLSQQFVYGALKQ---------GKKVYVITTEN-TSKSYLKQMESV   75 (234)
T ss_pred             CcEEEEECCCCCChHHHHHHHHHHHHhC---------CCEEEEEEcCC-CHHHHHHHHHHC
Confidence            4568999999999998754433333322         44477777543 334555555554

>cd00984 DnaB_C DnaB helicase C terminal domain

Probab=94.09  E-value=1  Score=38.82  Aligned_cols=39  Identities=23%  Similarity=0.229  Sum_probs=25.3

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeC
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVP  118 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~P  118 (316)
                      .|.-+++.|++|+|||...+--+.+....        .+..+++++.
T Consensus        12 ~G~l~lI~G~~G~GKT~~~~~~~~~~~~~--------~g~~vly~s~   50 (242)
T cd00984          12 PGDLIIIAARPSMGKTAFALNIAENIAKK--------QGKPVLFFSL   50 (242)
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHh--------CCCceEEEeC
Confidence            55678999999999997644333333332        1334888873

The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.

>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=94.06  E-value=0.1  Score=49.58  Aligned_cols=40  Identities=28%  Similarity=0.449  Sum_probs=30.3

Q ss_pred             cHHHHHHHHHHhCCCc--EEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           60 TKVQAQAIPVILSGRD--VLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        60 ~~~Q~~~i~~il~g~d--~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      ++.|...+..+++...  +++.+|||||||.. +..+++.+..
T Consensus       243 ~~~~~~~~~~~~~~p~GliLvTGPTGSGKTTT-LY~~L~~ln~  284 (500)
T COG2804         243 SPFQLARLLRLLNRPQGLILVTGPTGSGKTTT-LYAALSELNT  284 (500)
T ss_pred             CHHHHHHHHHHHhCCCeEEEEeCCCCCCHHHH-HHHHHHHhcC
Confidence            5677777777776655  89999999999986 4556666654

>PRK14723 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=94.04  E-value=0.46  Score=47.95  Aligned_cols=20  Identities=30%  Similarity=0.371  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCCchHHHHHH
Q 043110           73 GRDVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~l   92 (316)
                      |+-+.+.+|||+|||.+...
T Consensus       185 g~Vi~lVGpnGvGKTTTiaK  204 (767)
T PRK14723        185 GGVLALVGPTGVGKTTTTAK  204 (767)
T ss_pred             CeEEEEECCCCCcHHHHHHH
Confidence            34578999999999988643

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=94.02  E-value=0.69  Score=38.08  Aligned_cols=52  Identities=17%  Similarity=0.285  Sum_probs=38.1

Q ss_pred             CceeEEEEecchhhhcCCcH--HHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHH
Q 043110          185 TNLRWIIFDEADRILELGFG--KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK  251 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~--~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~  251 (316)
                      ...+++|+||+-..++.|+-  +++..+++..|.               ..-+|+.--..|+.+.+.+.
T Consensus       114 ~~~dlvVLDEi~~Al~~gli~~eeVl~~L~~rp~---------------~~evILTGR~~p~~Lie~AD  167 (178)
T PRK07414        114 GRYSLVVLDELSLAIQFGLIPETEVLEFLEKRPS---------------HVDVILTGPEMPESLLAIAD  167 (178)
T ss_pred             CCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCC---------------CCEEEEECCCCCHHHHHhCC
Confidence            46789999999999988754  455556655544               56777777778887777655

>PRK09111 DNA polymerase III subunits gamma and tau; Validated

Probab=94.01  E-value=0.86  Score=45.05  Aligned_cols=18  Identities=22%  Similarity=0.364  Sum_probs=15.6

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      .+++.||.|+|||..+.+
T Consensus        48 a~L~~Gp~GvGKTt~Ar~   65 (598)
T PRK09111         48 AFMLTGVRGVGKTTTARI   65 (598)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            489999999999988654

>PRK10867 signal recognition particle protein; Provisional

Probab=94.01  E-value=0.97  Score=42.78  Aligned_cols=17  Identities=24%  Similarity=0.348  Sum_probs=14.4

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      +++.+++|+|||.+..-
T Consensus       103 I~~vG~~GsGKTTtaak  119 (433)
T PRK10867        103 IMMVGLQGAGKTTTAGK  119 (433)
T ss_pred             EEEECCCCCcHHHHHHH
Confidence            78999999999987543

>PRK08691 DNA polymerase III subunits gamma and tau; Validated

Probab=94.00  E-value=0.56  Score=46.80  Aligned_cols=18  Identities=28%  Similarity=0.348  Sum_probs=15.4

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      .+++.||.|+|||....+
T Consensus        40 a~Lf~GP~GvGKTTlAri   57 (709)
T PRK08691         40 AYLLTGTRGVGKTTIARI   57 (709)
T ss_pred             EEEEECCCCCcHHHHHHH
Confidence            479999999999987644

>KOG0742 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.99  E-value=0.19  Score=46.47  Aligned_cols=17  Identities=41%  Similarity=0.630  Sum_probs=15.4

Q ss_pred             CcEEEEcCCCCchHHHH
Q 043110           74 RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~   90 (316)
                      +|++..+|+|+|||+++
T Consensus       385 RNilfyGPPGTGKTm~A  401 (630)
T KOG0742|consen  385 RNILFYGPPGTGKTMFA  401 (630)
T ss_pred             hheeeeCCCCCCchHHH
Confidence            58999999999999874

>PRK05973 replicative DNA helicase; Provisional

Probab=93.89  E-value=0.6  Score=40.43  Aligned_cols=55  Identities=25%  Similarity=0.267  Sum_probs=34.9

Q ss_pred             HHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           69 VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        69 ~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      -+..|.-+++.|++|+|||...+--+.+....         |-.++|++-- +-..|+.+.+..+
T Consensus        60 Gl~~Gsl~LIaG~PG~GKT~lalqfa~~~a~~---------Ge~vlyfSlE-es~~~i~~R~~s~  114 (237)
T PRK05973         60 QLKPGDLVLLGARPGHGKTLLGLELAVEAMKS---------GRTGVFFTLE-YTEQDVRDRLRAL  114 (237)
T ss_pred             CCCCCCEEEEEeCCCCCHHHHHHHHHHHHHhc---------CCeEEEEEEe-CCHHHHHHHHHHc
Confidence            34456679999999999998755444443322         3347777633 3356667666655

>PRK07994 DNA polymerase III subunits gamma and tau; Validated

Probab=93.89  E-value=1.2  Score=44.25  Aligned_cols=17  Identities=29%  Similarity=0.341  Sum_probs=14.7

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      +++.||.|+|||....+
T Consensus        41 yLf~Gp~GvGKTTlAr~   57 (647)
T PRK07994         41 YLFSGTRGVGKTTIARL   57 (647)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            58999999999987654

>TIGR01425 SRP54_euk signal recognition particle protein SRP54

Probab=93.81  E-value=1.1  Score=42.24  Aligned_cols=85  Identities=15%  Similarity=0.165  Sum_probs=41.7

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEe--CChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChH
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLV--PTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS  152 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~--Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (316)
                      -+.+.+++|+|||....--+. .+..        .|.++++++  |.|.-+   .++++.++...+ +.......+.+..
T Consensus       102 vi~lvG~~GvGKTTtaaKLA~-~l~~--------~G~kV~lV~~D~~R~aA---~eQLk~~a~~~~-vp~~~~~~~~dp~  168 (429)
T TIGR01425       102 VIMFVGLQGSGKTTTCTKLAY-YYQR--------KGFKPCLVCADTFRAGA---FDQLKQNATKAR-IPFYGSYTESDPV  168 (429)
T ss_pred             EEEEECCCCCCHHHHHHHHHH-HHHH--------CCCCEEEEcCcccchhH---HHHHHHHhhccC-CeEEeecCCCCHH
Confidence            378999999999976532222 2322        133355554  335433   334444444332 2222222233321


Q ss_pred             ----HHHHHHh-cCCc-EEEeCcHHH
Q 043110          153 ----KEKARLR-KGIS-ILVATPGHL  172 (316)
Q Consensus       153 ----~~~~~l~-~~~~-IlV~Tp~~l  172 (316)
                          .....+. .+++ |+|=|||++
T Consensus       169 ~i~~~~l~~~~~~~~DvViIDTaGr~  194 (429)
T TIGR01425       169 KIASEGVEKFKKENFDIIIVDTSGRH  194 (429)
T ss_pred             HHHHHHHHHHHhCCCCEEEEECCCCC
Confidence                1122222 2455 789999976

This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.

>TIGR00959 ffh signal recognition particle protein

Probab=93.76  E-value=1  Score=42.55  Aligned_cols=18  Identities=28%  Similarity=0.346  Sum_probs=15.0

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      -+++.+++|+|||....-
T Consensus       101 vi~~vG~~GsGKTTtaak  118 (428)
T TIGR00959       101 VILMVGLQGSGKTTTCGK  118 (428)
T ss_pred             EEEEECCCCCcHHHHHHH
Confidence            388999999999987543

This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle.

>PRK14964 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.74  E-value=0.89  Score=43.73  Aligned_cols=18  Identities=33%  Similarity=0.479  Sum_probs=15.6

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      .++++||.|+|||.++.+
T Consensus        37 a~Lf~Gp~G~GKTT~Ari   54 (491)
T PRK14964         37 SILLVGASGVGKTTCARI   54 (491)
T ss_pred             eEEEECCCCccHHHHHHH
Confidence            589999999999987654

>COG0630 VirB11 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=93.71  E-value=0.28  Score=44.36  Aligned_cols=76  Identities=20%  Similarity=0.258  Sum_probs=47.8

Q ss_pred             cccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHH-HHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCC
Q 043110           32 FASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQA-IPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSG  110 (316)
Q Consensus        32 ~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~-i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~  110 (316)
                      +....|..-+++..   .| .  ++..+++.|..- |-.+-.+++++++++||||||.. +.+++..+-.         .
T Consensus       107 ~~IRk~~~~~~t~~---~l-~--~~gt~~~~~~ayL~~~ie~~~siii~G~t~sGKTt~-lnall~~Ip~---------~  170 (312)
T COG0630         107 FTIRKFSDEPITPE---DL-I--EYGTISPEQAAYLWLAIEARKSIIICGGTASGKTTL-LNALLDFIPP---------E  170 (312)
T ss_pred             EEEEcCCCCCCCHH---HH-h--hcCCCCHHHHHHHHHHHHcCCcEEEECCCCCCHHHH-HHHHHHhCCc---------h
Confidence            34445555555544   33 1  244567777544 45555788999999999999964 4555554432         3


Q ss_pred             eeEEEEeCChHHH
Q 043110          111 TFALVLVPTSELC  123 (316)
Q Consensus       111 ~~~lil~Pt~~L~  123 (316)
                      .+.+.+--|.|+.
T Consensus       171 ~rivtIEdt~E~~  183 (312)
T COG0630         171 ERIVTIEDTPELK  183 (312)
T ss_pred             hcEEEEecccccc
Confidence            3478888887764

>PRK14961 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.71  E-value=0.72  Score=42.68  Aligned_cols=17  Identities=29%  Similarity=0.345  Sum_probs=14.5

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      +++.||.|+|||..+..
T Consensus        41 ~L~~Gp~G~GKTtla~~   57 (363)
T PRK14961         41 WLLSGTRGVGKTTIARL   57 (363)
T ss_pred             EEEecCCCCCHHHHHHH
Confidence            68999999999987644

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=93.70  E-value=0.22  Score=51.92  Aligned_cols=157  Identities=18%  Similarity=0.189  Sum_probs=89.2

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCC---------CCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCcee
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPR---------IDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVP  142 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~---------~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~  142 (316)
                      .|+++++.-..|.|||.+-+...+...-...+.         .......-.|||+|. ++..|+.+.+..-...   ...
T Consensus       373 ~g~~~~~ade~~~qk~~~~l~~~l~~~~k~~~~~cS~~~~e~~n~~~tgaTLII~P~-aIl~QW~~EI~kH~~~---~lK  448 (1394)
T KOG0298|consen  373 HGKRVQCADEMGWQKTSEKLILELSDLPKLCPSCCSELVKEGENLVETGATLIICPN-AILMQWFEEIHKHISS---LLK  448 (1394)
T ss_pred             CCcceeehhhhhccchHHHHHHHHhcccccchhhhhHHHhcccceeecCceEEECcH-HHHHHHHHHHHHhccc---cce
Confidence            456789999999999998765544432111100         000112338999998 5567888888776543   222


Q ss_pred             EEeeCCCChHH--HHHHHhcCCcEEEeCcHHHHHHHhcCC-------------cc----ccCcee--EEEEecchhhhcC
Q 043110          143 GYVMGGGNRSK--EKARLRKGISILVATPGHLLDHLKHTS-------------SF----LHTNLR--WIIFDEADRILEL  201 (316)
Q Consensus       143 ~~~~~~~~~~~--~~~~l~~~~~IlV~Tp~~l~~~l~~~~-------------~~----~~~~l~--~lViDEad~l~~~  201 (316)
                      .+.+-|.....  .... ..++|||++|...|..=+....             ..    .+..+.  -+++|||+.+-. 
T Consensus       449 v~~Y~Girk~~~~~~~e-l~~yDIVlTtYdiLr~El~hte~~~~~R~lR~qsr~~~~~SPL~~v~wWRIclDEaQMves-  526 (1394)
T KOG0298|consen  449 VLLYFGIRKTFWLSPFE-LLQYDIVLTTYDILRNELYHTEDFGSDRQLRHQSRYMRPNSPLLMVNWWRICLDEAQMVES-  526 (1394)
T ss_pred             EEEEechhhhcccCchh-hhccCEEEeehHHHHhHhhcccccCChhhhhcccCCCCCCCchHHHHHHHHhhhHHHhhcc-
Confidence            33443322111  1111 2358999999998865443220             00    111122  379999997654 


Q ss_pred             CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHH
Q 043110          202 GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK  251 (316)
Q Consensus       202 ~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~  251 (316)
                       -......++.+|+.                ...=++|.|.=..+.++-.
T Consensus       527 -ssS~~a~M~~rL~~----------------in~W~VTGTPiq~Iddl~~  559 (1394)
T KOG0298|consen  527 -SSSAAAEMVRRLHA----------------INRWCVTGTPIQKIDDLFP  559 (1394)
T ss_pred             -hHHHHHHHHHHhhh----------------hceeeecCCchhhhhhhHH
Confidence             45566666677763                3456778885555555443

>PRK12724 flagellar biosynthesis regulator FlhF; Provisional

Probab=93.69  E-value=1.8  Score=40.70  Aligned_cols=20  Identities=30%  Similarity=0.331  Sum_probs=15.7

Q ss_pred             cEEEEcCCCCchHHHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLAPI   94 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~   94 (316)
                      -+++.+|+|+|||....--+
T Consensus       225 vi~lvGptGvGKTTtaaKLA  244 (432)
T PRK12724        225 VVFFVGPTGSGKTTSIAKLA  244 (432)
T ss_pred             EEEEECCCCCCHHHHHHHHH
Confidence            37899999999998864433

>PRK00440 rfc replication factor C small subunit; Reviewed

Probab=93.66  E-value=1.5  Score=39.36  Aligned_cols=16  Identities=44%  Similarity=0.594  Sum_probs=14.3

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      ++++.||.|+|||.+.
T Consensus        40 ~~ll~G~~G~GKt~~~   55 (319)
T PRK00440         40 HLLFAGPPGTGKTTAA   55 (319)
T ss_pred             eEEEECCCCCCHHHHH
Confidence            5899999999999775

>KOG0739 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=93.64  E-value=2  Score=38.35  Aligned_cols=74  Identities=20%  Similarity=0.139  Sum_probs=41.2

Q ss_pred             ceeEEEEecchhhhcCCc---HHHHHHHHHHhccCcccccCCCCccccccceEEEEeeec-chhHHHHHHHhcCCCEEEE
Q 043110          186 NLRWIIFDEADRILELGF---GKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATL-NEKVNHLTKISLETPVLIG  261 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~~---~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~-~~~v~~~~~~~l~~p~~i~  261 (316)
                      .-+.+.|||+|.+-...-   .+..++|...+--       +-....+..--++.+.||- |=.+...+++.+..-++|-
T Consensus       225 kPSIIFiDEiDslcg~r~enEseasRRIKTEfLV-------QMqGVG~d~~gvLVLgATNiPw~LDsAIRRRFekRIYIP  297 (439)
T KOG0739|consen  225 KPSIIFIDEIDSLCGSRSENESEASRRIKTEFLV-------QMQGVGNDNDGVLVLGATNIPWVLDSAIRRRFEKRIYIP  297 (439)
T ss_pred             CCcEEEeehhhhhccCCCCCchHHHHHHHHHHHH-------hhhccccCCCceEEEecCCCchhHHHHHHHHhhcceecc
Confidence            456789999998775421   1222222222110       0011223344577778885 5556667777777777777


Q ss_pred             cCCCC
Q 043110          262 LDEKK  266 (316)
Q Consensus       262 ~~~~~  266 (316)
                      +.+..
T Consensus       298 LPe~~  302 (439)
T KOG0739|consen  298 LPEAH  302 (439)
T ss_pred             CCcHH
Confidence            66544

>PRK14949 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.62  E-value=0.58  Score=47.93  Aligned_cols=17  Identities=29%  Similarity=0.305  Sum_probs=14.6

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      +++.||.|+|||.+..+
T Consensus        41 yLFtGPpGtGKTTLARi   57 (944)
T PRK14949         41 YLFTGTRGVGKTSLARL   57 (944)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            58999999999988644

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=93.55  E-value=0.53  Score=43.94  Aligned_cols=49  Identities=16%  Similarity=0.176  Sum_probs=36.5

Q ss_pred             ceeEEEEecchhhhcC-CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHH
Q 043110          186 NLRWIIFDEADRILEL-GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNH  248 (316)
Q Consensus       186 ~l~~lViDEad~l~~~-~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~  248 (316)
                      ++++++||+++.+... .....+-.+++.+...              ..|+++.|...|.++..
T Consensus       175 ~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~--------------~kqIvltsdr~P~~l~~  224 (408)
T COG0593         175 SLDLLLIDDIQFLAGKERTQEEFFHTFNALLEN--------------GKQIVLTSDRPPKELNG  224 (408)
T ss_pred             ccCeeeechHhHhcCChhHHHHHHHHHHHHHhc--------------CCEEEEEcCCCchhhcc
Confidence            5789999999998764 4566677777777652              45888888888877663

>PRK14962 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.51  E-value=1.5  Score=42.01  Aligned_cols=17  Identities=29%  Similarity=0.362  Sum_probs=14.7

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      +++.||+|+|||..+.+
T Consensus        39 ~Lf~GPpGtGKTTlA~~   55 (472)
T PRK14962         39 YIFAGPRGTGKTTVARI   55 (472)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            69999999999987644

>TIGR03877 thermo_KaiC_1 KaiC domain protein, Ph0284 family

Probab=93.50  E-value=0.17  Score=43.87  Aligned_cols=53  Identities=23%  Similarity=0.226  Sum_probs=36.3

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      .|..+++.+++|+|||...+--+.+.+.+         |-.++|++ +.+-..|+.+.+..++
T Consensus        20 ~gs~~lI~G~pGsGKT~la~~~l~~~~~~---------ge~~lyvs-~ee~~~~i~~~~~~~g   72 (237)
T TIGR03877        20 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM---------GEPGIYVA-LEEHPVQVRRNMAQFG   72 (237)
T ss_pred             CCeEEEEEcCCCCCHHHHHHHHHHHHHHc---------CCcEEEEE-eeCCHHHHHHHHHHhC
Confidence            45679999999999998754444444432         33488888 4566777777776654

Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga.

>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]

Probab=93.50  E-value=0.26  Score=43.18  Aligned_cols=49  Identities=20%  Similarity=0.375  Sum_probs=33.1

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEIL  130 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~  130 (316)
                      .+.++++.|++|+|||..+. ++.+.+.. .       |. -++.+++.+|+.++....
T Consensus       104 ~~~nl~l~G~~G~GKThLa~-Ai~~~l~~-~-------g~-sv~f~~~~el~~~Lk~~~  152 (254)
T COG1484         104 RGENLVLLGPPGVGKTHLAI-AIGNELLK-A-------GI-SVLFITAPDLLSKLKAAF  152 (254)
T ss_pred             cCCcEEEECCCCCcHHHHHH-HHHHHHHH-c-------CC-eEEEEEHHHHHHHHHHHH
Confidence            67799999999999997653 34444443 1       22 456667888876665443

>TIGR02237 recomb_radB DNA repair and recombination protein RadB

Probab=93.47  E-value=2.1  Score=36.04  Aligned_cols=39  Identities=18%  Similarity=0.257  Sum_probs=26.0

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCC
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPT  119 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt  119 (316)
                      .|.-+.+.+++|+|||...+-.+.+....         +-.++++.-.
T Consensus        11 ~g~i~~i~G~~GsGKT~l~~~~~~~~~~~---------g~~v~yi~~e   49 (209)
T TIGR02237        11 RGTITQIYGPPGSGKTNICMILAVNAARQ---------GKKVVYIDTE   49 (209)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC---------CCeEEEEECC
Confidence            34568999999999998865444443322         3347777764

This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236).

>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=93.45  E-value=0.044  Score=45.07  Aligned_cols=45  Identities=27%  Similarity=0.368  Sum_probs=29.2

Q ss_pred             HHhcCCcEEEeCcHHHHHHHhcCCcc-ccCceeEEEEecchhhhcC
Q 043110          157 RLRKGISILVATPGHLLDHLKHTSSF-LHTNLRWIIFDEADRILEL  201 (316)
Q Consensus       157 ~l~~~~~IlV~Tp~~l~~~l~~~~~~-~~~~l~~lViDEad~l~~~  201 (316)
                      .....++|||++...|++........ ...+-.+|||||||.|.+.
T Consensus       115 ~~~~~adivi~~y~yl~~~~~~~~~~~~~~~~~ivI~DEAHNL~~~  160 (174)
T PF06733_consen  115 ELAKNADIVICNYNYLFDPSIRKSLFGIDLKDNIVIFDEAHNLEDA  160 (174)
T ss_dssp             HCGGG-SEEEEETHHHHSHHHHHHHCT--CCCEEEEETTGGGCGGG
T ss_pred             HhcccCCEEEeCHHHHhhHHHHhhhccccccCcEEEEecccchHHH
Confidence            33455899999999887755432221 1124468999999998763

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.

>PRK13900 type IV secretion system ATPase VirB11; Provisional

Probab=93.37  E-value=0.2  Score=45.73  Aligned_cols=44  Identities=16%  Similarity=0.328  Sum_probs=30.1

Q ss_pred             HhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           70 ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        70 il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      +..+++++++|+||||||.. +-+++..+-.         .-+++.+--+.||.
T Consensus       157 v~~~~nili~G~tgSGKTTl-l~aL~~~ip~---------~~ri~tiEd~~El~  200 (332)
T PRK13900        157 VISKKNIIISGGTSTGKTTF-TNAALREIPA---------IERLITVEDAREIV  200 (332)
T ss_pred             HHcCCcEEEECCCCCCHHHH-HHHHHhhCCC---------CCeEEEecCCCccc
Confidence            34678999999999999975 3444444422         23477776777764

>PRK06871 DNA polymerase III subunit delta'; Validated

Probab=93.33  E-value=1.1  Score=40.66  Aligned_cols=41  Identities=20%  Similarity=0.163  Sum_probs=27.9

Q ss_pred             CcHHHHHHHHHHh----CCC---cEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           59 PTKVQAQAIPVIL----SGR---DVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        59 p~~~Q~~~i~~il----~g~---d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      .+|||+..+..+.    .|+   -.++.||.|.||+..+.. +.+.+..
T Consensus         3 ~yPW~~~~~~~l~~~~~~~rl~HA~Lf~G~~G~GK~~lA~~-~A~~llC   50 (325)
T PRK06871          3 LYPWLQPTYQQITQAFQQGLGHHALLFKADSGLGTEQLIRA-LAQWLMC   50 (325)
T ss_pred             CCcchHHHHHHHHHHHHcCCcceeEEeECCCCCCHHHHHHH-HHHHHcC
Confidence            3678877776665    444   378999999999987543 3344444

>PRK07993 DNA polymerase III subunit delta'; Validated

Probab=93.29  E-value=2.5  Score=38.64  Aligned_cols=41  Identities=20%  Similarity=0.241  Sum_probs=28.7

Q ss_pred             CcHHHHHHHHHHh----CCC---cEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           59 PTKVQAQAIPVIL----SGR---DVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        59 p~~~Q~~~i~~il----~g~---d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      .+|||...|..+.    +|+   -.++.||.|.||+..+.. +.+.+..
T Consensus         3 ~yPWl~~~~~~l~~~~~~~rl~HA~Lf~G~~G~Gk~~lA~~-~A~~LlC   50 (334)
T PRK07993          3 WYPWLRPDYEQLVGSYQAGRGHHALLIQALPGMGDDALIYA-LSRWLMC   50 (334)
T ss_pred             CCCCChHHHHHHHHHHHcCCcceEEeeECCCCCCHHHHHHH-HHHHHcC
Confidence            5678888887765    344   378999999999987543 4444444

>PRK14969 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.25  E-value=2.1  Score=41.81  Aligned_cols=17  Identities=29%  Similarity=0.333  Sum_probs=14.6

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      +++.||.|+|||.++.+
T Consensus        41 ~Lf~Gp~G~GKTt~A~~   57 (527)
T PRK14969         41 YLFTGTRGVGKTTLARI   57 (527)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            68999999999987654

>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP

Probab=93.21  E-value=1  Score=41.60  Aligned_cols=112  Identities=19%  Similarity=0.188  Sum_probs=65.8

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS  152 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (316)
                      .+.+.+.|+.|.|||+.  +-++........      ..+    +...+.+.++++.+.++.            ++.+.-
T Consensus        62 ~~GlYl~G~vG~GKT~L--md~f~~~lp~~~------k~R----~HFh~Fm~~vh~~l~~~~------------~~~~~l  117 (362)
T PF03969_consen   62 PKGLYLWGPVGRGKTML--MDLFYDSLPIKR------KRR----VHFHEFMLDVHSRLHQLR------------GQDDPL  117 (362)
T ss_pred             CceEEEECCCCCchhHH--HHHHHHhCCccc------ccc----ccccHHHHHHHHHHHHHh------------CCCccH
Confidence            45799999999999974  322222111100      111    245677888887777754            111110


Q ss_pred             HHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCcccccc
Q 043110          153 KEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVK  232 (316)
Q Consensus       153 ~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~  232 (316)
                      .                 .+.+.+.       .+..+|++||.|. .|-+-...+..+++.+-..              .
T Consensus       118 ~-----------------~va~~l~-------~~~~lLcfDEF~V-~DiaDAmil~rLf~~l~~~--------------g  158 (362)
T PF03969_consen  118 P-----------------QVADELA-------KESRLLCFDEFQV-TDIADAMILKRLFEALFKR--------------G  158 (362)
T ss_pred             H-----------------HHHHHHH-------hcCCEEEEeeeec-cchhHHHHHHHHHHHHHHC--------------C
Confidence            0                 1122222       3567899999995 4555556677777776542              5


Q ss_pred             ceEEEEeeecchhHH
Q 043110          233 RQNLLLSATLNEKVN  247 (316)
Q Consensus       233 ~q~i~~SAT~~~~v~  247 (316)
                      .-+|+.|-+.|+++-
T Consensus       159 vvlVaTSN~~P~~Ly  173 (362)
T PF03969_consen  159 VVLVATSNRPPEDLY  173 (362)
T ss_pred             CEEEecCCCChHHHc
Confidence            677888888887743

AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding

>PRK12323 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.19  E-value=0.28  Score=48.52  Aligned_cols=23  Identities=26%  Similarity=0.356  Sum_probs=17.1

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHhh
Q 043110           76 VLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      +++.|+.|+|||....+ +...+.
T Consensus        41 ~LFtGP~GvGKTTLAri-LAkaLn   63 (700)
T PRK12323         41 YLFTGTRGVGKTTLSRI-LAKSLN   63 (700)
T ss_pred             EEEECCCCCCHHHHHHH-HHHHhc
Confidence            69999999999987654 333343

>PRK07940 DNA polymerase III subunit delta'; Validated

Probab=93.17  E-value=1.1  Score=42.06  Aligned_cols=18  Identities=33%  Similarity=0.470  Sum_probs=15.0

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      -+++.||.|+|||.....
T Consensus        38 a~Lf~Gp~G~GKt~lA~~   55 (394)
T PRK07940         38 AWLFTGPPGSGRSVAARA   55 (394)
T ss_pred             EEEEECCCCCcHHHHHHH
Confidence            489999999999987543

>PRK06904 replicative DNA helicase; Validated

Probab=93.13  E-value=2.3  Score=40.81  Aligned_cols=152  Identities=19%  Similarity=0.165  Sum_probs=72.3

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCC-CC
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGG-GN  150 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~-~~  150 (316)
                      .|.=+++.|.+|.|||... +-+.......       .+..+++.+.- .-..|+..++-.....   +....+..| .-
T Consensus       220 ~G~LiiIaarPg~GKTafa-lnia~~~a~~-------~g~~Vl~fSlE-Ms~~ql~~Rlla~~s~---v~~~~i~~g~~l  287 (472)
T PRK06904        220 PSDLIIVAARPSMGKTTFA-MNLCENAAMA-------SEKPVLVFSLE-MPAEQIMMRMLASLSR---VDQTKIRTGQNL  287 (472)
T ss_pred             CCcEEEEEeCCCCChHHHH-HHHHHHHHHh-------cCCeEEEEecc-CCHHHHHHHHHHhhCC---CCHHHhccCCCC
Confidence            3444888999999999754 4444443321       12336666533 3345555544333221   111111122 22


Q ss_pred             hHHHHH-------HHhcCCcEEEe-----CcHHHHHHHhcCCccccCceeEEEEecchhhhcCC----cHHHHHHHHHHh
Q 043110          151 RSKEKA-------RLRKGISILVA-----TPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELG----FGKEIEEILDIL  214 (316)
Q Consensus       151 ~~~~~~-------~l~~~~~IlV~-----Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~----~~~~i~~i~~~l  214 (316)
                      ...++.       .+...+++.|-     |+..+...++.... ....++++|||=.+.|...+    ....+..|.+.|
T Consensus       288 ~~~e~~~~~~a~~~l~~~~~l~I~d~~~~t~~~i~~~~r~~~~-~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~L  366 (472)
T PRK06904        288 DQQDWAKISSTVGMFKQKPNLYIDDSSGLTPTELRSRARRVYR-ENGGLSLIMVDYLQLMRAPGFEDNRTLEIAEISRSL  366 (472)
T ss_pred             CHHHHHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHHHHHHHH-hCCCCCEEEEecHHhcCCCCCCCcHHHHHHHHHHHH
Confidence            222222       22233446553     44444443332111 11257899999998775332    233455555555


Q ss_pred             ccCcccccCCCCccccccceEEEEeeecchhHH
Q 043110          215 GSRNIASIGEGNEVSNVKRQNLLLSATLNEKVN  247 (316)
Q Consensus       215 ~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~  247 (316)
                      +...          ..-++.++++| -++..++
T Consensus       367 K~lA----------kel~ipVi~ls-QLnR~~e  388 (472)
T PRK06904        367 KALA----------KELKVPVVALS-QLNRTLE  388 (472)
T ss_pred             HHHH----------HHhCCeEEEEE-ecCchhh
Confidence            4211          01156677766 4554443

>PRK14963 DNA polymerase III subunits gamma and tau; Provisional

Probab=93.07  E-value=1.1  Score=43.49  Aligned_cols=28  Identities=21%  Similarity=0.306  Sum_probs=19.5

Q ss_pred             CceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          185 TNLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      ...+++||||+|.+..    ..++.+++.+..
T Consensus       115 ~~~kVVIIDEad~ls~----~a~naLLk~LEe  142 (504)
T PRK14963        115 GGRKVYILDEAHMMSK----SAFNALLKTLEE  142 (504)
T ss_pred             CCCeEEEEECccccCH----HHHHHHHHHHHh
Confidence            4678999999998743    445566666643

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=93.07  E-value=0.87  Score=46.33  Aligned_cols=55  Identities=22%  Similarity=0.340  Sum_probs=33.1

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcC--CCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLG--FEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g--~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|++++-....++.+.+...  +.+|.-++...   +..++.+++.||+|+|||...
T Consensus       173 ~~~~~~di~G~~~~~~~l~~~i~~~~~~~~~~~~~g---i~~~~giLL~GppGtGKT~la  229 (733)
T TIGR01243       173 PKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLG---IEPPKGVLLYGPPGTGKTLLA  229 (733)
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHHHHhhCHHHHHhcC---CCCCceEEEECCCCCChHHHH
Confidence            45678888766666666633222  22222222111   134577999999999999763

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>PF03796 DnaB_C: DnaB-like helicase C terminal domain; InterPro: IPR007694 The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork

Probab=93.06  E-value=0.72  Score=40.40  Aligned_cols=130  Identities=18%  Similarity=0.132  Sum_probs=65.0

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS  152 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (316)
                      |.=+++.|.||.|||...+=-+.+....        .+..++|++.--. ..++..++-........   .-+..+....
T Consensus        19 g~L~vi~a~pg~GKT~~~l~ia~~~a~~--------~~~~vly~SlEm~-~~~l~~R~la~~s~v~~---~~i~~g~l~~   86 (259)
T PF03796_consen   19 GELTVIAARPGVGKTAFALQIALNAALN--------GGYPVLYFSLEMS-EEELAARLLARLSGVPY---NKIRSGDLSD   86 (259)
T ss_dssp             T-EEEEEESTTSSHHHHHHHHHHHHHHT--------TSSEEEEEESSS--HHHHHHHHHHHHHTSTH---HHHHCCGCHH
T ss_pred             CcEEEEEecccCCchHHHHHHHHHHHHh--------cCCeEEEEcCCCC-HHHHHHHHHHHhhcchh---hhhhccccCH
Confidence            3458999999999997654444444433        1344888875322 23334333333222111   1111222222


Q ss_pred             HHHHH-------HhcCCcEEEeCcH----HHHHHHhcCCccccCceeEEEEecchhhhcC----CcHHHHHHHHHHhc
Q 043110          153 KEKAR-------LRKGISILVATPG----HLLDHLKHTSSFLHTNLRWIIFDEADRILEL----GFGKEIEEILDILG  215 (316)
Q Consensus       153 ~~~~~-------l~~~~~IlV~Tp~----~l~~~l~~~~~~~~~~l~~lViDEad~l~~~----~~~~~i~~i~~~l~  215 (316)
                      .+...       +....-.+..+|.    .+...+....... ..++++|||=.|.|-..    +....+..+...|.
T Consensus        87 ~e~~~~~~~~~~l~~~~l~i~~~~~~~~~~i~~~i~~~~~~~-~~~~~v~IDyl~ll~~~~~~~~~~~~~~~i~~~Lk  163 (259)
T PF03796_consen   87 EEFERLQAAAEKLSDLPLYIEDTPSLTIDDIESKIRRLKREG-KKVDVVFIDYLQLLKSEDSSDNRRQEIGEISRELK  163 (259)
T ss_dssp             HHHHHHHHHHHHHHTSEEEEEESSS-BHHHHHHHHHHHHHHS-TTEEEEEEEEGGGSBTSCSSSCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhhCcEEEECCCCCCHHHHHHHHHHHHhhc-cCCCEEEechHHHhcCCCCCCCHHHHHHHHHHHHH
Confidence            32222       2222223344443    4555444322222 57899999999987663    34455555555544

Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1Q57_E 1E0K_D 1E0J_B 1CR2_A 1CR4_A 1CR1_A 1CR0_A 1MI8_A 2R6D_B 2R6C_C ....

>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]

Probab=92.99  E-value=0.86  Score=46.01  Aligned_cols=44  Identities=9%  Similarity=0.133  Sum_probs=36.2

Q ss_pred             ceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecch
Q 043110          186 NLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                      +--++|+|+-|.+.+......++.+++..|.               +.+.++.|=+-|+
T Consensus       129 ~pl~LVlDDyHli~~~~l~~~l~fLl~~~P~---------------~l~lvv~SR~rP~  172 (894)
T COG2909         129 GPLYLVLDDYHLISDPALHEALRFLLKHAPE---------------NLTLVVTSRSRPQ  172 (894)
T ss_pred             CceEEEeccccccCcccHHHHHHHHHHhCCC---------------CeEEEEEeccCCC
Confidence            3459999999999998888889999999887               7778877766653

>PRK14965 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.93  E-value=2.6  Score=41.64  Aligned_cols=17  Identities=35%  Similarity=0.407  Sum_probs=14.7

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      .++.||.|+|||.+..+
T Consensus        41 yLf~Gp~G~GKtt~A~~   57 (576)
T PRK14965         41 FLFTGARGVGKTSTARI   57 (576)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            68999999999988654

>PRK03992 proteasome-activating nucleotidase; Provisional

Probab=92.89  E-value=1.1  Score=41.91  Aligned_cols=53  Identities=23%  Similarity=0.348  Sum_probs=28.8

Q ss_pred             CCcccCCCCHHHHHHHHHHc--CCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           35 CCFSSLGLDSTLCDQLRERL--GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~--g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      .+|++++-.++.++.+.+..  .+.+|..++...   +...+.+++.||+|+|||+..
T Consensus       128 ~~~~di~Gl~~~~~~l~~~i~~pl~~~~~~~~~g---~~~p~gvLL~GppGtGKT~lA  182 (389)
T PRK03992        128 VTYEDIGGLEEQIREVREAVELPLKKPELFEEVG---IEPPKGVLLYGPPGTGKTLLA  182 (389)
T ss_pred             CCHHHhCCcHHHHHHHHHHHHHHhhCHHHHHhcC---CCCCCceEEECCCCCChHHHH
Confidence            45677765555555553322  222222222110   112356999999999999864

>PHA00012 I assembly protein

Probab=92.88  E-value=1.5  Score=39.68  Aligned_cols=25  Identities=28%  Similarity=0.429  Sum_probs=20.0

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           76 VLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      .++.+..|+|||+..+.-++..+.+
T Consensus         4 ylITGkPGSGKSl~aV~~I~~~L~~   28 (361)
T PHA00012          4 YVVTGKLGAGKTLVAVSRIQDKLVK   28 (361)
T ss_pred             EEEecCCCCCchHHHHHHHHHHHHc
Confidence            5789999999999987766666654

>PRK14952 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.87  E-value=1.1  Score=44.09  Aligned_cols=17  Identities=29%  Similarity=0.350  Sum_probs=14.9

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      ++++||.|+|||.++.+
T Consensus        38 ~Lf~Gp~G~GKTt~A~~   54 (584)
T PRK14952         38 YLFSGPRGCGKTSSARI   54 (584)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            68999999999988754

>PRK14721 flhF flagellar biosynthesis regulator FlhF; Provisional

Probab=92.76  E-value=0.85  Score=42.97  Aligned_cols=92  Identities=16%  Similarity=0.072  Sum_probs=45.4

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS  152 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (316)
                      |.-+.+.||||+|||.....-+...+....      ....+++.+.+.-.+  ..+.+..++..++ +............
T Consensus       191 g~vi~lvGpnG~GKTTtlakLA~~~~~~~~------~~~v~~i~~d~~rig--alEQL~~~a~ilG-vp~~~v~~~~dl~  261 (420)
T PRK14721        191 GGVYALIGPTGVGKTTTTAKLAARAVIRHG------ADKVALLTTDSYRIG--GHEQLRIYGKLLG-VSVRSIKDIADLQ  261 (420)
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHHHHHhcC------CCeEEEEecCCcchh--HHHHHHHHHHHcC-CceecCCCHHHHH
Confidence            455899999999999886432222222211      112255666553332  2333455554433 2222222222222


Q ss_pred             HHHHHHhcCCcEEEeCcHHHH
Q 043110          153 KEKARLRKGISILVATPGHLL  173 (316)
Q Consensus       153 ~~~~~l~~~~~IlV~Tp~~l~  173 (316)
                      .....+...-.|+|-|+|+..
T Consensus       262 ~al~~l~~~d~VLIDTaGrsq  282 (420)
T PRK14721        262 LMLHELRGKHMVLIDTVGMSQ  282 (420)
T ss_pred             HHHHHhcCCCEEEecCCCCCc
Confidence            223333333458899998643

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=92.75  E-value=0.95  Score=37.46  Aligned_cols=54  Identities=15%  Similarity=0.244  Sum_probs=37.2

Q ss_pred             CceeEEEEecchhhhcCCcH--HHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHh
Q 043110          185 TNLRWIIFDEADRILELGFG--KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKIS  253 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~--~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~  253 (316)
                      ...+++|+||.-..+..++.  +++..+++.-|.               ..-+|+..-..|+.+.+++...
T Consensus       121 ~~ydlviLDEl~~al~~g~l~~eeV~~~l~~kP~---------------~~~vIiTGr~ap~~lie~ADlV  176 (198)
T COG2109         121 GKYDLVILDELNYALRYGLLPLEEVVALLKARPE---------------HTHVIITGRGAPPELIELADLV  176 (198)
T ss_pred             CCCCEEEEehhhHHHHcCCCCHHHHHHHHhcCCC---------------CcEEEEECCCCCHHHHHHHHHH
Confidence            36889999999999887754  445455544433               4556666666788888877654

>PRK10865 protein disaggregation chaperone; Provisional

Probab=92.75  E-value=1.3  Score=45.77  Aligned_cols=17  Identities=24%  Similarity=0.317  Sum_probs=15.1

Q ss_pred             cEEEEcCCCCchHHHHH
Q 043110           75 DVLVNAATGTGKTVAYL   91 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~   91 (316)
                      +.++.||+|+|||...-
T Consensus       201 n~lL~G~pGvGKT~l~~  217 (857)
T PRK10865        201 NPVLIGEPGVGKTAIVE  217 (857)
T ss_pred             ceEEECCCCCCHHHHHH
Confidence            79999999999998753

>PF01637 Arch_ATPase: Archaeal ATPase; InterPro: IPR011579 This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP

Probab=92.70  E-value=0.79  Score=38.80  Aligned_cols=17  Identities=29%  Similarity=0.562  Sum_probs=14.6

Q ss_pred             CCcEEEEcCCCCchHHH
Q 043110           73 GRDVLVNAATGTGKTVA   89 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~   89 (316)
                      ++.+++.||.|+|||..
T Consensus        20 ~~~~~l~G~rg~GKTsL   36 (234)
T PF01637_consen   20 SQHILLYGPRGSGKTSL   36 (234)
T ss_dssp             SSEEEEEESTTSSHHHH
T ss_pred             CcEEEEEcCCcCCHHHH
Confidence            35699999999999974

; GO: 0005524 ATP binding; PDB: 2FNA_A 2QEN_A.

>KOG0732 consensus AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones]

Probab=92.69  E-value=0.28  Score=50.67  Aligned_cols=53  Identities=30%  Similarity=0.345  Sum_probs=33.1

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCC---CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFE---APTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~---~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      .-+|++.|....+...| +.+-+.   .|--+|...   +..-+-++..+|.|+|||+..
T Consensus       261 ~v~fd~vggl~~~i~~L-KEmVl~PLlyPE~f~~~~---itpPrgvL~~GppGTGkTl~a  316 (1080)
T KOG0732|consen  261 SVGFDSVGGLENYINQL-KEMVLLPLLYPEFFDNFN---ITPPRGVLFHGPPGTGKTLMA  316 (1080)
T ss_pred             ccCccccccHHHHHHHH-HHHHHhHhhhhhHhhhcc---cCCCcceeecCCCCCchhHHH
Confidence            35788998777777777 333322   222222111   123355999999999999874

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=92.67  E-value=0.87  Score=37.33  Aligned_cols=53  Identities=15%  Similarity=0.263  Sum_probs=33.6

Q ss_pred             CceeEEEEecchhhhcCCcH--HHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHH
Q 043110          185 TNLRWIIFDEADRILELGFG--KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKI  252 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~--~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~  252 (316)
                      ...++||+||+-..++.++-  +++..+++.-|.               ..-+|+.--..|+.+.+.+..
T Consensus        95 ~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~---------------~~evVlTGR~~~~~l~e~ADl  149 (172)
T PF02572_consen   95 GEYDLVILDEINYAVDYGLLSEEEVLDLLENRPE---------------SLEVVLTGRNAPEELIEAADL  149 (172)
T ss_dssp             TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-T---------------T-EEEEE-SS--HHHHHH-SE
T ss_pred             CCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCC---------------CeEEEEECCCCCHHHHHhCCe
Confidence            46889999999999988764  445555554333               667788777788888887763

5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents the ATP:cob(I)alamin adenosyltransferases CobA (Salmonella typhimurium), CobO (Pseudomonas denitrificans), and ButR (Escherichia coli). There is a high degree of sequence identity between these proteins []. CobA is responsible for attaching the adenosyl moiety from ATP to the cobalt ion of the corrin ring, necessary for the convertion of cobalamin to adenosylcobalamin [, ]. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 1G64_A 1G5T_A 1G5R_A.

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=92.66  E-value=2.1  Score=43.60  Aligned_cols=18  Identities=28%  Similarity=0.337  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 043110           74 RDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~   91 (316)
                      .++++.||+|+|||...-
T Consensus       204 ~n~lL~G~pG~GKT~l~~  221 (731)
T TIGR02639       204 NNPLLVGEPGVGKTAIAE  221 (731)
T ss_pred             CceEEECCCCCCHHHHHH
Confidence            479999999999998753

>TIGR00416 sms DNA repair protein RadA

Probab=92.63  E-value=1.3  Score=42.35  Aligned_cols=51  Identities=20%  Similarity=0.223  Sum_probs=31.9

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      |.-+++.+++|+|||...+- ++..+..        .+.+++|+..- +-..|+...+..+
T Consensus        94 GsvilI~G~pGsGKTTL~lq-~a~~~a~--------~g~kvlYvs~E-Es~~qi~~ra~rl  144 (454)
T TIGR00416        94 GSLILIGGDPGIGKSTLLLQ-VACQLAK--------NQMKVLYVSGE-ESLQQIKMRAIRL  144 (454)
T ss_pred             CeEEEEEcCCCCCHHHHHHH-HHHHHHh--------cCCcEEEEECc-CCHHHHHHHHHHc
Confidence            45689999999999987543 3333322        12348888754 4456666555543

The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=92.59  E-value=0.46  Score=39.56  Aligned_cols=106  Identities=17%  Similarity=0.201  Sum_probs=57.3

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS  152 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (316)
                      |+=.++.+|..||||...+--+-....         .|.++++..|-..-         .    +..-.+..-. |..  
T Consensus         4 g~l~~i~gpM~SGKT~eLl~r~~~~~~---------~g~~v~vfkp~iD~---------R----~~~~~V~Sr~-G~~--   58 (201)
T COG1435           4 GWLEFIYGPMFSGKTEELLRRARRYKE---------AGMKVLVFKPAIDT---------R----YGVGKVSSRI-GLS--   58 (201)
T ss_pred             EEEEEEEccCcCcchHHHHHHHHHHHH---------cCCeEEEEeccccc---------c----cccceeeecc-CCc--
Confidence            344689999999999864333322222         24558888876331         0    0111111111 111  


Q ss_pred             HHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHh
Q 043110          153 KEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDIL  214 (316)
Q Consensus       153 ~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l  214 (316)
                              ..-++|-.+..+.+.+......  ..++.+.||||+-+.+ ..-..+..+...+
T Consensus        59 --------~~A~~i~~~~~i~~~i~~~~~~--~~~~~v~IDEaQF~~~-~~v~~l~~lad~l  109 (201)
T COG1435          59 --------SEAVVIPSDTDIFDEIAALHEK--PPVDCVLIDEAQFFDE-ELVYVLNELADRL  109 (201)
T ss_pred             --------ccceecCChHHHHHHHHhcccC--CCcCEEEEehhHhCCH-HHHHHHHHHHhhc
Confidence                    1246666777777777653221  1278999999997433 2334445554443

>PRK14957 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.59  E-value=1.1  Score=43.76  Aligned_cols=17  Identities=29%  Similarity=0.290  Sum_probs=14.7

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      +++.||.|+|||.....
T Consensus        41 ~Lf~Gp~GvGKTTlAr~   57 (546)
T PRK14957         41 YLFTGTRGVGKTTLGRL   57 (546)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            78999999999987644

>PRK09354 recA recombinase A; Provisional

Probab=92.51  E-value=0.56  Score=42.97  Aligned_cols=42  Identities=26%  Similarity=0.275  Sum_probs=29.5

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      |+-+.+.+|+|+|||...+-.+.+....         +..++|+..-..+-
T Consensus        60 G~IteI~G~~GsGKTtLal~~~~~~~~~---------G~~~~yId~E~s~~  101 (349)
T PRK09354         60 GRIVEIYGPESSGKTTLALHAIAEAQKA---------GGTAAFIDAEHALD  101 (349)
T ss_pred             CeEEEEECCCCCCHHHHHHHHHHHHHHc---------CCcEEEECCccchH
Confidence            4568899999999998876555444332         44588887666555

>PRK09087 hypothetical protein; Validated

Probab=92.45  E-value=1.2  Score=38.35  Aligned_cols=18  Identities=28%  Similarity=0.355  Sum_probs=14.7

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      +.-+++.||+|+|||-..
T Consensus        44 ~~~l~l~G~~GsGKThLl   61 (226)
T PRK09087         44 SPVVVLAGPVGSGKTHLA   61 (226)
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            334899999999999753

>TIGR01243 CDC48 AAA family ATPase, CDC48 subfamily

Probab=92.38  E-value=1.4  Score=44.88  Aligned_cols=54  Identities=26%  Similarity=0.367  Sum_probs=32.4

Q ss_pred             cCCcccCCCCHHHHHHHHHHcC--CCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           34 SCCFSSLGLDSTLCDQLRERLG--FEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g--~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      ..+|++++-.+.+++.|.+...  +..|..++..-   +...+.+++.||+|+|||+..
T Consensus       449 ~~~~~di~g~~~~k~~l~~~v~~~~~~~~~~~~~g---~~~~~giLL~GppGtGKT~la  504 (733)
T TIGR01243       449 NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMG---IRPPKGVLLFGPPGTGKTLLA  504 (733)
T ss_pred             ccchhhcccHHHHHHHHHHHHHhhhhCHHHHHhcC---CCCCceEEEECCCCCCHHHHH
Confidence            3468888877777777744322  22222221111   112346899999999999864

This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.

>TIGR00678 holB DNA polymerase III, delta' subunit

Probab=92.37  E-value=1.8  Score=35.78  Aligned_cols=27  Identities=26%  Similarity=0.468  Sum_probs=18.9

Q ss_pred             CceeEEEEecchhhhcCCcHHHHHHHHHHhc
Q 043110          185 TNLRWIIFDEADRILELGFGKEIEEILDILG  215 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~~~i~~i~~~l~  215 (316)
                      ..-+++||||+|.+..    ...+.++..+.
T Consensus        95 ~~~kviiide~~~l~~----~~~~~Ll~~le  121 (188)
T TIGR00678        95 SGRRVVIIEDAERMNE----AAANALLKTLE  121 (188)
T ss_pred             CCeEEEEEechhhhCH----HHHHHHHHHhc
Confidence            4678999999999854    33445555554

At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau.

>PF02534 T4SS-DNA_transf: Type IV secretory system Conjugative DNA transfer; InterPro: IPR003688 This entry represents TraG proteins and their homologues

Probab=92.36  E-value=0.11  Score=49.91  Aligned_cols=49  Identities=29%  Similarity=0.331  Sum_probs=34.8

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .++++.||||||||..+++|.+-...   .        -+||.=|--||........++.
T Consensus        45 ~h~lvig~tgSGKt~~~viP~ll~~~---~--------s~iV~D~KgEl~~~t~~~r~~~   93 (469)
T PF02534_consen   45 THVLVIGPTGSGKTTSFVIPNLLNYP---G--------SMIVTDPKGELYEKTAGYRKKR   93 (469)
T ss_pred             eEEEEEeCCCCCccceeeHhHHHhcc---C--------CEEEEECCCcHHHHHHHHHHHC
Confidence            46999999999999999999763211   1        1667777777776665555544

These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems [, ].; GO: 0009291 unidirectional conjugation, 0016020 membrane

>TIGR02655 circ_KaiC circadian clock protein KaiC

Probab=92.33  E-value=1.2  Score=43.08  Aligned_cols=60  Identities=18%  Similarity=0.094  Sum_probs=39.9

Q ss_pred             HHHHHHhC-----CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           65 QAIPVILS-----GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        65 ~~i~~il~-----g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      ..++.++.     |.-+++.+|+|+|||...+--+.+.+.+         |-+++|++ .-|-..|+...++.++
T Consensus       250 ~~lD~~lgGG~~~gs~~li~G~~G~GKt~l~~~f~~~~~~~---------ge~~~y~s-~eEs~~~i~~~~~~lg  314 (484)
T TIGR02655       250 VRLDEMCGGGFFKDSIILATGATGTGKTLLVSKFLENACAN---------KERAILFA-YEESRAQLLRNAYSWG  314 (484)
T ss_pred             HhHHHHhcCCccCCcEEEEECCCCCCHHHHHHHHHHHHHHC---------CCeEEEEE-eeCCHHHHHHHHHHcC
Confidence            34555554     3569999999999998654433333322         34488887 5666788888877654

Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (Pfam model pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.

>PRK07471 DNA polymerase III subunit delta'; Validated

Probab=92.32  E-value=4  Score=37.83  Aligned_cols=25  Identities=20%  Similarity=0.307  Sum_probs=18.3

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      -.++.||.|+||+..+. .+...+..
T Consensus        43 A~Lf~Gp~G~GK~~lA~-~~A~~Llc   67 (365)
T PRK07471         43 AWLIGGPQGIGKATLAY-RMARFLLA   67 (365)
T ss_pred             eEEEECCCCCCHHHHHH-HHHHHHhC
Confidence            38999999999998753 34455544

>KOG0060 consensus Long-chain acyl-CoA transporter, ABC superfamily (involved in peroxisome organization and biogenesis) [Lipid transport and metabolism; General function prediction only]

Probab=92.29  E-value=0.24  Score=47.70  Aligned_cols=30  Identities=10%  Similarity=0.129  Sum_probs=23.6

Q ss_pred             CceeEEEEecchhhhcCCcHHHHHHHHHHh
Q 043110          185 TNLRWIIFDEADRILELGFGKEIEEILDIL  214 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~~~i~~i~~~l  214 (316)
                      ..-++.|+|||-.-++.+.+..+.++.+..
T Consensus       587 ~kPk~AiLDE~TSAv~~dvE~~~Yr~~r~~  616 (659)
T KOG0060|consen  587 HKPKFAILDECTSAVTEDVEGALYRKCREM  616 (659)
T ss_pred             cCCceEEeechhhhccHHHHHHHHHHHHHc
Confidence            456899999999988877777777766654

>PRK05896 DNA polymerase III subunits gamma and tau; Validated

Probab=92.27  E-value=1.4  Score=43.38  Aligned_cols=18  Identities=22%  Similarity=0.268  Sum_probs=15.2

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      -+++.||.|+|||..+..
T Consensus        40 A~Lf~GP~GvGKTTlA~~   57 (605)
T PRK05896         40 AYIFSGPRGIGKTSIAKI   57 (605)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            478999999999987644

>COG2874 FlaH Predicted ATPases involved in biogenesis of archaeal flagella [Cell motility and secretion / Intracellular trafficking and secretion]

Probab=92.26  E-value=3.2  Score=35.23  Aligned_cols=133  Identities=15%  Similarity=0.092  Sum_probs=66.2

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEe---CChHHHHHHHHHHHHHHhhcCCceeEEe---eC
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLV---PTSELCLLVYEILQKLLHRFRWIVPGYV---MG  147 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~---Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~---~~  147 (316)
                      .=+++.++.|+|||....--+.-.+..         +.++.+++   ++++...|....=-.+...+-+-....+   ..
T Consensus        29 sL~lIEGd~~tGKSvLsqr~~YG~L~~---------g~~v~yvsTe~T~refi~qm~sl~ydv~~~~l~G~l~~~~~~~~   99 (235)
T COG2874          29 SLILIEGDNGTGKSVLSQRFAYGFLMN---------GYRVTYVSTELTVREFIKQMESLSYDVSDFLLSGRLLFFPVNLE   99 (235)
T ss_pred             eEEEEECCCCccHHHHHHHHHHHHHhC---------CceEEEEEechhHHHHHHHHHhcCCCchHHHhcceeEEEEeccc
Confidence            348999999999998754444444433         44466665   5666666653321111111100011111   11


Q ss_pred             CCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCc
Q 043110          148 GGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNE  227 (316)
Q Consensus       148 ~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~  227 (316)
                      +..+.....             ..+++.+-+...  ..+-+++|+|-...+....-...+..++..+.+.+         
T Consensus       100 ~~~~~~~~~-------------~~~L~~l~~~~k--~~~~dViIIDSls~~~~~~~~~~vl~fm~~~r~l~---------  155 (235)
T COG2874         100 PVNWGRRSA-------------RKLLDLLLEFIK--RWEKDVIIIDSLSAFATYDSEDAVLNFMTFLRKLS---------  155 (235)
T ss_pred             ccccChHHH-------------HHHHHHHHhhHH--hhcCCEEEEecccHHhhcccHHHHHHHHHHHHHHH---------
Confidence            222211111             112222221111  13456899999988776554455666666655421         


Q ss_pred             cccccceEEEEeeec
Q 043110          228 VSNVKRQNLLLSATL  242 (316)
Q Consensus       228 ~~~~~~q~i~~SAT~  242 (316)
                         ..-.+|++|+..
T Consensus       156 ---d~gKvIilTvhp  167 (235)
T COG2874         156 ---DLGKVIILTVHP  167 (235)
T ss_pred             ---hCCCEEEEEeCh
Confidence               155788888763

>PRK14948 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.22  E-value=1.6  Score=43.50  Aligned_cols=19  Identities=32%  Similarity=0.338  Sum_probs=15.8

Q ss_pred             CcEEEEcCCCCchHHHHHH
Q 043110           74 RDVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~l   92 (316)
                      ..+++.||.|+|||..+..
T Consensus        39 ~a~Lf~Gp~G~GKttlA~~   57 (620)
T PRK14948         39 PAYLFTGPRGTGKTSSARI   57 (620)
T ss_pred             ceEEEECCCCCChHHHHHH
Confidence            3579999999999987644

>TIGR03880 KaiC_arch_3 KaiC domain protein, AF_0351 family

Probab=92.22  E-value=1.7  Score=37.12  Aligned_cols=52  Identities=23%  Similarity=0.217  Sum_probs=32.4

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .|.-+++.+++|+|||...+--+...+.+         +-.++|++-. +-..|+.+.+..+
T Consensus        15 ~g~~~li~G~~G~GKt~~~~~~~~~~~~~---------g~~~~y~s~e-~~~~~l~~~~~~~   66 (224)
T TIGR03880        15 EGHVIVVIGEYGTGKTTFSLQFLYQGLKN---------GEKAMYISLE-EREERILGYAKSK   66 (224)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC---------CCeEEEEECC-CCHHHHHHHHHHc
Confidence            34568999999999987643334333332         3347777654 4466666666554

This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself.

>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily

Probab=92.20  E-value=1.2  Score=42.17  Aligned_cols=22  Identities=27%  Similarity=0.409  Sum_probs=16.8

Q ss_pred             hCCCcEEEEcCCCCchHHHHHH
Q 043110           71 LSGRDVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        71 l~g~d~li~a~TGsGKT~~~~l   92 (316)
                      ..|.=+++.|++|+|||...+-
T Consensus       192 ~~g~liviag~pg~GKT~~al~  213 (421)
T TIGR03600       192 VKGDLIVIGARPSMGKTTLALN  213 (421)
T ss_pred             CCCceEEEEeCCCCCHHHHHHH
Confidence            3455689999999999976543

Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.

>PRK09376 rho transcription termination factor Rho; Provisional

Probab=92.13  E-value=0.62  Score=43.30  Aligned_cols=64  Identities=28%  Similarity=0.373  Sum_probs=39.7

Q ss_pred             cccccCCcccC-CCCHHHHHHHHHHcCCCC--CcHHHHHHHHHHh---CCCcEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           30 EIFASCCFSSL-GLDSTLCDQLRERLGFEA--PTKVQAQAIPVIL---SGRDVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        30 ~~~~~~~f~~~-~l~~~l~~~l~~~~g~~~--p~~~Q~~~i~~il---~g~d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      .......|+++ ++++.-      ++.+++  |.+.=.++|+.+.   .|+..++.||.|+|||... --+.+.+..
T Consensus       126 ~~~~r~~f~~l~p~~p~~------R~~le~~~~~~~~~rvID~l~PIGkGQR~lIvgppGvGKTTLa-K~Ian~I~~  195 (416)
T PRK09376        126 KARNRPLFENLTPLYPNE------RLRLETGNPEDLSTRIIDLIAPIGKGQRGLIVAPPKAGKTVLL-QNIANSITT  195 (416)
T ss_pred             HhcCCCCcccCCCCChhh------cccccCCCCcccceeeeeeecccccCceEEEeCCCCCChhHHH-HHHHHHHHh
Confidence            33455677777 355553      333433  4555566666654   7889999999999999643 234444443

>PRK14970 DNA polymerase III subunits gamma and tau; Provisional

Probab=92.12  E-value=5.5  Score=36.77  Aligned_cols=17  Identities=29%  Similarity=0.382  Sum_probs=14.5

Q ss_pred             cEEEEcCCCCchHHHHH
Q 043110           75 DVLVNAATGTGKTVAYL   91 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~   91 (316)
                      .++++||.|+|||....
T Consensus        41 ~~L~~G~~G~GKt~~a~   57 (367)
T PRK14970         41 ALLFCGPRGVGKTTCAR   57 (367)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            58899999999997653

>PF12846 AAA_10: AAA-like domain

Probab=92.12  E-value=0.3  Score=43.34  Aligned_cols=26  Identities=27%  Similarity=0.411  Sum_probs=19.4

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      .++++.|+||+|||.... .++..+..
T Consensus         2 ~h~~i~G~tGsGKT~~~~-~l~~~~~~   27 (304)
T PF12846_consen    2 PHTLILGKTGSGKTTLLK-NLLEQLIR   27 (304)
T ss_pred             CeEEEECCCCCcHHHHHH-HHHHHHHH
Confidence            578999999999998766 44444433

>PRK06090 DNA polymerase III subunit delta'; Validated

Probab=92.03  E-value=5.2  Score=36.30  Aligned_cols=42  Identities=14%  Similarity=0.076  Sum_probs=29.0

Q ss_pred             CCcHHHHHHHHHHh----CCC---cEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           58 APTKVQAQAIPVIL----SGR---DVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        58 ~p~~~Q~~~i~~il----~g~---d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      .++|||...+..+.    .|+   -.++.||.|.||+..+.. +.+.+..
T Consensus         3 ~~yPWl~~~~~~l~~~~~~~rl~hA~L~~G~~G~Gk~~lA~~-~a~~llC   51 (319)
T PRK06090          3 NDYPWLVPVWQNWKAGLDAGRIPGALLLQSDEGLGVESLVEL-FSRALLC   51 (319)
T ss_pred             cCcccHHHHHHHHHHHHHcCCcceeEeeECCCCCCHHHHHHH-HHHHHcC
Confidence            36788888876665    344   489999999999976543 4444443

>TIGR00763 lon ATP-dependent protease La

Probab=91.97  E-value=0.78  Score=46.96  Aligned_cols=18  Identities=28%  Similarity=0.287  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      |..+++.+|+|+|||..+
T Consensus       347 ~~~lll~GppG~GKT~lA  364 (775)
T TIGR00763       347 GPILCLVGPPGVGKTSLG  364 (775)
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            456999999999999764

This protein is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.

>cd01126 TraG_VirD4 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion

Probab=91.96  E-value=0.072  Score=49.68  Aligned_cols=48  Identities=33%  Similarity=0.348  Sum_probs=35.0

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      ++++.|+||||||.++++|-+....           .-+||+=|--|+........+..
T Consensus         1 H~lv~g~tGsGKt~~~viP~ll~~~-----------~s~vv~D~Kge~~~~t~~~r~~~   48 (384)
T cd01126           1 HVLVFAPTRSGKGVGFVIPNLLTWP-----------GSVVVLDPKGENFELTSEHRRAL   48 (384)
T ss_pred             CeeEecCCCCCCccEEEccchhcCC-----------CCEEEEccchhHHHHHHHHHHHc
Confidence            5789999999999999888654321           12788888888887666555443

These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer to plant cells and is required for virulence.

>PF00437 T2SE: Type II/IV secretion system protein; InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group [, ]

Probab=91.89  E-value=0.33  Score=42.83  Aligned_cols=44  Identities=18%  Similarity=0.328  Sum_probs=30.2

Q ss_pred             hCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           71 LSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        71 l~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      ..+.++++.|+||||||... -.++..+...        ..+++++-.+.|+-
T Consensus       125 ~~~~~ili~G~tGSGKTT~l-~all~~i~~~--------~~~iv~iEd~~E~~  168 (270)
T PF00437_consen  125 RGRGNILISGPTGSGKTTLL-NALLEEIPPE--------DERIVTIEDPPELR  168 (270)
T ss_dssp             HTTEEEEEEESTTSSHHHHH-HHHHHHCHTT--------TSEEEEEESSS-S-
T ss_pred             ccceEEEEECCCccccchHH-HHHhhhcccc--------ccceEEecccccee
Confidence            45779999999999999764 4455555431        24478888887764

These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1NLZ_C 2PT7_B 1OPX_A 1NLY_A 1G6O_B 2OAQ_2 2OAP_1 2JNQ_A 2JMZ_A 2GZA_B ....

>COG3972 Superfamily I DNA and RNA helicases [General function prediction only]

Probab=91.79  E-value=0.99  Score=42.86  Aligned_cols=79  Identities=18%  Similarity=0.138  Sum_probs=53.9

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH
Q 043110           46 LCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL  125 (316)
Q Consensus        46 l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q  125 (316)
                      +++.+ ++ .+..+...|.++.-..-.|+. .+.+=.|||||....+-+.. +...      .+.-++++-+-|+.|+.+
T Consensus       152 ~l~~i-es-kIanfD~~Q~kaa~~~~~G~q-rIrGLAGSGKT~~La~Kaa~-lh~k------nPd~~I~~Tfftk~L~s~  221 (660)
T COG3972         152 LLDTI-ES-KIANFDTDQTKAAFQSGFGKQ-RIRGLAGSGKTELLAHKAAE-LHSK------NPDSRIAFTFFTKILAST  221 (660)
T ss_pred             HHHHH-HH-HHhcccchhheeeeecCCchh-hhhcccCCCchhHHHHHHHH-HhcC------CCCceEEEEeehHHHHHH
Confidence            44445 22 344566678776655556666 77899999999875443333 2221      234569999999999999


Q ss_pred             HHHHHHHHH
Q 043110          126 VYEILQKLL  134 (316)
Q Consensus       126 ~~~~~~~~~  134 (316)
                      +...+.+++
T Consensus       222 ~r~lv~~F~  230 (660)
T COG3972         222 MRTLVPEFF  230 (660)
T ss_pred             HHHHHHHHH
Confidence            999888887

>TIGR00602 rad24 checkpoint protein rad24

Probab=91.76  E-value=2.4  Score=42.15  Aligned_cols=18  Identities=28%  Similarity=0.516  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 043110           74 RDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~   91 (316)
                      +-+++.||+|+|||..+-
T Consensus       111 ~illL~GP~GsGKTTl~~  128 (637)
T TIGR00602       111 RILLITGPSGCGKSTTIK  128 (637)
T ss_pred             cEEEEECCCCCCHHHHHH
Confidence            348999999999998753

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

>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain

Probab=91.76  E-value=0.19  Score=47.37  Aligned_cols=32  Identities=22%  Similarity=0.419  Sum_probs=22.3

Q ss_pred             HHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           67 IPVILSGRDVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        67 i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      +|.-...+++++.|+||+|||.+ +..++..+.
T Consensus        36 ~~~~~~~~h~~i~g~tGsGKt~~-i~~l~~~~~   67 (410)
T cd01127          36 FPKDAEEAHTMIIGTTGTGKTTQ-IRELLASIR   67 (410)
T ss_pred             CCcchhhccEEEEcCCCCCHHHH-HHHHHHHHH
Confidence            44444567999999999999986 334444443

TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.

>KOG0058 consensus Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport]

Probab=91.74  E-value=0.31  Score=48.20  Aligned_cols=32  Identities=34%  Similarity=0.342  Sum_probs=27.6

Q ss_pred             CceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          185 TNLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      ++-+.||+|||-.-+|..-+..+...+..+..
T Consensus       621 r~P~VLILDEATSALDaeSE~lVq~aL~~~~~  652 (716)
T KOG0058|consen  621 RNPRVLILDEATSALDAESEYLVQEALDRLMQ  652 (716)
T ss_pred             cCCCEEEEechhhhcchhhHHHHHHHHHHhhc
Confidence            46789999999999999888888888887764

>PRK14950 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.72  E-value=2.4  Score=41.94  Aligned_cols=18  Identities=28%  Similarity=0.318  Sum_probs=15.1

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      .+++.||.|+|||.+...
T Consensus        40 a~Lf~Gp~G~GKTtlA~~   57 (585)
T PRK14950         40 AYLFTGPRGVGKTSTARI   57 (585)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            369999999999987644

>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ

Probab=91.72  E-value=0.58  Score=43.39  Aligned_cols=28  Identities=29%  Similarity=0.336  Sum_probs=20.2

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      .+..+++++|||||||... -.++..+..
T Consensus       148 ~~GlilI~G~TGSGKTT~l-~al~~~i~~  175 (372)
T TIGR02525       148 AAGLGLICGETGSGKSTLA-ASIYQHCGE  175 (372)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHHh
Confidence            3446899999999999763 455665543

Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).

>PRK13764 ATPase; Provisional

Probab=91.69  E-value=0.49  Score=46.57  Aligned_cols=27  Identities=19%  Similarity=0.377  Sum_probs=20.4

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      .+++++++++||||||... -+++..+.
T Consensus       256 ~~~~ILIsG~TGSGKTTll-~AL~~~i~  282 (602)
T PRK13764        256 RAEGILIAGAPGAGKSTFA-QALAEFYA  282 (602)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            4678999999999999753 44555554

>PRK14959 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.69  E-value=2.1  Score=42.34  Aligned_cols=18  Identities=28%  Similarity=0.324  Sum_probs=15.5

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      .+++.+|.|+|||.++.+
T Consensus        40 a~Lf~GPpG~GKTtiAri   57 (624)
T PRK14959         40 AYLFSGTRGVGKTTIARI   57 (624)
T ss_pred             eEEEECCCCCCHHHHHHH
Confidence            478999999999998754

>PRK10416 signal recognition particle-docking protein FtsY; Provisional

Probab=91.59  E-value=1.8  Score=39.30  Aligned_cols=18  Identities=33%  Similarity=0.329  Sum_probs=14.6

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 043110           74 RDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~   91 (316)
                      +-+.+.+|+|+|||....
T Consensus       115 ~vi~lvGpnGsGKTTt~~  132 (318)
T PRK10416        115 FVILVVGVNGVGKTTTIG  132 (318)
T ss_pred             eEEEEECCCCCcHHHHHH
Confidence            347889999999998753

>COG4626 Phage terminase-like protein, large subunit [General function prediction only]

Probab=91.57  E-value=3.3  Score=39.99  Aligned_cols=74  Identities=15%  Similarity=0.240  Sum_probs=52.5

Q ss_pred             CCcHHHHHHHHHHh------CC----CcEEEEcCCCCchHHHHH-HHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           58 APTKVQAQAIPVIL------SG----RDVLVNAATGTGKTVAYL-APIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        58 ~p~~~Q~~~i~~il------~g----~d~li~a~TGsGKT~~~~-lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .+-|+|+-.+-.+.      .|    +..+|..|-+-|||.... +.+...+...      ..+-...|++|+.+-+.+.
T Consensus        61 ~l~PwQkFiia~l~G~~~k~T~~rrf~e~fI~v~RkngKt~l~A~i~~~~~l~~~------~~~~~~~i~A~s~~qa~~~  134 (546)
T COG4626          61 SLEPWQKFIVAALFGFYDKQTGIRRFKEAFIFIPRKNGKSTLAAGIMMTALLLNW------RSGAGIYILAPSVEQAANS  134 (546)
T ss_pred             ccchHHHHHHHHHhceeecCCCceEEEEEEEEEecCCchHHHHHHHHHHHHHhhh------hcCCcEEEEeccHHHHHHh
Confidence            36799999888776      12    257999999999997643 2222222221      2355599999999999999


Q ss_pred             HHHHHHHHhhc
Q 043110          127 YEILQKLLHRF  137 (316)
Q Consensus       127 ~~~~~~~~~~~  137 (316)
                      +..++.+....
T Consensus       135 F~~ar~mv~~~  145 (546)
T COG4626         135 FNPARDMVKRD  145 (546)
T ss_pred             hHHHHHHHHhC
Confidence            99888877543

>PTZ00293 thymidine kinase; Provisional

Probab=91.57  E-value=2.4  Score=35.93  Aligned_cols=39  Identities=15%  Similarity=0.123  Sum_probs=24.8

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCCh
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTS  120 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~  120 (316)
                      |+=-++.||.+||||.-.+-.+-.....         +.+++++-|..
T Consensus         4 G~i~vi~GpMfSGKTteLLr~i~~y~~a---------g~kv~~~kp~~   42 (211)
T PTZ00293          4 GTISVIIGPMFSGKTTELMRLVKRFTYS---------EKKCVVIKYSK   42 (211)
T ss_pred             eEEEEEECCCCChHHHHHHHHHHHHHHc---------CCceEEEEecc
Confidence            4456889999999997543333322222         33488888864

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

Probab=91.54  E-value=1.3  Score=46.33  Aligned_cols=145  Identities=21%  Similarity=0.213  Sum_probs=99.9

Q ss_pred             ccCCcccCCC---CHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcC-CCC---
Q 043110           33 ASCCFSSLGL---DSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYS-PRI---  105 (316)
Q Consensus        33 ~~~~f~~~~l---~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~-~~~---  105 (316)
                      +.-.|.++||   +++      .+||..     |++-+..+...-|++--+.|--=.|+-..+.-+..+.--. +..   
T Consensus       710 kdv~FkdLGLlIIDEE------qRFGVk-----~KEkLK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~~R~  778 (1139)
T COG1197         710 KDVKFKDLGLLIIDEE------QRFGVK-----HKEKLKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPEDRL  778 (1139)
T ss_pred             CCcEEecCCeEEEech------hhcCcc-----HHHHHHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCCCCc
Confidence            4467999984   454      567775     7888888888888888888888888765444333332111 110   


Q ss_pred             --------------------CCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHH---HHHh-cC
Q 043110          106 --------------------DRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK---ARLR-KG  161 (316)
Q Consensus       106 --------------------~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~l~-~~  161 (316)
                                          .-..|.++-||.|..+-..++.+.++.+.   +.....+.+|.....+..   ..+. ..
T Consensus       779 pV~T~V~~~d~~~ireAI~REl~RgGQvfYv~NrV~~Ie~~~~~L~~LV---PEarI~vaHGQM~e~eLE~vM~~F~~g~  855 (1139)
T COG1197         779 PVKTFVSEYDDLLIREAILRELLRGGQVFYVHNRVESIEKKAERLRELV---PEARIAVAHGQMRERELEEVMLDFYNGE  855 (1139)
T ss_pred             ceEEEEecCChHHHHHHHHHHHhcCCEEEEEecchhhHHHHHHHHHHhC---CceEEEEeecCCCHHHHHHHHHHHHcCC
Confidence                                11357889999999999999988888875   446667777766654332   2333 45


Q ss_pred             CcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhh
Q 043110          162 ISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRI  198 (316)
Q Consensus       162 ~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l  198 (316)
                      .||+|||.     .+.  .+++..+...+||+-||++
T Consensus       856 ~dVLv~TT-----IIE--tGIDIPnANTiIIe~AD~f  885 (1139)
T COG1197         856 YDVLVCTT-----IIE--TGIDIPNANTIIIERADKF  885 (1139)
T ss_pred             CCEEEEee-----eee--cCcCCCCCceEEEeccccc
Confidence            89999994     122  5667778899999999985

>PRK13897 type IV secretion system component VirD4; Provisional

Probab=91.52  E-value=0.14  Score=50.50  Aligned_cols=25  Identities=32%  Similarity=0.541  Sum_probs=21.9

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHh
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHL   98 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l   98 (316)
                      .++++.||||||||..+++|-+...
T Consensus       159 ~hvLviapTgSGKg~g~VIPnLL~~  183 (606)
T PRK13897        159 QHALLFAPTGSGKGVGFVIPNLLFW  183 (606)
T ss_pred             ceEEEEcCCCCCcceEEehhhHHhC
Confidence            4799999999999999999987653

>PF03237 Terminase_6: Terminase-like family; InterPro: IPR004921 The terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging []

Probab=91.50  E-value=3.1  Score=37.83  Aligned_cols=42  Identities=21%  Similarity=0.237  Sum_probs=24.4

Q ss_pred             EEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH
Q 043110           77 LVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL  125 (316)
Q Consensus        77 li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q  125 (316)
                      ++.++.|+|||.+..+.++..+.....      +..++++ |+..-+..
T Consensus         1 ~i~~~r~~GKT~~~~~~~~~~~~~~~~------~~~vi~~-~~~~~~~~   42 (384)
T PF03237_consen    1 LINGGRGSGKTTLIAIWFLWWALTRPP------GRRVIIA-STYRQARD   42 (384)
T ss_dssp             -EEE-SSS-HHHHHHHHHHHHHHSSSS--------EEEEE-ESSHHHHH
T ss_pred             CCcCCccccHHHHHHHHHHHHHhhCCC------CcEEEEe-cCHHHHHH
Confidence            467899999999987777777655221      2345555 66555444

The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein may have or induce an endonuclease activity to cleave DNA after encapsidation. This entry represents a family of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. Homologues are also found in Gene Transfer Agents (GTA) [], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in ].; PDB: 2O0K_A 3CPE_A 2O0J_A 2O0H_A 3C6H_A 3C6A_A.

>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]

Probab=91.49  E-value=2  Score=42.74  Aligned_cols=112  Identities=21%  Similarity=0.318  Sum_probs=67.2

Q ss_pred             CcHHHHHHHHHHh--------CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHH
Q 043110           59 PTKVQAQAIPVIL--------SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEIL  130 (316)
Q Consensus        59 p~~~Q~~~i~~il--------~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~  130 (316)
                      +..+-.+.+..+.        .|+=+++.+|+|.|||-..                             ++.|       
T Consensus       416 m~dVKeRILEfiAV~kLrgs~qGkIlCf~GPPGVGKTSI~-----------------------------kSIA-------  459 (906)
T KOG2004|consen  416 MEDVKERILEFIAVGKLRGSVQGKILCFVGPPGVGKTSIA-----------------------------KSIA-------  459 (906)
T ss_pred             hHHHHHHHHHHHHHHhhcccCCCcEEEEeCCCCCCcccHH-----------------------------HHHH-------
Confidence            4556666666554        4567899999999999653                             1111       


Q ss_pred             HHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHH
Q 043110          131 QKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEI  210 (316)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i  210 (316)
                      +.+.+    -......||.....+...=+.  -.+=+-||++.+.++.-+.-.    -++.|||+|.+-....++--..+
T Consensus       460 ~ALnR----kFfRfSvGG~tDvAeIkGHRR--TYVGAMPGkiIq~LK~v~t~N----PliLiDEvDKlG~g~qGDPasAL  529 (906)
T KOG2004|consen  460 RALNR----KFFRFSVGGMTDVAEIKGHRR--TYVGAMPGKIIQCLKKVKTEN----PLILIDEVDKLGSGHQGDPASAL  529 (906)
T ss_pred             HHhCC----ceEEEeccccccHHhhcccce--eeeccCChHHHHHHHhhCCCC----ceEEeehhhhhCCCCCCChHHHH
Confidence            11111    122234466555444322111  245567999999998643322    37889999998743455556677


Q ss_pred             HHHhcc
Q 043110          211 LDILGS  216 (316)
Q Consensus       211 ~~~l~~  216 (316)
                      ++.|..
T Consensus       530 LElLDP  535 (906)
T KOG2004|consen  530 LELLDP  535 (906)
T ss_pred             HHhcCh
Confidence            777654

>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]

Probab=91.48  E-value=0.13  Score=46.06  Aligned_cols=17  Identities=35%  Similarity=0.593  Sum_probs=15.1

Q ss_pred             CcEEEEcCCCCchHHHH
Q 043110           74 RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~   90 (316)
                      .|+++.+|||||||+.+
T Consensus        98 SNILLiGPTGsGKTlLA  114 (408)
T COG1219          98 SNILLIGPTGSGKTLLA  114 (408)
T ss_pred             ccEEEECCCCCcHHHHH
Confidence            47999999999999865

>PRK14955 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.44  E-value=2.6  Score=39.53  Aligned_cols=17  Identities=29%  Similarity=0.370  Sum_probs=15.0

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      +++.||.|+|||.++..
T Consensus        41 ~lf~Gp~G~GKtt~A~~   57 (397)
T PRK14955         41 YIFSGLRGVGKTTAARV   57 (397)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            88999999999988654

>PRK14951 DNA polymerase III subunits gamma and tau; Provisional

Probab=91.35  E-value=1.5  Score=43.42  Aligned_cols=17  Identities=29%  Similarity=0.364  Sum_probs=14.9

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      +++.||.|+|||....+
T Consensus        41 ~Lf~Gp~GvGKTtlAr~   57 (618)
T PRK14951         41 YLFTGTRGVGKTTVSRI   57 (618)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            59999999999988655

>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB

Probab=91.32  E-value=2.2  Score=44.25  Aligned_cols=18  Identities=22%  Similarity=0.305  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 043110           74 RDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~   91 (316)
                      .+.++.||+|+|||...-
T Consensus       195 ~n~lL~G~pGvGKT~l~~  212 (852)
T TIGR03346       195 NNPVLIGEPGVGKTAIVE  212 (852)
T ss_pred             CceEEEcCCCCCHHHHHH
Confidence            479999999999998753

Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.

>PRK04841 transcriptional regulator MalT; Provisional

Probab=91.24  E-value=3.3  Score=43.05  Aligned_cols=42  Identities=14%  Similarity=0.160  Sum_probs=31.7

Q ss_pred             eEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecch
Q 043110          188 RWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       188 ~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                      -+||||++|.+-+......+..++...+.               ...+|+.|-+.|+
T Consensus       123 ~~lvlDD~h~~~~~~~~~~l~~l~~~~~~---------------~~~lv~~sR~~~~  164 (903)
T PRK04841        123 LYLVIDDYHLITNPEIHEAMRFFLRHQPE---------------NLTLVVLSRNLPP  164 (903)
T ss_pred             EEEEEeCcCcCCChHHHHHHHHHHHhCCC---------------CeEEEEEeCCCCC
Confidence            48999999998655566678888887766               6778787777543

>KOG0729 consensus 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones]

Probab=91.20  E-value=2.8  Score=36.83  Aligned_cols=17  Identities=41%  Similarity=0.647  Sum_probs=15.5

Q ss_pred             CcEEEEcCCCCchHHHH
Q 043110           74 RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~   90 (316)
                      +-+++.+|.|+|||+++
T Consensus       212 kgvllygppgtgktl~a  228 (435)
T KOG0729|consen  212 KGVLLYGPPGTGKTLCA  228 (435)
T ss_pred             CceEEeCCCCCchhHHH
Confidence            56999999999999986

>KOG2228 consensus Origin recognition complex, subunit 4 [Replication, recombination and repair]

Probab=91.01  E-value=5.4  Score=36.33  Aligned_cols=45  Identities=24%  Similarity=0.227  Sum_probs=28.1

Q ss_pred             HHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          171 HLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       171 ~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      .++..+....... +.--++|+||.|.......+..+..++..-.+
T Consensus       123 ~lL~~L~~~~~~t-~~~ViFIldEfDlf~~h~rQtllYnlfDisqs  167 (408)
T KOG2228|consen  123 KLLEALKKGDETT-SGKVIFILDEFDLFAPHSRQTLLYNLFDISQS  167 (408)
T ss_pred             HHHHHHhcCCCCC-CceEEEEeehhhccccchhhHHHHHHHHHHhh
Confidence            4555555422221 22247899999988777777777777766553

>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP)

Probab=90.98  E-value=0.67  Score=40.88  Aligned_cols=43  Identities=28%  Similarity=0.442  Sum_probs=27.5

Q ss_pred             HHcCCCCCcHHHHHHHHHHhC--CCcEEEEcCCCCchHHHHHHHHHHHh
Q 043110           52 ERLGFEAPTKVQAQAIPVILS--GRDVLVNAATGTGKTVAYLAPIINHL   98 (316)
Q Consensus        52 ~~~g~~~p~~~Q~~~i~~il~--g~d~li~a~TGsGKT~~~~lp~l~~l   98 (316)
                      ..+|+   .+-|.+.+..++.  +..+++.++||||||... -.++..+
T Consensus        60 ~~lg~---~~~~~~~l~~~~~~~~GlilisG~tGSGKTT~l-~all~~i  104 (264)
T cd01129          60 EKLGL---KPENLEIFRKLLEKPHGIILVTGPTGSGKTTTL-YSALSEL  104 (264)
T ss_pred             HHcCC---CHHHHHHHHHHHhcCCCEEEEECCCCCcHHHHH-HHHHhhh
Confidence            44554   3456666655543  335899999999999764 3344444

It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.

>PHA00729 NTP-binding motif containing protein

Probab=90.98  E-value=5.2  Score=34.32  Aligned_cols=16  Identities=25%  Similarity=0.387  Sum_probs=14.3

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      ++++.|++|+|||..+
T Consensus        19 nIlItG~pGvGKT~LA   34 (226)
T PHA00729         19 SAVIFGKQGSGKTTYA   34 (226)
T ss_pred             EEEEECCCCCCHHHHH
Confidence            7999999999999754

>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases

Probab=90.97  E-value=0.37  Score=40.00  Aligned_cols=32  Identities=25%  Similarity=0.428  Sum_probs=24.4

Q ss_pred             CcHHHHHHHHHHh-CCCcEEEEcCCCCchHHHH
Q 043110           59 PTKVQAQAIPVIL-SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        59 p~~~Q~~~i~~il-~g~d~li~a~TGsGKT~~~   90 (316)
                      .++-|...+.... .|..+++.+|||||||...
T Consensus        10 ~~~~~~~~l~~~v~~g~~i~I~G~tGSGKTTll   42 (186)
T cd01130          10 FSPLQAAYLWLAVEARKNILISGGTGSGKTTLL   42 (186)
T ss_pred             CCHHHHHHHHHHHhCCCEEEEECCCCCCHHHHH
Confidence            4566666665544 6788999999999999763

The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.

>PF10412 TrwB_AAD_bind: Type IV secretion-system coupling protein DNA-binding domain; InterPro: IPR019476 The plasmid conjugative coupling protein TraD (also known as TrwB) is a basic integral inner-membrane nucleoside-triphosphate-binding protein

Probab=90.83  E-value=0.38  Score=44.96  Aligned_cols=32  Identities=31%  Similarity=0.577  Sum_probs=21.7

Q ss_pred             HHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           68 PVILSGRDVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        68 ~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      |.-...+++++.|.||||||.+ +-.++..+..
T Consensus        10 ~~~~e~~~~li~G~~GsGKT~~-i~~ll~~~~~   41 (386)
T PF10412_consen   10 PKDSENRHILIIGATGSGKTQA-IRHLLDQIRA   41 (386)
T ss_dssp             -GGGGGG-EEEEE-TTSSHHHH-HHHHHHHHHH
T ss_pred             ccchhhCcEEEECCCCCCHHHH-HHHHHHHHHH
Confidence            3344668999999999999974 4667766654

It is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells []. This protein forms hexamers from six structurally very similar protomers []. This hexamer contains a central channel running from the cytosolic pole (formed by the all-alpha domains) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB all-alpha domain appears to be the DNA-binding domain of the structure. ; PDB: 1E9S_D 1E9R_F 1GKI_B 1GL7_G 1GL6_A.

>PRK04328 hypothetical protein; Provisional

Probab=90.81  E-value=0.53  Score=41.09  Aligned_cols=53  Identities=23%  Similarity=0.230  Sum_probs=34.3

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      .|.-+++.+++|+|||...+--+.+.+.+         |-.++|++ +.+-..++.+.++.++
T Consensus        22 ~gs~ili~G~pGsGKT~l~~~fl~~~~~~---------ge~~lyis-~ee~~~~i~~~~~~~g   74 (249)
T PRK04328         22 ERNVVLLSGGPGTGKSIFSQQFLWNGLQM---------GEPGVYVA-LEEHPVQVRRNMRQFG   74 (249)
T ss_pred             CCcEEEEEcCCCCCHHHHHHHHHHHHHhc---------CCcEEEEE-eeCCHHHHHHHHHHcC
Confidence            45568999999999987654434444433         33377777 5555666666666654

>TIGR02012 tigrfam_recA protein RecA

Probab=90.78  E-value=0.61  Score=42.29  Aligned_cols=43  Identities=23%  Similarity=0.264  Sum_probs=28.0

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      .|.-+.+.+|+|+|||...+-.+.+....         +..++++..-..+.
T Consensus        54 ~G~iteI~G~~GsGKTtLaL~~~~~~~~~---------g~~v~yId~E~~~~   96 (321)
T TIGR02012        54 RGRIIEIYGPESSGKTTLALHAIAEAQKA---------GGTAAFIDAEHALD   96 (321)
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHHc---------CCcEEEEcccchhH
Confidence            44568999999999998765444443322         34477776554443

This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage.

>cd01394 radB RadB

Probab=90.71  E-value=1.5  Score=37.26  Aligned_cols=42  Identities=21%  Similarity=0.245  Sum_probs=26.7

Q ss_pred             HHHHhC-----CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEe
Q 043110           67 IPVILS-----GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLV  117 (316)
Q Consensus        67 i~~il~-----g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~  117 (316)
                      ++.++.     |.-+.+.+++|+|||...+--+.+....         +..++++.
T Consensus         8 LD~~l~GGi~~g~i~~i~G~~GsGKT~l~~~~a~~~~~~---------g~~v~yi~   54 (218)
T cd01394           8 LDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQ---------GKKVAYID   54 (218)
T ss_pred             HHHHhcCCccCCeEEEEECCCCCCHHHHHHHHHHHHHhc---------CCeEEEEE
Confidence            455554     4458999999999998764444333221         34477774

The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.

>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes

Probab=90.71  E-value=7.8  Score=31.37  Aligned_cols=16  Identities=31%  Similarity=0.461  Sum_probs=13.6

Q ss_pred             EEEEcCCCCchHHHHH
Q 043110           76 VLVNAATGTGKTVAYL   91 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~   91 (316)
                      +++.+++|+|||....
T Consensus         3 ~~~~G~~G~GKTt~~~   18 (173)
T cd03115           3 ILLVGLQGVGKTTTAA   18 (173)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5788999999998753

SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.

>PRK07133 DNA polymerase III subunits gamma and tau; Validated

Probab=90.67  E-value=4.9  Score=40.57  Aligned_cols=17  Identities=35%  Similarity=0.391  Sum_probs=14.7

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      .++.||.|+|||.++..
T Consensus        43 YLF~GP~GtGKTt~Ari   59 (725)
T PRK07133         43 YLFSGPRGTGKTSVAKI   59 (725)
T ss_pred             EEEECCCCCcHHHHHHH
Confidence            68999999999988644

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=90.66  E-value=3.3  Score=42.86  Aligned_cols=28  Identities=18%  Similarity=0.391  Sum_probs=20.2

Q ss_pred             HHHHHHHHh----CC--CcEEEEcCCCCchHHHH
Q 043110           63 QAQAIPVIL----SG--RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        63 Q~~~i~~il----~g--~d~li~a~TGsGKT~~~   90 (316)
                      |...+..+.    .+  .+.++.||.|+|||...
T Consensus       192 r~~ei~~~i~~l~r~~~~n~lLvG~pGvGKTal~  225 (852)
T TIGR03345       192 RDDEIRQMIDILLRRRQNNPILTGEAGVGKTAVV  225 (852)
T ss_pred             CHHHHHHHHHHHhcCCcCceeEECCCCCCHHHHH
Confidence            555554443    22  37999999999999875

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK08840 replicative DNA helicase; Provisional

Probab=90.65  E-value=5.3  Score=38.31  Aligned_cols=151  Identities=17%  Similarity=0.139  Sum_probs=69.1

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCCh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR  151 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (316)
                      .|.=+++.|.+|.|||...+ -+.......       .+..++|.+.- .-..|+..++-.....   +...-+..|.-.
T Consensus       216 ~g~LiviaarPg~GKTafal-nia~~~a~~-------~~~~v~~fSlE-Ms~~ql~~Rlla~~s~---v~~~~i~~~~l~  283 (464)
T PRK08840        216 GSDLIIVAARPSMGKTTFAM-NLCENAAMD-------QDKPVLIFSLE-MPAEQLMMRMLASLSR---VDQTKIRTGQLD  283 (464)
T ss_pred             CCceEEEEeCCCCchHHHHH-HHHHHHHHh-------CCCeEEEEecc-CCHHHHHHHHHHhhCC---CCHHHHhcCCCC
Confidence            44458889999999997653 333333221       12336666533 2244554443332211   111111122222


Q ss_pred             HHHHHH-------HhcCCcEEEe-Cc----HHHHHHHhcCCccccCceeEEEEecchhhhcCC----cHHHHHHHHHHhc
Q 043110          152 SKEKAR-------LRKGISILVA-TP----GHLLDHLKHTSSFLHTNLRWIIFDEADRILELG----FGKEIEEILDILG  215 (316)
Q Consensus       152 ~~~~~~-------l~~~~~IlV~-Tp----~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~----~~~~i~~i~~~l~  215 (316)
                      ..++..       +....++.|- +|    ..+...++.... ....++++|||=.+.|...+    ....+..|.+.|+
T Consensus       284 ~~e~~~~~~a~~~l~~~~~l~I~d~~~~ti~~i~~~~r~~~~-~~~~~~lvvIDYLql~~~~~~~~~r~~ei~~isr~LK  362 (464)
T PRK08840        284 DEDWARISSTMGILMEKKNMYIDDSSGLTPTEVRSRARRIAR-EHGGLSMIMVDYLQLMRVPALSDNRTLEIAEISRSLK  362 (464)
T ss_pred             HHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCCEEEEccHHhcCCCCCCCchHHHHHHHHHHHH
Confidence            222222       2223345443 33    333332222111 11247899999999875222    2334555555554


Q ss_pred             cCcccccCCCCccccccceEEEEeeecchhH
Q 043110          216 SRNIASIGEGNEVSNVKRQNLLLSATLNEKV  246 (316)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v  246 (316)
                      ...          ..-++.++++| -++..+
T Consensus       363 ~lA----------kel~ipVi~Ls-QLnR~~  382 (464)
T PRK08840        363 ALA----------KELNVPVVALS-QLNRSL  382 (464)
T ss_pred             HHH----------HHhCCeEEEEE-ecCccc
Confidence            311          01156677766 455444

>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]

Probab=90.62  E-value=2.5  Score=42.11  Aligned_cols=68  Identities=21%  Similarity=0.323  Sum_probs=46.6

Q ss_pred             EEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          143 GYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       143 ~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      ....||.....+.+.=++  --+=+=||++.+.+...+...    -++++||+|.|.....++=-..+++-|..
T Consensus       380 R~sLGGvrDEAEIRGHRR--TYIGamPGrIiQ~mkka~~~N----Pv~LLDEIDKm~ss~rGDPaSALLEVLDP  447 (782)
T COG0466         380 RISLGGVRDEAEIRGHRR--TYIGAMPGKIIQGMKKAGVKN----PVFLLDEIDKMGSSFRGDPASALLEVLDP  447 (782)
T ss_pred             EEecCccccHHHhccccc--cccccCChHHHHHHHHhCCcC----CeEEeechhhccCCCCCChHHHHHhhcCH
Confidence            445577666655543222  244567999999998754433    27899999999887777777777777764

>TIGR00665 DnaB replicative DNA helicase

Probab=90.57  E-value=4.1  Score=38.60  Aligned_cols=129  Identities=16%  Similarity=0.119  Sum_probs=60.1

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCCh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR  151 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (316)
                      .|.=+++.|++|+|||...+ -++..+...       .+..+++++.- .-..|+.+++........   ...+..|.-.
T Consensus       194 ~G~l~vi~g~pg~GKT~~~l-~~a~~~a~~-------~g~~vl~~SlE-m~~~~i~~R~~~~~~~v~---~~~~~~g~l~  261 (434)
T TIGR00665       194 PSDLIILAARPSMGKTAFAL-NIAENAAIK-------EGKPVAFFSLE-MSAEQLAMRMLSSESRVD---SQKLRTGKLS  261 (434)
T ss_pred             CCeEEEEEeCCCCChHHHHH-HHHHHHHHh-------CCCeEEEEeCc-CCHHHHHHHHHHHhcCCC---HHHhccCCCC
Confidence            34458999999999997543 333333221       12336666533 334455544433322211   1111122111


Q ss_pred             HHHH-------HHHhcCCcEEE-eC----cHHHHHHHhcCCccccCceeEEEEecchhhhcCC----cHHHHHHHHHHhc
Q 043110          152 SKEK-------ARLRKGISILV-AT----PGHLLDHLKHTSSFLHTNLRWIIFDEADRILELG----FGKEIEEILDILG  215 (316)
Q Consensus       152 ~~~~-------~~l~~~~~IlV-~T----p~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~----~~~~i~~i~~~l~  215 (316)
                      ..++       ..+.. ..+.| .+    +..+...++....  -..++++|||=.+.+...+    ....+..+.+.|.
T Consensus       262 ~~~~~~~~~a~~~l~~-~~l~i~d~~~~~~~~i~~~i~~~~~--~~~~~~vvID~l~~i~~~~~~~~r~~~i~~i~~~Lk  338 (434)
T TIGR00665       262 DEDWEKLTSAAGKLSE-APLYIDDTPGLTITELRAKARRLKR--EHGLGLIVIDYLQLMSGSGRSENRQQEVSEISRSLK  338 (434)
T ss_pred             HHHHHHHHHHHHHHhc-CCEEEECCCCCCHHHHHHHHHHHHH--hcCCCEEEEcchHhcCCCCCCCCHHHHHHHHHHHHH
Confidence            2222       22222 23444 33    3444443332111  1247899999988774322    2334555555554

This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites.

>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN

Probab=90.55  E-value=0.31  Score=42.92  Aligned_cols=28  Identities=32%  Similarity=0.461  Sum_probs=22.2

Q ss_pred             HHHHHHHhCCCcEEEEcCCCCchHHHHH
Q 043110           64 AQAIPVILSGRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        64 ~~~i~~il~g~d~li~a~TGsGKT~~~~   91 (316)
                      ++++..+..|+++++.+|+|+|||....
T Consensus        12 ~~~l~~l~~g~~vLL~G~~GtGKT~lA~   39 (262)
T TIGR02640        12 SRALRYLKSGYPVHLRGPAGTGKTTLAM   39 (262)
T ss_pred             HHHHHHHhcCCeEEEEcCCCCCHHHHHH
Confidence            3444556688999999999999998753

Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728).

>COG0210 UvrD Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]

Probab=90.51  E-value=0.88  Score=45.63  Aligned_cols=71  Identities=24%  Similarity=0.148  Sum_probs=53.3

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      .+++-|++++...  ...++|.|..|||||.+..--+...+....-.     .-.++.++=|+.-|.++.+++..+..
T Consensus         2 ~Ln~~Q~~av~~~--~gp~lV~AGaGsGKT~vlt~Ria~li~~~~v~-----p~~Il~vTFTnkAA~em~~Rl~~~~~   72 (655)
T COG0210           2 KLNPEQREAVLHP--DGPLLVLAGAGSGKTRVLTERIAYLIAAGGVD-----PEQILAITFTNKAAAEMRERLLKLLG   72 (655)
T ss_pred             CCCHHHHHHHhcC--CCCeEEEECCCCCchhhHHHHHHHHHHcCCcC-----hHHeeeeechHHHHHHHHHHHHHHhC
Confidence            5789999998765  56799999999999998655555555442111     11388999999999999888888775

>PRK08006 replicative DNA helicase; Provisional

Probab=90.51  E-value=5.8  Score=38.13  Aligned_cols=151  Identities=18%  Similarity=0.150  Sum_probs=70.6

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCCh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR  151 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (316)
                      .|.=+++.|.+|.|||...+ -++..+...       .+..++|.+.- .-..|+..++-.....   +....+..|.-.
T Consensus       223 ~G~LiiIaarPgmGKTafal-nia~~~a~~-------~g~~V~~fSlE-M~~~ql~~Rlla~~~~---v~~~~i~~~~l~  290 (471)
T PRK08006        223 PSDLIIVAARPSMGKTTFAM-NLCENAAML-------QDKPVLIFSLE-MPGEQIMMRMLASLSR---VDQTRIRTGQLD  290 (471)
T ss_pred             CCcEEEEEeCCCCCHHHHHH-HHHHHHHHh-------cCCeEEEEecc-CCHHHHHHHHHHHhcC---CCHHHhhcCCCC
Confidence            34448889999999997543 333333221       12336666533 2344444443322211   111111122222


Q ss_pred             HHHHHH-------HhcCCcEEEe-----CcHHHHHHHhcCCccccCceeEEEEecchhhhcC----CcHHHHHHHHHHhc
Q 043110          152 SKEKAR-------LRKGISILVA-----TPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL----GFGKEIEEILDILG  215 (316)
Q Consensus       152 ~~~~~~-------l~~~~~IlV~-----Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~----~~~~~i~~i~~~l~  215 (316)
                      ..++..       +....++.|-     |+..+...++.... ....++++|||=.+.|-..    .....+..|.+.|+
T Consensus       291 ~~e~~~~~~a~~~~~~~~~l~I~d~~~~t~~~i~~~~r~~~~-~~~~~~lvvIDYLqli~~~~~~~~r~~ei~~isr~LK  369 (471)
T PRK08006        291 DEDWARISGTMGILLEKRNMYIDDSSGLTPTEVRSRARRIFR-EHGGLSLIMIDYLQLMRVPSLSDNRTLEIAEISRSLK  369 (471)
T ss_pred             HHHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCCEEEEccHHHccCCCCCCCcHHHHHHHHHHHH
Confidence            222222       2133445553     34444443322111 1125889999999987522    23345666655554


Q ss_pred             cCcccccCCCCccccccceEEEEeeecchhH
Q 043110          216 SRNIASIGEGNEVSNVKRQNLLLSATLNEKV  246 (316)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v  246 (316)
                      ....          .-++.++++| -++..+
T Consensus       370 ~lAk----------el~ipVi~Ls-QLnR~~  389 (471)
T PRK08006        370 ALAK----------ELQVPVVALS-QLNRSL  389 (471)
T ss_pred             HHHH----------HhCCeEEEEE-ecCccc
Confidence            3110          1156777776 445544

>CHL00176 ftsH cell division protein; Validated

Probab=90.50  E-value=2.2  Score=42.54  Aligned_cols=55  Identities=20%  Similarity=0.288  Sum_probs=30.0

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcC-CCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLG-FEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g-~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|++..-.++..+.+.+-.. +..|..++...   ....+.+++.+|+|+|||+..
T Consensus       178 ~~~~f~dv~G~~~~k~~l~eiv~~lk~~~~~~~~g---~~~p~gVLL~GPpGTGKT~LA  233 (638)
T CHL00176        178 TGITFRDIAGIEEAKEEFEEVVSFLKKPERFTAVG---AKIPKGVLLVGPPGTGKTLLA  233 (638)
T ss_pred             CCCCHHhccChHHHHHHHHHHHHHHhCHHHHhhcc---CCCCceEEEECCCCCCHHHHH
Confidence            34677877655555555532211 11222211111   112356999999999999864

>PRK05748 replicative DNA helicase; Provisional

Probab=90.39  E-value=4.7  Score=38.47  Aligned_cols=129  Identities=17%  Similarity=0.137  Sum_probs=60.0

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS  152 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (316)
                      |.-+++.|++|.|||... +-++......       .+..+++++ .-.-..|+..++-.....   +....+..|.-..
T Consensus       203 G~livIaarpg~GKT~~a-l~ia~~~a~~-------~g~~v~~fS-lEms~~~l~~R~l~~~~~---v~~~~i~~~~l~~  270 (448)
T PRK05748        203 NDLIIVAARPSVGKTAFA-LNIAQNVATK-------TDKNVAIFS-LEMGAESLVMRMLCAEGN---IDAQRLRTGQLTD  270 (448)
T ss_pred             CceEEEEeCCCCCchHHH-HHHHHHHHHh-------CCCeEEEEe-CCCCHHHHHHHHHHHhcC---CCHHHhhcCCCCH
Confidence            345899999999999754 3344433321       122366664 333445555544322111   1111111222222


Q ss_pred             HHHHHH------hcCCcEEEe-Cc----HHHHHHHhcCCccccCceeEEEEecchhhhcCC-----cHHHHHHHHHHh
Q 043110          153 KEKARL------RKGISILVA-TP----GHLLDHLKHTSSFLHTNLRWIIFDEADRILELG-----FGKEIEEILDIL  214 (316)
Q Consensus       153 ~~~~~l------~~~~~IlV~-Tp----~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~-----~~~~i~~i~~~l  214 (316)
                      .++..+      ..+.++.|. +|    ..+...++.... ....++++|||=.+.+-..+     ....+..|.+.|
T Consensus       271 ~e~~~~~~a~~~l~~~~~~i~d~~~~ti~~i~~~~r~~~~-~~~~~~~vvIDyL~li~~~~~~~~~r~~~i~~i~~~L  347 (448)
T PRK05748        271 DDWPKLTIAMGSLSDAPIYIDDTPGIKVTEIRARCRRLAQ-EHGGLGLILIDYLQLIQGSGRSGENRQQEVSEISRSL  347 (448)
T ss_pred             HHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hcCCCCEEEEccchhcCCCCCCCcCHHHHHHHHHHHH
Confidence            232222      122345543 33    444443332111 10257899999999874221     223455555555

>CHL00095 clpC Clp protease ATP binding subunit

Probab=90.37  E-value=2.3  Score=43.83  Aligned_cols=18  Identities=22%  Similarity=0.303  Sum_probs=15.7

Q ss_pred             CcEEEEcCCCCchHHHHH
Q 043110           74 RDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~   91 (316)
                      .++++.||+|+|||...-
T Consensus       201 ~n~lL~G~pGvGKTal~~  218 (821)
T CHL00095        201 NNPILIGEPGVGKTAIAE  218 (821)
T ss_pred             CCeEEECCCCCCHHHHHH
Confidence            479999999999998763

>TIGR03743 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily

Probab=90.33  E-value=0.76  Score=45.77  Aligned_cols=52  Identities=23%  Similarity=0.247  Sum_probs=34.4

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH--HHHHHHHHHHHHH
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE--LCLLVYEILQKLL  134 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~--L~~Q~~~~~~~~~  134 (316)
                      +++++.|+||+|||..+..-+.+.+..         |..++++=|-..  |...+...++..+
T Consensus       177 ~H~lv~G~TGsGKT~l~~~l~~q~i~~---------g~~viv~DpKgD~~l~~~~~~~~~~~G  230 (634)
T TIGR03743       177 GHTLVLGTTGVGKTRLAELLITQDIRR---------GDVVIVIDPKGDADLKRRMRAEAKRAG  230 (634)
T ss_pred             CcEEEECCCCCCHHHHHHHHHHHHHHc---------CCeEEEEeCCCchHHHHHHHHHHHHhC
Confidence            579999999999998875545555543         233556656543  6666666665554

Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains.

>TIGR02524 dot_icm_DotB Dot/Icm secretion system ATPase DotB

Probab=90.24  E-value=0.33  Score=44.82  Aligned_cols=27  Identities=37%  Similarity=0.524  Sum_probs=20.0

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      .+.-+++++|||||||... -.++..+.
T Consensus       133 ~~glilI~GpTGSGKTTtL-~aLl~~i~  159 (358)
T TIGR02524       133 QEGIVFITGATGSGKSTLL-AAIIRELA  159 (358)
T ss_pred             cCCEEEEECCCCCCHHHHH-HHHHHHHh
Confidence            5667999999999999763 44555543

Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems.

>PRK14953 DNA polymerase III subunits gamma and tau; Provisional

Probab=90.24  E-value=7.8  Score=37.44  Aligned_cols=17  Identities=29%  Similarity=0.345  Sum_probs=14.2

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      .++.||.|+|||.+..+
T Consensus        41 yLf~Gp~G~GKTtlAr~   57 (486)
T PRK14953         41 YIFAGPRGTGKTTIARI   57 (486)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            57899999999987644

>COG1074 RecB ATP-dependent exoDNAse (exonuclease V) beta subunit (contains helicase and exonuclease domains) [DNA replication, recombination, and repair]

Probab=90.21  E-value=0.75  Score=49.11  Aligned_cols=61  Identities=28%  Similarity=0.314  Sum_probs=46.5

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHR  136 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~  136 (316)
                      .+.++++.|..|||||.+...-++..+....+    -.--.+|+|+-|+.-+..+..++..-...
T Consensus        15 ~~~~~lveASAGSGKT~vL~~r~lrlLl~~~~----~~v~~ILvvTFT~aAa~Emk~RI~~~L~~   75 (1139)
T COG1074          15 PGQSVLVEASAGTGKTFVLAERVLRLLLEGGP----LDVDEILVVTFTKAAAAEMKERIRDRLKE   75 (1139)
T ss_pred             CCCcEEEEEcCCCCchhHHHHHHHHHHhhcCC----CChhHeeeeeccHHHHHHHHHHHHHHHHH
Confidence            56799999999999999977777777766321    01224999999999999988877766544

>COG0467 RAD55 RecA-superfamily ATPases implicated in signal transduction [Signal transduction mechanisms]

Probab=90.06  E-value=0.66  Score=40.68  Aligned_cols=53  Identities=26%  Similarity=0.253  Sum_probs=34.7

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      .|+.+++.+++|+|||...+=-+.+.+..         |-.+++++ +.+...++.+.+..++
T Consensus        22 ~g~~~lI~G~pGsGKT~f~~qfl~~~~~~---------ge~vlyvs-~~e~~~~l~~~~~~~g   74 (260)
T COG0467          22 RGSVVLITGPPGTGKTIFALQFLYEGARE---------GEPVLYVS-TEESPEELLENARSFG   74 (260)
T ss_pred             CCcEEEEEcCCCCcHHHHHHHHHHHHHhc---------CCcEEEEE-ecCCHHHHHHHHHHcC
Confidence            56789999999999998643323332222         33377776 5566677777776654

>KOG2543 consensus Origin recognition complex, subunit 5 [Replication, recombination and repair]

Probab=90.02  E-value=11  Score=35.01  Aligned_cols=63  Identities=19%  Similarity=0.276  Sum_probs=39.3

Q ss_pred             ceeEEEEecchhhhcCC--cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcC
Q 043110          186 NLRWIIFDEADRILELG--FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD  263 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~--~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~  263 (316)
                      ..-++|+|-||.+-|++  ..+.+-.+-+.++.               ..=.+++|+++++..- ..+.....|+.+.+.
T Consensus       115 ~~~~liLDnad~lrD~~a~ll~~l~~L~el~~~---------------~~i~iils~~~~e~~y-~~n~g~~~i~~l~fP  178 (438)
T KOG2543|consen  115 QKVFLILDNADALRDMDAILLQCLFRLYELLNE---------------PTIVIILSAPSCEKQY-LINTGTLEIVVLHFP  178 (438)
T ss_pred             ceEEEEEcCHHhhhccchHHHHHHHHHHHHhCC---------------CceEEEEeccccHHHh-hcccCCCCceEEecC
Confidence            34589999999998875  33445555555554               4456778888875432 223345566666655


Q ss_pred             C
Q 043110          264 E  264 (316)
Q Consensus       264 ~  264 (316)
                      .
T Consensus       179 ~  179 (438)
T KOG2543|consen  179 Q  179 (438)
T ss_pred             C
Confidence            4

>PRK09112 DNA polymerase III subunit delta'; Validated

Probab=89.96  E-value=3.8  Score=37.75  Aligned_cols=30  Identities=27%  Similarity=0.478  Sum_probs=20.3

Q ss_pred             HhCCC---cEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           70 ILSGR---DVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        70 il~g~---d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      +.+|+   -+++.||.|+|||.... .+...+..
T Consensus        39 ~~~grl~ha~L~~G~~G~GKttlA~-~lA~~Llc   71 (351)
T PRK09112         39 YREGKLHHALLFEGPEGIGKATLAF-HLANHILS   71 (351)
T ss_pred             HHcCCCCeeEeeECCCCCCHHHHHH-HHHHHHcC
Confidence            33554   38999999999997653 34444444

>PF01443 Viral_helicase1: Viral (Superfamily 1) RNA helicase; InterPro: IPR000606 This entry includes RNA and DNA helicases

Probab=89.96  E-value=0.49  Score=40.44  Aligned_cols=14  Identities=29%  Similarity=0.676  Sum_probs=12.4

Q ss_pred             EEEEcCCCCchHHH
Q 043110           76 VLVNAATGTGKTVA   89 (316)
Q Consensus        76 ~li~a~TGsGKT~~   89 (316)
                      +++.|+.|||||..
T Consensus         1 ~vv~G~pGsGKSt~   14 (234)
T PF01443_consen    1 IVVHGVPGSGKSTL   14 (234)
T ss_pred             CEEEcCCCCCHHHH
Confidence            47899999999986

Some of the members are found in positive-strand single stranded RNA viruses. The helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis [].; GO: 0004386 helicase activity

>PRK08506 replicative DNA helicase; Provisional

Probab=89.95  E-value=4  Score=39.23  Aligned_cols=113  Identities=13%  Similarity=0.081  Sum_probs=54.2

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS  152 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (316)
                      |.=+++.|.||.|||...+- ++..+...        +..+++++.- .-..|+..++-.......   ...+..|.-..
T Consensus       192 G~LivIaarpg~GKT~fal~-ia~~~~~~--------g~~V~~fSlE-Ms~~ql~~Rlla~~s~v~---~~~i~~~~l~~  258 (472)
T PRK08506        192 GDLIIIAARPSMGKTTLCLN-MALKALNQ--------DKGVAFFSLE-MPAEQLMLRMLSAKTSIP---LQNLRTGDLDD  258 (472)
T ss_pred             CceEEEEcCCCCChHHHHHH-HHHHHHhc--------CCcEEEEeCc-CCHHHHHHHHHHHhcCCC---HHHHhcCCCCH
Confidence            34589999999999976543 33333321        2336666533 345555554433222111   11111122122


Q ss_pred             HHHH-------HHhcCCcEEEe-----CcHHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          153 KEKA-------RLRKGISILVA-----TPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       153 ~~~~-------~l~~~~~IlV~-----Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                      .++.       .+.. ..+.|-     |+..+...++.... ....++++|||=.+.|..
T Consensus       259 ~e~~~~~~a~~~l~~-~~l~I~d~~~~ti~~I~~~~r~l~~-~~~~~~lvvIDyLql~~~  316 (472)
T PRK08506        259 DEWERLSDACDELSK-KKLFVYDSGYVNIHQVRAQLRKLKS-QHPEIGLAVIDYLQLMSG  316 (472)
T ss_pred             HHHHHHHHHHHHHHc-CCeEEECCCCCCHHHHHHHHHHHHH-hCCCCCEEEEcChhhccC
Confidence            2222       2222 344443     34444444432111 112578999999987753

>KOG0652 consensus 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones]

Probab=89.95  E-value=1.8  Score=37.91  Aligned_cols=18  Identities=39%  Similarity=0.556  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      -+-++..+|+|+|||+.+
T Consensus       205 PKGvLmYGPPGTGKTlmA  222 (424)
T KOG0652|consen  205 PKGVLMYGPPGTGKTLMA  222 (424)
T ss_pred             CCceEeeCCCCCcHHHHH
Confidence            357999999999999875

>cd01393 recA_like RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response

Probab=89.84  E-value=2.2  Score=36.35  Aligned_cols=45  Identities=16%  Similarity=0.060  Sum_probs=26.6

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCCh
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTS  120 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~  120 (316)
                      |+-+.+.+++|+|||...+.-+...+... ..  .+....++++....
T Consensus        19 g~v~~I~G~~GsGKT~l~~~ia~~~~~~~-~~--~g~~~~v~yi~~e~   63 (226)
T cd01393          19 GRITEIFGEFGSGKTQLCLQLAVEAQLPG-EL--GGLEGKVVYIDTEG   63 (226)
T ss_pred             CcEEEEeCCCCCChhHHHHHHHHHhhccc-cc--CCCcceEEEEecCC
Confidence            45689999999999987654333332221 00  01124578877643

RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs radA and radB.

>PRK14954 DNA polymerase III subunits gamma and tau; Provisional

Probab=89.83  E-value=3.5  Score=40.97  Aligned_cols=28  Identities=21%  Similarity=0.277  Sum_probs=19.7

Q ss_pred             CceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          185 TNLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      .+-+++||||+|.|..    ...+.+++.+..
T Consensus       126 ~~~KVvIIdEad~Lt~----~a~naLLK~LEe  153 (620)
T PRK14954        126 GRYRVYIIDEVHMLST----AAFNAFLKTLEE  153 (620)
T ss_pred             CCCEEEEEeChhhcCH----HHHHHHHHHHhC
Confidence            4678999999999864    334556665543

>PRK08451 DNA polymerase III subunits gamma and tau; Validated

Probab=89.77  E-value=3.5  Score=40.20  Aligned_cols=22  Identities=27%  Similarity=0.335  Sum_probs=16.3

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHh
Q 043110           76 VLVNAATGTGKTVAYLAPIINHL   98 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l   98 (316)
                      .++.||.|+|||.++.. +...+
T Consensus        39 yLf~Gp~G~GKTt~Ar~-LAk~L   60 (535)
T PRK08451         39 YLFSGLRGSGKTSSARI-FARAL   60 (535)
T ss_pred             EEEECCCCCcHHHHHHH-HHHHh
Confidence            58999999999987644 33333

>PRK10436 hypothetical protein; Provisional

Probab=89.63  E-value=0.56  Score=44.82  Aligned_cols=38  Identities=29%  Similarity=0.359  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHh--CCCcEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           61 KVQAQAIPVIL--SGRDVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        61 ~~Q~~~i~~il--~g~d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      +-|.+.+..++  .+.-+++.+|||||||... ..++..+.
T Consensus       204 ~~~~~~l~~~~~~~~GliLvtGpTGSGKTTtL-~a~l~~~~  243 (462)
T PRK10436        204 PAQLAQFRQALQQPQGLILVTGPTGSGKTVTL-YSALQTLN  243 (462)
T ss_pred             HHHHHHHHHHHHhcCCeEEEECCCCCChHHHH-HHHHHhhC
Confidence            44555555444  3345999999999999864 34555553

>PRK13850 type IV secretion system protein VirD4; Provisional

Probab=89.52  E-value=0.26  Score=49.15  Aligned_cols=24  Identities=33%  Similarity=0.383  Sum_probs=21.2

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHH
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINH   97 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~   97 (316)
                      .++++.||||||||.++++|-+-.
T Consensus       140 ~hvlviApTgSGKgvg~VIPnLL~  163 (670)
T PRK13850        140 PHSLVVAPTRAGKGVGVVIPTLLT  163 (670)
T ss_pred             ceEEEEecCCCCceeeehHhHHhc
Confidence            479999999999999999997654

>KOG0740 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=89.37  E-value=3.3  Score=38.97  Aligned_cols=70  Identities=20%  Similarity=0.195  Sum_probs=44.3

Q ss_pred             ceeEEEEecchhhhcCC--------cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeee-cchhHHHHHHHhcCC
Q 043110          186 NLRWIIFDEADRILELG--------FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSAT-LNEKVNHLTKISLET  256 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~--------~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT-~~~~v~~~~~~~l~~  256 (316)
                      ...+++|||+|.++..-        .....+.++.....           ...++-++++++|| +|..+++-++..+..
T Consensus       245 qPsvifidEidslls~Rs~~e~e~srr~ktefLiq~~~~-----------~s~~~drvlvigaTN~P~e~Dea~~Rrf~k  313 (428)
T KOG0740|consen  245 QPSVIFIDEIDSLLSKRSDNEHESSRRLKTEFLLQFDGK-----------NSAPDDRVLVIGATNRPWELDEAARRRFVK  313 (428)
T ss_pred             CCeEEEechhHHHHhhcCCcccccchhhhhHHHhhhccc-----------cCCCCCeEEEEecCCCchHHHHHHHHHhhc
Confidence            34577899999988531        22333333333321           22334588888888 588888887777777


Q ss_pred             CEEEEcCCCC
Q 043110          257 PVLIGLDEKK  266 (316)
Q Consensus       257 p~~i~~~~~~  266 (316)
                      -.+|...+.+
T Consensus       314 r~yiplPd~e  323 (428)
T KOG0740|consen  314 RLYIPLPDYE  323 (428)
T ss_pred             eeeecCCCHH
Confidence            7777666553

>KOG2036 consensus Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only]

Probab=89.33  E-value=5.6  Score=39.56  Aligned_cols=61  Identities=25%  Similarity=0.226  Sum_probs=41.8

Q ss_pred             cHHHHHHHHHHhCC-------CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           60 TKVQAQAIPVILSG-------RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        60 ~~~Q~~~i~~il~g-------~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      |--|.+|+-.+...       --+-+.|.-|-||+.+.-+++...+.-.        ..-+-|-+|+-+=..-+++
T Consensus       255 T~dQakav~~f~dai~eK~lr~~vsLtA~RGRGKSAALGlsiA~AVa~G--------ysnIyvtSPspeNlkTlFe  322 (1011)
T KOG2036|consen  255 TLDQAKAVLTFFDAIVEKTLRSTVSLTASRGRGKSAALGLSIAGAVAFG--------YSNIYVTSPSPENLKTLFE  322 (1011)
T ss_pred             hHHHHHHHHHHHHHHHHhhhcceEEEEecCCCCchhhhhHHHHHHHhcC--------cceEEEcCCChHHHHHHHH
Confidence            66788776554421       2478899999999999888887777542        1226667799776554444

>PRK06305 DNA polymerase III subunits gamma and tau; Validated

Probab=89.17  E-value=8.5  Score=36.80  Aligned_cols=18  Identities=33%  Similarity=0.337  Sum_probs=15.2

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      ..++.||.|+|||.++..
T Consensus        41 a~Lf~Gp~G~GKtt~A~~   58 (451)
T PRK06305         41 AYLFSGIRGTGKTTLARI   58 (451)
T ss_pred             EEEEEcCCCCCHHHHHHH
Confidence            478999999999987644

>PRK08760 replicative DNA helicase; Provisional

Probab=89.17  E-value=4.8  Score=38.73  Aligned_cols=129  Identities=19%  Similarity=0.106  Sum_probs=60.5

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS  152 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (316)
                      |.=+++.|.+|.|||...+ -++..+...       .+..++|.+.- .-..|+..++..........   .+..|.-..
T Consensus       229 G~LivIaarPg~GKTafal-~iA~~~a~~-------~g~~V~~fSlE-Ms~~ql~~Rl~a~~s~i~~~---~i~~g~l~~  296 (476)
T PRK08760        229 TDLIILAARPAMGKTTFAL-NIAEYAAIK-------SKKGVAVFSME-MSASQLAMRLISSNGRINAQ---RLRTGALED  296 (476)
T ss_pred             CceEEEEeCCCCChhHHHH-HHHHHHHHh-------cCCceEEEecc-CCHHHHHHHHHHhhCCCcHH---HHhcCCCCH
Confidence            3448999999999997644 333333221       12236666533 23445555554433221111   111222222


Q ss_pred             HHHHHH------hcCCcEEEe-----CcHHHHHHHhcCCccccCceeEEEEecchhhhcC----CcHHHHHHHHHHhc
Q 043110          153 KEKARL------RKGISILVA-----TPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL----GFGKEIEEILDILG  215 (316)
Q Consensus       153 ~~~~~l------~~~~~IlV~-----Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~----~~~~~i~~i~~~l~  215 (316)
                      .++..+      .....+.|.     |++.+...++...  .-..++++|||=.+.|...    .....+..|.+.|+
T Consensus       297 ~e~~~~~~a~~~l~~~~l~I~d~~~~t~~~I~~~~r~l~--~~~~~~lVvIDyLql~~~~~~~~~r~~ei~~Isr~LK  372 (476)
T PRK08760        297 EDWARVTGAIKMLKETKIFIDDTPGVSPEVLRSKCRRLK--REHDLGLIVIDYLQLMSVPGNSENRATEISEISRSLK  372 (476)
T ss_pred             HHHHHHHHHHHHHhcCCEEEeCCCCCCHHHHHHHHHHHH--HhcCCCEEEEecHHhcCCCCCCcccHHHHHHHHHHHH
Confidence            222221      112345444     3344444333211  1135789999999877422    22334555555443

>TIGR03754 conj_TOL_TraD conjugative coupling factor TraD, TOL family

Probab=89.08  E-value=1.2  Score=44.22  Aligned_cols=54  Identities=22%  Similarity=0.237  Sum_probs=38.4

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCCh--HHHHHHHHHHHHHHh
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTS--ELCLLVYEILQKLLH  135 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~--~L~~Q~~~~~~~~~~  135 (316)
                      ..+.++.++||+|||..+.+-+.+.+..         +..++++=|-.  ++...++..++..+.
T Consensus       180 ~gHtlV~GtTGsGKT~l~~~li~q~i~~---------g~~vi~fDpkgD~el~~~~~~~~~~~GR  235 (643)
T TIGR03754       180 VGHTLVLGTTRVGKTRLAELLITQDIRR---------GDVVIVFDPKGDADLLKRMYAEAKRAGR  235 (643)
T ss_pred             cCceEEECCCCCCHHHHHHHHHHHHHHc---------CCeEEEEeCCCCHHHHHHHHHHHHHhCC
Confidence            3579999999999999987766666643         33477777765  566666666666654

Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion.

>PRK07004 replicative DNA helicase; Provisional

Probab=88.94  E-value=2.1  Score=41.07  Aligned_cols=131  Identities=17%  Similarity=0.110  Sum_probs=60.1

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCCh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR  151 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (316)
                      .|.=+++.|.+|+|||...+ -+...+...       .+..+++.+. -.-..|+..++-....   .+....+..|.-.
T Consensus       212 ~g~liviaarpg~GKT~~al-~ia~~~a~~-------~~~~v~~fSl-EM~~~ql~~R~la~~~---~v~~~~i~~g~l~  279 (460)
T PRK07004        212 GGELIIVAGRPSMGKTAFSM-NIGEYVAVE-------YGLPVAVFSM-EMPGTQLAMRMLGSVG---RLDQHRMRTGRLT  279 (460)
T ss_pred             CCceEEEEeCCCCCccHHHH-HHHHHHHHH-------cCCeEEEEeC-CCCHHHHHHHHHHhhc---CCCHHHHhcCCCC
Confidence            34458899999999997643 333333221       1223555542 2234444444322111   1111111122222


Q ss_pred             HHHHHHHh------cCCcEEEe-C----cHHHHHHHhcCCccccCceeEEEEecchhhhcC----CcHHHHHHHHHHhc
Q 043110          152 SKEKARLR------KGISILVA-T----PGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL----GFGKEIEEILDILG  215 (316)
Q Consensus       152 ~~~~~~l~------~~~~IlV~-T----p~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~----~~~~~i~~i~~~l~  215 (316)
                      ..++..+.      ...++.|. +    +..+....+.... ....++++|||=.+.|...    .....+..|.+.|+
T Consensus       280 ~~e~~~~~~a~~~l~~~~l~I~d~~~~~~~~i~~~~r~l~~-~~~~~~lviIDYLql~~~~~~~~~r~~ei~~Isr~LK  357 (460)
T PRK07004        280 DEDWPKLTHAVQKMSEAQLFIDETGGLNPMELRSRARRLAR-QCGKLGLIIIDYLQLMSGSSQGENRATEISEISRSLK  357 (460)
T ss_pred             HHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHHH-hCCCCCEEEEChhhhccCCCCCCcHHHHHHHHHHHHH
Confidence            23332221      23455553 3    3344333322111 1124789999999887532    23344556655554

>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]

Probab=88.79  E-value=0.48  Score=44.12  Aligned_cols=52  Identities=25%  Similarity=0.349  Sum_probs=40.0

Q ss_pred             CCCHHHHHHHHHHcCCCCCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHH
Q 043110           41 GLDSTLCDQLRERLGFEAPTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPI   94 (316)
Q Consensus        41 ~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~   94 (316)
                      +++.+++..+ +.||.. -+.+|..++..+.    .|.-+.+.+++|+|||..+-+-+
T Consensus       375 ~lp~e~~~Il-eSFGv~-~r~ieryvlr~vNL~ikpGdvvaVvGqSGaGKttllRmi~  430 (593)
T COG2401         375 GLPNEFQDIL-ESFGVR-QRVIERYVLRNLNLEIKPGDVVAVVGQSGAGKTTLLRMIL  430 (593)
T ss_pred             cCChHHHHHH-HHhcch-heeeeeeeeeceeeEecCCCeEEEEecCCCCcchHHHHHH
Confidence            7999999999 778887 4677777765543    45568999999999998754433

>PRK14971 DNA polymerase III subunits gamma and tau; Provisional

Probab=88.79  E-value=4.8  Score=40.09  Aligned_cols=17  Identities=29%  Similarity=0.315  Sum_probs=14.4

Q ss_pred             EEEEcCCCCchHHHHHH
Q 043110           76 VLVNAATGTGKTVAYLA   92 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~l   92 (316)
                      ++++||.|+|||.+..+
T Consensus        42 yLf~Gp~G~GKtt~A~~   58 (614)
T PRK14971         42 YLFCGPRGVGKTTCARI   58 (614)
T ss_pred             EEEECCCCCCHHHHHHH
Confidence            79999999999996543

>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB

Probab=88.75  E-value=0.67  Score=45.60  Aligned_cols=44  Identities=34%  Similarity=0.453  Sum_probs=28.5

Q ss_pred             HHcCCCCCcHHHHHHHHHHhC--CCcEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           52 ERLGFEAPTKVQAQAIPVILS--GRDVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        52 ~~~g~~~p~~~Q~~~i~~il~--g~d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      ..+|+   .+-|.+.+..++.  +.-++++||||||||... ..++..+.
T Consensus       296 ~~lg~---~~~~~~~l~~~~~~~~Glilv~G~tGSGKTTtl-~a~l~~~~  341 (564)
T TIGR02538       296 DKLGF---EPDQKALFLEAIHKPQGMVLVTGPTGSGKTVSL-YTALNILN  341 (564)
T ss_pred             HHcCC---CHHHHHHHHHHHHhcCCeEEEECCCCCCHHHHH-HHHHHhhC
Confidence            34555   3556666655544  345899999999999874 44555553

This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.

>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11

Probab=88.65  E-value=0.88  Score=41.08  Aligned_cols=20  Identities=35%  Similarity=0.674  Sum_probs=17.4

Q ss_pred             HhCCCcEEEEcCCCCchHHH
Q 043110           70 ILSGRDVLVNAATGTGKTVA   89 (316)
Q Consensus        70 il~g~d~li~a~TGsGKT~~   89 (316)
                      +..|+++++.++||||||..
T Consensus       141 v~~~~~ili~G~tGsGKTTl  160 (308)
T TIGR02788       141 IASRKNIIISGGTGSGKTTF  160 (308)
T ss_pred             hhCCCEEEEECCCCCCHHHH
Confidence            34678999999999999975

The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA.

>KOG0744 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=88.62  E-value=2.8  Score=37.87  Aligned_cols=98  Identities=18%  Similarity=0.241  Sum_probs=54.2

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee-EEEEe-----------CChHHHHHHHHHHHHHHhhcCCce
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF-ALVLV-----------PTSELCLLVYEILQKLLHRFRWIV  141 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~-~lil~-----------Pt~~L~~Q~~~~~~~~~~~~~~~~  141 (316)
                      +=+++.||+|+|||... -++.+.+.-+..    +...+ .+|=.           -+--|+.++++.++.+...-+..+
T Consensus       178 RliLlhGPPGTGKTSLC-KaLaQkLSIR~~----~~y~~~~liEinshsLFSKWFsESgKlV~kmF~kI~ELv~d~~~lV  252 (423)
T KOG0744|consen  178 RLILLHGPPGTGKTSLC-KALAQKLSIRTN----DRYYKGQLIEINSHSLFSKWFSESGKLVAKMFQKIQELVEDRGNLV  252 (423)
T ss_pred             eEEEEeCCCCCChhHHH-HHHHHhheeeec----CccccceEEEEehhHHHHHHHhhhhhHHHHHHHHHHHHHhCCCcEE
Confidence            44899999999999653 445555533211    11222 33333           344577778888888877655444


Q ss_pred             eEEee-------------CCC-C---------hHHHHHHHhcCCcEEEeCcHHHHHHH
Q 043110          142 PGYVM-------------GGG-N---------RSKEKARLRKGISILVATPGHLLDHL  176 (316)
Q Consensus       142 ~~~~~-------------~~~-~---------~~~~~~~l~~~~~IlV~Tp~~l~~~l  176 (316)
                      +..+-             .+. .         .-.|.+++...++++|-|...+.+.+
T Consensus       253 fvLIDEVESLa~aR~s~~S~~EpsDaIRvVNalLTQlDrlK~~~NvliL~TSNl~~si  310 (423)
T KOG0744|consen  253 FVLIDEVESLAAARTSASSRNEPSDAIRVVNALLTQLDRLKRYPNVLILATSNLTDSI  310 (423)
T ss_pred             EEEeHHHHHHHHHHHhhhcCCCCchHHHHHHHHHHHHHHhccCCCEEEEeccchHHHH
Confidence            43321             011 0         12345556666777776665555544

>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional

Probab=88.51  E-value=3.9  Score=41.70  Aligned_cols=17  Identities=35%  Similarity=0.485  Sum_probs=14.6

Q ss_pred             cEEEEcCCCCchHHHHH
Q 043110           75 DVLVNAATGTGKTVAYL   91 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~   91 (316)
                      .+++.||||+|||..+-
T Consensus       490 ~~Lf~GP~GvGKT~lAk  506 (758)
T PRK11034        490 SFLFAGPTGVGKTEVTV  506 (758)
T ss_pred             eEEEECCCCCCHHHHHH
Confidence            48999999999998753

>PF12775 AAA_7: P-loop containing dynein motor region D3; PDB: 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 3VKH_A 3VKG_A

Probab=88.14  E-value=0.37  Score=42.71  Aligned_cols=19  Identities=47%  Similarity=0.665  Sum_probs=16.9

Q ss_pred             hCCCcEEEEcCCCCchHHH
Q 043110           71 LSGRDVLVNAATGTGKTVA   89 (316)
Q Consensus        71 l~g~d~li~a~TGsGKT~~   89 (316)
                      ..++.++++||+|+|||..
T Consensus        31 ~~~~pvLl~G~~GtGKT~l   49 (272)
T PF12775_consen   31 SNGRPVLLVGPSGTGKTSL   49 (272)
T ss_dssp             HCTEEEEEESSTTSSHHHH
T ss_pred             HcCCcEEEECCCCCchhHH
Confidence            4677899999999999986

>PF13555 AAA_29: P-loop containing region of AAA domain

Probab=88.06  E-value=0.52  Score=31.56  Aligned_cols=18  Identities=28%  Similarity=0.562  Sum_probs=15.3

Q ss_pred             CCCcEEEEcCCCCchHHH
Q 043110           72 SGRDVLVNAATGTGKTVA   89 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~   89 (316)
                      .|...++.+++|+|||..
T Consensus        22 ~g~~tli~G~nGsGKSTl   39 (62)
T PF13555_consen   22 RGDVTLITGPNGSGKSTL   39 (62)
T ss_pred             CCcEEEEECCCCCCHHHH
Confidence            345799999999999976

>KOG0741 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=88.06  E-value=6.9  Score=37.84  Aligned_cols=18  Identities=28%  Similarity=0.556  Sum_probs=15.7

Q ss_pred             CceeEEEEecchhhhcCC
Q 043110          185 TNLRWIIFDEADRILELG  202 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~  202 (316)
                      +.+..+|+|+..+|+|+.
T Consensus       597 S~lsiivvDdiErLiD~v  614 (744)
T KOG0741|consen  597 SPLSIIVVDDIERLLDYV  614 (744)
T ss_pred             CcceEEEEcchhhhhccc
Confidence            468899999999999983

>PRK10689 transcription-repair coupling factor; Provisional

Probab=87.81  E-value=2.9  Score=44.65  Aligned_cols=79  Identities=18%  Similarity=0.144  Sum_probs=55.7

Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHH---HHh-cCCcEEEeCcHHHHHHHhcCCccccC
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA---RLR-KGISILVATPGHLLDHLKHTSSFLHT  185 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~  185 (316)
                      +.+++|++|+++-+..+++.+++..   ....+.+++|+.+......   .+. ...+|+|||.  +   +.  .++++.
T Consensus       809 ~gqv~vf~n~i~~ie~la~~L~~~~---p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTd--I---ie--rGIDIP  878 (1147)
T PRK10689        809 GGQVYYLYNDVENIQKAAERLAELV---PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT--I---IE--TGIDIP  878 (1147)
T ss_pred             CCeEEEEECCHHHHHHHHHHHHHhC---CCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECc--h---hh--cccccc
Confidence            4569999999998888888777654   2345666777766544322   223 3589999994  2   22  567778


Q ss_pred             ceeEEEEecchhh
Q 043110          186 NLRWIIFDEADRI  198 (316)
Q Consensus       186 ~l~~lViDEad~l  198 (316)
                      +++++|++.+|+.
T Consensus       879 ~v~~VIi~~ad~f  891 (1147)
T PRK10689        879 TANTIIIERADHF  891 (1147)
T ss_pred             cCCEEEEecCCCC
Confidence            9999999999863

>TIGR00767 rho transcription termination factor Rho

Probab=87.79  E-value=4  Score=38.17  Aligned_cols=19  Identities=37%  Similarity=0.462  Sum_probs=16.8

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .|+-+++.+|+|+|||...
T Consensus       167 ~Gq~~~IvG~~g~GKTtL~  185 (415)
T TIGR00767       167 KGQRGLIVAPPKAGKTVLL  185 (415)
T ss_pred             CCCEEEEECCCCCChhHHH
Confidence            7888999999999999753

Members of this family differ in the specificity of RNA binding.

>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]

Probab=87.78  E-value=1.5  Score=43.06  Aligned_cols=32  Identities=28%  Similarity=0.264  Sum_probs=25.5

Q ss_pred             CceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          185 TNLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      ++-.++|+|||-.-+|..-+..+...+..+.+
T Consensus       482 ~~~~ILILDEaTSalD~~tE~~I~~~l~~l~~  513 (567)
T COG1132         482 RNPPILILDEATSALDTETEALIQDALKKLLK  513 (567)
T ss_pred             cCCCEEEEeccccccCHHhHHHHHHHHHHHhc
Confidence            34579999999999998888878777776554

>PRK05636 replicative DNA helicase; Provisional

Probab=87.69  E-value=3.2  Score=40.28  Aligned_cols=17  Identities=35%  Similarity=0.518  Sum_probs=14.0

Q ss_pred             cEEEEcCCCCchHHHHH
Q 043110           75 DVLVNAATGTGKTVAYL   91 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~   91 (316)
                      =+++.|.+|.|||...+
T Consensus       267 Liiiaarpg~GKT~~al  283 (505)
T PRK05636        267 MIIVAARPGVGKSTLAL  283 (505)
T ss_pred             eEEEEeCCCCCHHHHHH
Confidence            36889999999997654

>PRK13876 conjugal transfer coupling protein TraG; Provisional

Probab=87.54  E-value=0.44  Score=47.54  Aligned_cols=25  Identities=32%  Similarity=0.416  Sum_probs=21.9

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHh
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHL   98 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l   98 (316)
                      .++++.||||||||.++++|-+-..
T Consensus       145 ~hvLviApTrSGKgvg~VIPnLL~~  169 (663)
T PRK13876        145 EHVLCFAPTRSGKGVGLVVPTLLTW  169 (663)
T ss_pred             ceEEEEecCCCCcceeEehhhHHhC
Confidence            5799999999999999999976643

>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA

Probab=87.49  E-value=4.6  Score=41.16  Aligned_cols=16  Identities=38%  Similarity=0.461  Sum_probs=13.9

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      .+++.||||+|||..+
T Consensus       486 ~~lf~Gp~GvGKT~lA  501 (731)
T TIGR02639       486 SFLFTGPTGVGKTELA  501 (731)
T ss_pred             eEEEECCCCccHHHHH
Confidence            3799999999999765

>PF13481 AAA_25: AAA domain; PDB: 1G8Y_J 1OLO_A 1NLF_C

Probab=87.47  E-value=2.7  Score=34.65  Aligned_cols=62  Identities=21%  Similarity=0.236  Sum_probs=34.6

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCC--CCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRID--RSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~--~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      .|.-+++.|++|+|||...+- +...+....+...  ...+.+++++..-.. ..++.+++..+..
T Consensus        31 ~g~l~~i~g~~g~GKT~~~~~-l~~~~~~g~~~~g~~~~~~~~Vl~i~~E~~-~~~~~~rl~~~~~   94 (193)
T PF13481_consen   31 RGELTLIAGPPGSGKTTLALQ-LAAALATGRPFLGELPPRPGRVLYISLEDS-ESQIARRLRALLQ   94 (193)
T ss_dssp             TTSEEEEEECSTSSHHHHHHH-HHHHHHT---TT---------EEEEESSS--HHHHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHH-HHHHHHhCCccCCcccccCceEEEEeccCC-HHHHHHHHHHHhc
Confidence            456699999999999986543 3333333211111  113456888876655 5677777777664

>PF04665 Pox_A32: Poxvirus A32 protein; InterPro: IPR006758 This entry contains uncharacterised proteins belonging to the B354L family which include the pox virus A32 protein

Probab=87.39  E-value=0.94  Score=39.27  Aligned_cols=23  Identities=22%  Similarity=0.479  Sum_probs=17.3

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHh
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHL   98 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l   98 (316)
                      .+++.|++|||||.. ++-++..+
T Consensus        15 r~viIG~sGSGKT~l-i~~lL~~~   37 (241)
T PF04665_consen   15 RMVIIGKSGSGKTTL-IKSLLYYL   37 (241)
T ss_pred             eEEEECCCCCCHHHH-HHHHHHhh
Confidence            689999999999974 44455444

This is thought to be an ATPase involved in viral DNA packaging [].

>PRK09165 replicative DNA helicase; Provisional

Probab=87.38  E-value=7.8  Score=37.56  Aligned_cols=120  Identities=9%  Similarity=0.059  Sum_probs=55.5

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhc-CCCC------CCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEee
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSY-SPRI------DRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVM  146 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~-~~~~------~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~  146 (316)
                      .=+++.|+||.|||...+- +...+... ....      ....|..++|++. -.-..|+..++.........   ..+.
T Consensus       218 ~livIaarpg~GKT~~al~-ia~~~a~~~~~~~~~~~~~~~~~g~~vl~fSl-EMs~~ql~~R~la~~s~v~~---~~i~  292 (497)
T PRK09165        218 DLIILAGRPSMGKTALATN-IAFNAAKAYRREAQPDGSKKAVNGGVVGFFSL-EMSAEQLATRILSEQSEISS---SKIR  292 (497)
T ss_pred             ceEEEEeCCCCChHHHHHH-HHHHHHHhhcccccccccccccCCCeEEEEeC-cCCHHHHHHHHHHHhcCCCH---HHHh
Confidence            3489999999999976533 33333221 1000      0012445666653 33345555554433222111   1111


Q ss_pred             CCCChHHHHHHHh------cCCcEEEe-----CcHHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          147 GGGNRSKEKARLR------KGISILVA-----TPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       147 ~~~~~~~~~~~l~------~~~~IlV~-----Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                      .|.-...++..+.      ...++.|-     |+..+...++....  -..++++|||=.+.|..
T Consensus       293 ~~~l~~~e~~~l~~a~~~l~~~~l~I~d~~~~ti~~i~~~ir~l~~--~~~~~lvvIDyLqli~~  355 (497)
T PRK09165        293 RGKISEEDFEKLVDASQELQKLPLYIDDTPALSISQLRARARRLKR--QHGLDLLVVDYLQLIRG  355 (497)
T ss_pred             cCCCCHHHHHHHHHHHHHHhcCCeEEeCCCCCCHHHHHHHHHHHHH--hcCCCEEEEcchHhccC
Confidence            2222222222222      12345543     33444444432111  13578999999997753

>cd01128 rho_factor Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase

Probab=87.38  E-value=3.7  Score=35.86  Aligned_cols=19  Identities=32%  Similarity=0.326  Sum_probs=16.7

Q ss_pred             hCCCcEEEEcCCCCchHHH
Q 043110           71 LSGRDVLVNAATGTGKTVA   89 (316)
Q Consensus        71 l~g~d~li~a~TGsGKT~~   89 (316)
                      -.|+.+++.++.|+|||..
T Consensus        14 ~~Gqr~~I~G~~G~GKTTL   32 (249)
T cd01128          14 GKGQRGLIVAPPKAGKTTL   32 (249)
T ss_pred             CCCCEEEEECCCCCCHHHH
Confidence            3788999999999999964

It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the C-terminal ATP binding domain.

>TIGR01420 pilT_fam pilus retraction protein PilT

Probab=87.33  E-value=1.2  Score=40.94  Aligned_cols=43  Identities=21%  Similarity=0.348  Sum_probs=26.4

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSEL  122 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L  122 (316)
                      .+..+++++|||||||... -.++..+...       .+.+++.+-...|+
T Consensus       121 ~~g~ili~G~tGSGKTT~l-~al~~~i~~~-------~~~~i~tiEdp~E~  163 (343)
T TIGR01420       121 PRGLILVTGPTGSGKSTTL-ASMIDYINKN-------AAGHIITIEDPIEY  163 (343)
T ss_pred             cCcEEEEECCCCCCHHHHH-HHHHHhhCcC-------CCCEEEEEcCChhh
Confidence            4567999999999999864 3344444321       12345555555554

This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.

>PRK13695 putative NTPase; Provisional

Probab=87.23  E-value=3.1  Score=33.86  Aligned_cols=17  Identities=29%  Similarity=0.477  Sum_probs=14.4

Q ss_pred             cEEEEcCCCCchHHHHH
Q 043110           75 DVLVNAATGTGKTVAYL   91 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~   91 (316)
                      .+.+.++.|+|||....
T Consensus         2 ~i~ltG~~G~GKTTll~   18 (174)
T PRK13695          2 KIGITGPPGVGKTTLVL   18 (174)
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47899999999998754

>PRK05595 replicative DNA helicase; Provisional

Probab=87.23  E-value=3.1  Score=39.67  Aligned_cols=129  Identities=15%  Similarity=0.089  Sum_probs=58.8

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS  152 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (316)
                      |.=+++.|.||.|||...+ -+...+...       .|..+++++.- .-..|+..++........   ...+..|.-..
T Consensus       201 g~liviaarpg~GKT~~al-~ia~~~a~~-------~g~~vl~fSlE-ms~~~l~~R~~a~~~~v~---~~~~~~~~l~~  268 (444)
T PRK05595        201 GDMILIAARPSMGKTTFAL-NIAEYAALR-------EGKSVAIFSLE-MSKEQLAYKLLCSEANVD---MLRLRTGNLED  268 (444)
T ss_pred             CcEEEEEecCCCChHHHHH-HHHHHHHHH-------cCCcEEEEecC-CCHHHHHHHHHHHhcCCC---HHHHhcCCCCH
Confidence            3347889999999997643 333333211       13337776543 234455444333222111   11111222122


Q ss_pred             HHHHHHhc------CCcEEEe-Cc----HHHHHHHhcCCccccCceeEEEEecchhhhcCC----cHHHHHHHHHHhc
Q 043110          153 KEKARLRK------GISILVA-TP----GHLLDHLKHTSSFLHTNLRWIIFDEADRILELG----FGKEIEEILDILG  215 (316)
Q Consensus       153 ~~~~~l~~------~~~IlV~-Tp----~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~----~~~~i~~i~~~l~  215 (316)
                      .++..+..      ...+.|- +|    ..+...++...  .-..++++|||=.+.|...+    ....+..|.+.|+
T Consensus       269 ~e~~~~~~~~~~l~~~~l~i~d~~~~t~~~i~~~~r~~~--~~~~~~~vvIDylql~~~~~~~~~r~~~v~~is~~LK  344 (444)
T PRK05595        269 KDWENIARASGPLAAAKIFIDDTAGVSVMEMRSKCRRLK--IEHGIDMILIDYLQLMSGGKGSESRQQEVSEISRSIK  344 (444)
T ss_pred             HHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHH--HhcCCCEEEEeHHHhccCCCCCccHHHHHHHHHHHHH
Confidence            22222221      1234443 32    33333332211  11358899999999876332    2234555544443

>TIGR02784 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type

Probab=87.19  E-value=1.9  Score=46.18  Aligned_cols=59  Identities=20%  Similarity=0.137  Sum_probs=44.5

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHR  136 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~  136 (316)
                      -.+++++.|+.|||||...+--++..+....      ..-.+++|+-|+.-|.++.+++...+..
T Consensus         9 p~~~~~~~a~agsgkt~~l~~~~~~~~~~~~------~~~~i~~~t~t~~aa~em~~Ri~~~L~~   67 (1141)
T TIGR02784         9 PKTSAWVSANAGSGKTHVLTQRVIRLLLNGV------PPSKILCLTYTKAAAAEMQNRVFDRLGE   67 (1141)
T ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHHHHcCC------CCCeEEEEecCHHHHHHHHHHHHHHHHH
Confidence            3567999999999999987666666654421      1235999999999999998887776643

AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species.

>PF08423 Rad51: Rad51; InterPro: IPR013632 This domain is found at the C terminus of the DNA repair and recombination protein Rad51

Probab=87.12  E-value=2.9  Score=36.69  Aligned_cols=116  Identities=18%  Similarity=0.248  Sum_probs=58.4

Q ss_pred             HHHHHHhCC-----CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCC
Q 043110           65 QAIPVILSG-----RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRW  139 (316)
Q Consensus        65 ~~i~~il~g-----~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~  139 (316)
                      ..++.++.|     .=+=++++.|+|||-..+--++.......   ..+.+.+++|+.-....-   .+++.+++..++ 
T Consensus        25 ~~lD~~L~GGi~~g~itEi~G~~gsGKTql~l~l~~~~~l~~~---~~g~~~~vvyidTe~~f~---~~Rl~~i~~~~~-   97 (256)
T PF08423_consen   25 KSLDELLGGGIPTGSITEIVGESGSGKTQLCLQLAVNVQLPEE---IGGLGGKVVYIDTEGTFS---PERLQQIAERFG-   97 (256)
T ss_dssp             HHHHHHTTSSEETTSEEEEEESTTSSHHHHHHHHHHHTTSGGC---TTSSSSEEEEEESSSSS----HHHHHHHHHHTT-
T ss_pred             HHHHHhhCCCCCCCcEEEEEEecccccchHHHHHHHHhhcccc---cccCCCceEEEeCCCCCC---HHHHHHHhhccc-
Confidence            367777755     33678999999999875443333322211   123356799997544333   223333333221 


Q ss_pred             ceeEEeeCCCChHHHHHHHhcCCcE-EEeCcHHHHHHHhcCCc-cccCceeEEEEecchhhhc
Q 043110          140 IVPGYVMGGGNRSKEKARLRKGISI-LVATPGHLLDHLKHTSS-FLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~l~~~~~I-lV~Tp~~l~~~l~~~~~-~~~~~l~~lViDEad~l~~  200 (316)
                               .+..    .+..+..+ -+.+.+.+...+..... +.-.++++||||-+-.++.
T Consensus        98 ---------~~~~----~~l~~I~v~~~~~~~~l~~~L~~l~~~l~~~~ikLIVIDSIaalfr  147 (256)
T PF08423_consen   98 ---------LDPE----EILDNIFVIRVFDLEELLELLEQLPKLLSESKIKLIVIDSIAALFR  147 (256)
T ss_dssp             ---------S-HH----HHHHTEEEEE-SSHHHHHHHHHHHHHHHHHSCEEEEEEETSSHHHH
T ss_pred             ---------cccc----hhhhceeeeecCCHHHHHHHHHHHHhhccccceEEEEecchHHHHH
Confidence                     1111    11222111 12344455444433211 1124799999999988763

It is critical for DNA binding []. Rad51 is a homologue of the bacterial RecA protein. Rad51 and RecA share a core ATPase domain.; PDB: 2ZUC_A 2Z43_C 2ZUD_B 2DFL_A 2ZUB_A 2BKE_A 2KZ3_A 2CVH_B 2CVF_B 1SZP_D ....

>cd01131 PilT Pilus retraction ATPase PilT

Probab=87.11  E-value=1.2  Score=37.30  Aligned_cols=22  Identities=41%  Similarity=0.706  Sum_probs=16.3

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHh
Q 043110           76 VLVNAATGTGKTVAYLAPIINHL   98 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l   98 (316)
                      +++.+|||||||... -.++..+
T Consensus         4 ilI~GptGSGKTTll-~~ll~~~   25 (198)
T cd01131           4 VLVTGPTGSGKSTTL-AAMIDYI   25 (198)
T ss_pred             EEEECCCCCCHHHHH-HHHHHHh
Confidence            689999999999874 3344444

PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.

>PRK06321 replicative DNA helicase; Provisional

Probab=87.03  E-value=11  Score=36.15  Aligned_cols=126  Identities=13%  Similarity=0.121  Sum_probs=59.5

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE  154 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (316)
                      =+++.|.+|.|||...+ -+...+...       .+..+++.+. -.-..|+..++-.....   +...-+..+.-...+
T Consensus       228 LiiiaarPgmGKTafal-~ia~~~a~~-------~g~~v~~fSL-EMs~~ql~~Rlla~~s~---v~~~~i~~~~l~~~e  295 (472)
T PRK06321        228 LMILAARPAMGKTALAL-NIAENFCFQ-------NRLPVGIFSL-EMTVDQLIHRIICSRSE---VESKKISVGDLSGRD  295 (472)
T ss_pred             EEEEEeCCCCChHHHHH-HHHHHHHHh-------cCCeEEEEec-cCCHHHHHHHHHHhhcC---CCHHHhhcCCCCHHH
Confidence            37889999999997643 344444321       1223555542 22344444444322111   111111122222223


Q ss_pred             HH-------HHhcCCcEEEe-----CcHHHHHHHhcCCccccCceeEEEEecchhhhcCC-------cHHHHHHHHHHhc
Q 043110          155 KA-------RLRKGISILVA-----TPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELG-------FGKEIEEILDILG  215 (316)
Q Consensus       155 ~~-------~l~~~~~IlV~-----Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~-------~~~~i~~i~~~l~  215 (316)
                      +.       .+.. ..+.|-     |...+..-++....  -..++++|||=.+.|...+       ....+..|.+.|+
T Consensus       296 ~~~~~~a~~~l~~-~~~~idd~~~~ti~~i~~~~r~~~~--~~~~~lvvIDyLql~~~~~~~~~~~~r~~ei~~Isr~LK  372 (472)
T PRK06321        296 FQRIVSVVNEMQE-HTLLIDDQPGLKITDLRARARRMKE--SYDIQFLIIDYLQLLSGSGNLRNSESRQTEISEISRMLK  372 (472)
T ss_pred             HHHHHHHHHHHHc-CCEEEeCCCCCCHHHHHHHHHHHHH--hcCCCEEEEcchHHcCCCCccCCcchHHHHHHHHHHHHH
Confidence            32       2222 345554     33344443332111  1357899999998875322       2244555555554

>TIGR03819 heli_sec_ATPase helicase/secretion neighborhood ATPase

Probab=86.89  E-value=2.2  Score=39.09  Aligned_cols=58  Identities=19%  Similarity=0.259  Sum_probs=36.0

Q ss_pred             cCCCCCcHHHHHHHHHHh-CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           54 LGFEAPTKVQAQAIPVIL-SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        54 ~g~~~p~~~Q~~~i~~il-~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      .|+  +++.+...+..+. .++++++.++||+|||... -.++..+..         ..+.+++-.+.||.
T Consensus       160 ~g~--~~~~~~~~L~~~v~~~~~ili~G~tGsGKTTll-~al~~~i~~---------~~riv~iEd~~El~  218 (340)
T TIGR03819       160 SGT--FPPGVARLLRAIVAARLAFLISGGTGSGKTTLL-SALLALVAP---------DERIVLVEDAAELR  218 (340)
T ss_pred             cCC--CCHHHHHHHHHHHhCCCeEEEECCCCCCHHHHH-HHHHccCCC---------CCcEEEECCcceec
Confidence            354  3456666665544 5679999999999999753 223332211         23367777777773

Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer.

>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau

Probab=86.87  E-value=7.1  Score=35.67  Aligned_cols=24  Identities=29%  Similarity=0.303  Sum_probs=17.0

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      .+++.||.|+|||.... .+...+.
T Consensus        38 ~~Ll~G~~G~GKt~~a~-~la~~l~   61 (355)
T TIGR02397        38 AYLFSGPRGTGKTSIAR-IFAKALN   61 (355)
T ss_pred             EEEEECCCCCCHHHHHH-HHHHHhc
Confidence            47899999999997653 3444443

This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=86.84  E-value=3.2  Score=37.07  Aligned_cols=60  Identities=20%  Similarity=0.238  Sum_probs=38.7

Q ss_pred             eeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcC
Q 043110          187 LRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLE  255 (316)
Q Consensus       187 l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~  255 (316)
                      -.++|+||+|.|-. +.-+.+.-.+.+.+.        .......+.=.|++|-+-...+.+++-.+++
T Consensus       179 rslFIFDE~DKmp~-gLld~lkpfLdyyp~--------v~gv~frkaIFIfLSN~gg~eI~~~aL~~~~  238 (344)
T KOG2170|consen  179 RSLFIFDEVDKLPP-GLLDVLKPFLDYYPQ--------VSGVDFRKAIFIFLSNAGGSEIARIALENAR  238 (344)
T ss_pred             CceEEechhhhcCH-hHHHHHhhhhccccc--------cccccccceEEEEEcCCcchHHHHHHHHHHH
Confidence            35899999998743 444555555554332        2233445677889998888888776665544

>COG1674 FtsK DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]

Probab=86.84  E-value=9.4  Score=39.69  Aligned_cols=29  Identities=38%  Similarity=0.500  Sum_probs=21.7

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcC
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYS  102 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~  102 (316)
                      .++++.+.||||||.+.---++..+.+..
T Consensus       531 ~hllv~G~tgsGKSv~lnt~i~Sll~~~~  559 (858)
T COG1674         531 GHLLIAGATGSGKSVALNTMILSLLYTHS  559 (858)
T ss_pred             CcEEEEcCCCCcHHHHHHHHHHHHHHhCC
Confidence            57999999999999986555555555433

>TIGR02868 CydC thiol reductant ABC exporter, CydC subunit

Probab=86.82  E-value=1  Score=43.87  Aligned_cols=31  Identities=23%  Similarity=0.212  Sum_probs=23.7

Q ss_pred             CceeEEEEecchhhhcCCcHHHHHHHHHHhc
Q 043110          185 TNLRWIIFDEADRILELGFGKEIEEILDILG  215 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~~~i~~i~~~l~  215 (316)
                      ++-+++|+||+-.-+|......+...+..+.
T Consensus       487 ~~~~iliLDE~TSaLD~~te~~I~~~l~~~~  517 (529)
T TIGR02868       487 ADAPILLLDEPTEHLDAGTESELLEDLLAAL  517 (529)
T ss_pred             cCCCEEEEeCCcccCCHHHHHHHHHHHHHhc
Confidence            4667999999999898877777766666553

The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex.

>PRK10787 DNA-binding ATP-dependent protease La; Provisional

Probab=86.75  E-value=4.3  Score=41.65  Aligned_cols=44  Identities=20%  Similarity=0.413  Sum_probs=27.0

Q ss_pred             CcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhc
Q 043110          168 TPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILG  215 (316)
Q Consensus       168 Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~  215 (316)
                      .||++...+.....    .-.++++||+|.+.....++-...+++.+.
T Consensus       402 ~~G~~~~~l~~~~~----~~~villDEidk~~~~~~g~~~~aLlevld  445 (784)
T PRK10787        402 MPGKLIQKMAKVGV----KNPLFLLDEIDKMSSDMRGDPASALLEVLD  445 (784)
T ss_pred             CCcHHHHHHHhcCC----CCCEEEEEChhhcccccCCCHHHHHHHHhc
Confidence            57788777765321    113689999999876433333455555554

>TIGR02533 type_II_gspE general secretory pathway protein E

Probab=86.74  E-value=0.83  Score=44.02  Aligned_cols=38  Identities=21%  Similarity=0.308  Sum_probs=25.6

Q ss_pred             cHHHHHHHHHHhCCC--cEEEEcCCCCchHHHHHHHHHHHh
Q 043110           60 TKVQAQAIPVILSGR--DVLVNAATGTGKTVAYLAPIINHL   98 (316)
Q Consensus        60 ~~~Q~~~i~~il~g~--d~li~a~TGsGKT~~~~lp~l~~l   98 (316)
                      .+-|.+.+..+....  -+++.+|||||||... ..++..+
T Consensus       227 ~~~~~~~l~~~~~~~~GlilitGptGSGKTTtL-~a~L~~l  266 (486)
T TIGR02533       227 SPELLSRFERLIRRPHGIILVTGPTGSGKTTTL-YAALSRL  266 (486)
T ss_pred             CHHHHHHHHHHHhcCCCEEEEEcCCCCCHHHHH-HHHHhcc
Confidence            456666666655433  3789999999999864 3345544

This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=86.73  E-value=3.4  Score=43.07  Aligned_cols=79  Identities=16%  Similarity=0.159  Sum_probs=56.1

Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHH---HHh-cCCcEEEeCcHHHHHHHhcCCccccC
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA---RLR-KGISILVATPGHLLDHLKHTSSFLHT  185 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~  185 (316)
                      +.+++|++|+++-+..+++.++++.   ....+..++|+........   .+. ...+|+|||.  +   +.  .++++.
T Consensus       660 g~qv~if~n~i~~~e~l~~~L~~~~---p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~--i---ie--~GIDIp  729 (926)
T TIGR00580       660 GGQVFYVHNRIESIEKLATQLRELV---PEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTT--I---IE--TGIDIP  729 (926)
T ss_pred             CCeEEEEECCcHHHHHHHHHHHHhC---CCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECC--h---hh--cccccc
Confidence            4569999999998888888877653   3356677777766543332   233 3479999994  2   22  566778


Q ss_pred             ceeEEEEecchhh
Q 043110          186 NLRWIIFDEADRI  198 (316)
Q Consensus       186 ~l~~lViDEad~l  198 (316)
                      +++++|++.+|+.
T Consensus       730 ~v~~VIi~~a~~~  742 (926)
T TIGR00580       730 NANTIIIERADKF  742 (926)
T ss_pred             cCCEEEEecCCCC
Confidence            8999999999873

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.

>PF01078 Mg_chelatase: Magnesium chelatase, subunit ChlI; InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX

Probab=86.71  E-value=0.78  Score=38.71  Aligned_cols=19  Identities=37%  Similarity=0.585  Sum_probs=14.2

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .++++++.+|.|+|||+..
T Consensus        21 G~h~lLl~GppGtGKTmlA   39 (206)
T PF01078_consen   21 GGHHLLLIGPPGTGKTMLA   39 (206)
T ss_dssp             CC--EEEES-CCCTHHHHH
T ss_pred             CCCCeEEECCCCCCHHHHH
Confidence            5678999999999999874

This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 2X31_J 1G8P_A 3K1J_B.

>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]

Probab=86.55  E-value=4.2  Score=36.17  Aligned_cols=41  Identities=32%  Similarity=0.309  Sum_probs=27.3

Q ss_pred             HHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           68 PVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        68 ~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      |+-..|+-+++.+..|.|||.+.    .+....         .+.++++-|..+
T Consensus        89 ~A~k~g~l~~vyg~~g~gKt~a~----~~y~~s---------~p~~~l~~~~p~  129 (297)
T COG2842          89 PASKTGSLVVVYGYAGLGKTQAA----KNYAPS---------NPNALLIEADPS  129 (297)
T ss_pred             hhhhcCceEEEeccccchhHHHH----Hhhccc---------CccceeecCChh
Confidence            34446777899999999999873    232222         444777777655

>PF01580 FtsK_SpoIIIE: FtsK/SpoIIIE family; InterPro: IPR002543 The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids [] some of which contain up to three copies

Probab=86.51  E-value=1.7  Score=36.48  Aligned_cols=27  Identities=22%  Similarity=0.372  Sum_probs=17.3

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      ..++++.+.||||||.+...-+...+.
T Consensus        38 ~~h~li~G~tgsGKS~~l~~ll~~l~~   64 (205)
T PF01580_consen   38 NPHLLIAGATGSGKSTLLRTLLLSLAL   64 (205)
T ss_dssp             S-SEEEE--TTSSHHHHHHHHHHHHHT
T ss_pred             CceEEEEcCCCCCccHHHHHHHHHHHH
Confidence            348999999999999876544444443

The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification []. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer []. ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2IUS_E 2IUU_A 2IUT_A.

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

Probab=86.28  E-value=19  Score=35.11  Aligned_cols=99  Identities=19%  Similarity=0.201  Sum_probs=70.5

Q ss_pred             cCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChH---HHHH
Q 043110           80 AATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS---KEKA  156 (316)
Q Consensus        80 a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~  156 (316)
                      .-.++||+..-++++.+.+...       -.+-+||.+-+.+-|.|++..+.    .+..+.+.+++|.....   ....
T Consensus       364 elvF~gse~~K~lA~rq~v~~g-------~~PP~lIfVQs~eRak~L~~~L~----~~~~i~v~vIh~e~~~~qrde~~~  432 (593)
T KOG0344|consen  364 ELVFCGSEKGKLLALRQLVASG-------FKPPVLIFVQSKERAKQLFEELE----IYDNINVDVIHGERSQKQRDETME  432 (593)
T ss_pred             hheeeecchhHHHHHHHHHhcc-------CCCCeEEEEecHHHHHHHHHHhh----hccCcceeeEecccchhHHHHHHH
Confidence            3457888888888888777653       34559999999999999998886    24567777888775543   3344


Q ss_pred             HHhcC-CcEEEeCcHHHHHHHhcCCccccCceeEEEEecch
Q 043110          157 RLRKG-ISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEAD  196 (316)
Q Consensus       157 ~l~~~-~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad  196 (316)
                      .++.+ ..++|||     +.+.  .++++..+.++|-++.-
T Consensus       433 ~FR~g~IwvLicT-----dll~--RGiDf~gvn~VInyD~p  466 (593)
T KOG0344|consen  433 RFRIGKIWVLICT-----DLLA--RGIDFKGVNLVINYDFP  466 (593)
T ss_pred             HHhccCeeEEEeh-----hhhh--ccccccCcceEEecCCC
Confidence            45544 6899999     3444  34777899999987653

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=86.27  E-value=2.8  Score=33.10  Aligned_cols=29  Identities=28%  Similarity=0.349  Sum_probs=21.9

Q ss_pred             ceeEEEEecchhhhcCCcHHHHHHHHHHh
Q 043110          186 NLRWIIFDEADRILELGFGKEIEEILDIL  214 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~~~~~i~~i~~~l  214 (316)
                      +-+++++||.-.-+|......+..+++.+
T Consensus        88 ~p~illlDEP~~~LD~~~~~~l~~~l~~~  116 (144)
T cd03221          88 NPNLLLLDEPTNHLDLESIEALEEALKEY  116 (144)
T ss_pred             CCCEEEEeCCccCCCHHHHHHHHHHHHHc
Confidence            56789999999888876666666666554

EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.

>PF06309 Torsin: Torsin; InterPro: IPR010448 This family consists of several eukaryotic torsin proteins

Probab=86.25  E-value=3.4  Score=32.01  Aligned_cols=59  Identities=20%  Similarity=0.113  Sum_probs=31.5

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           76 VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      +...|+||+|||.+.-+ +.+.+.....+..--....+..-.|....+.+-.+.++.+..
T Consensus        56 lSfHG~tGtGKn~v~~l-iA~~ly~~G~~S~~V~~f~~~~hFP~~~~v~~Yk~~L~~~I~  114 (127)
T PF06309_consen   56 LSFHGWTGTGKNFVSRL-IAEHLYKSGMKSPFVHQFIATHHFPHNSNVDEYKEQLKSWIR  114 (127)
T ss_pred             EEeecCCCCcHHHHHHH-HHHHHHhcccCCCceeeecccccCCCchHHHHHHHHHHHHHH
Confidence            45899999999988655 334433322111110111122334666666666666665543

Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia [].; GO: 0005524 ATP binding, 0051085 chaperone mediated protein folding requiring cofactor

>TIGR02767 TraG-Ti Ti-type conjugative transfer system protien TraG

Probab=86.24  E-value=0.6  Score=46.27  Aligned_cols=23  Identities=22%  Similarity=0.250  Sum_probs=20.3

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHH
Q 043110           74 RDVLVNAATGTGKTVAYLAPIIN   96 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~   96 (316)
                      .++++.||||||||.++++|-+-
T Consensus       212 ~H~lv~ApTgsGKgvg~VIPnLL  234 (623)
T TIGR02767       212 THMIFFAGSGGFKTTSVVVPTAL  234 (623)
T ss_pred             ceEEEEeCCCCCccceeehhhhh
Confidence            47999999999999999999643

This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems.

>TIGR03575 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic

Probab=86.06  E-value=4.2  Score=37.27  Aligned_cols=15  Identities=13%  Similarity=0.228  Sum_probs=12.7

Q ss_pred             EEEEcCCCCchHHHH
Q 043110           76 VLVNAATGTGKTVAY   90 (316)
Q Consensus        76 ~li~a~TGsGKT~~~   90 (316)
                      ++++|..|+|||...
T Consensus         2 ~~l~Gl~GaGKST~~   16 (340)
T TIGR03575         2 CVLCGLPAAGKSTLA   16 (340)
T ss_pred             eEEECCCCCCHHHHH
Confidence            578999999999763

Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity.

>PRK05917 DNA polymerase III subunit delta'; Validated

Probab=85.79  E-value=14  Score=33.06  Aligned_cols=28  Identities=21%  Similarity=0.177  Sum_probs=18.8

Q ss_pred             CceeEEEEecchhhhcCCcHHHHHHHHHH
Q 043110          185 TNLRWIIFDEADRILELGFGKEIEEILDI  213 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~~~i~~i~~~  213 (316)
                      ...+++|||+||.|... -...+.++++.
T Consensus        94 ~~~kv~ii~~ad~mt~~-AaNaLLK~LEE  121 (290)
T PRK05917         94 SPYKIYIIHEADRMTLD-AISAFLKVLED  121 (290)
T ss_pred             CCceEEEEechhhcCHH-HHHHHHHHhhc
Confidence            46789999999998653 33444444444

>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family

Probab=85.76  E-value=3.7  Score=42.51  Aligned_cols=16  Identities=38%  Similarity=0.530  Sum_probs=14.2

Q ss_pred             EEEEcCCCCchHHHHH
Q 043110           76 VLVNAATGTGKTVAYL   91 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~   91 (316)
                      +++.||||+|||...-
T Consensus       599 ~lf~Gp~GvGKT~lA~  614 (852)
T TIGR03345       599 FLLVGPSGVGKTETAL  614 (852)
T ss_pred             EEEECCCCCCHHHHHH
Confidence            7999999999998753

Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.

>PRK13531 regulatory ATPase RavA; Provisional

Probab=85.74  E-value=1.7  Score=41.60  Aligned_cols=27  Identities=22%  Similarity=0.333  Sum_probs=22.2

Q ss_pred             HHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           64 AQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        64 ~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      ..++-.++.|.++++.+|+|+|||..+
T Consensus        30 ~lll~aalag~hVLL~GpPGTGKT~LA   56 (498)
T PRK13531         30 RLCLLAALSGESVFLLGPPGIAKSLIA   56 (498)
T ss_pred             HHHHHHHccCCCEEEECCCChhHHHHH
Confidence            444556678999999999999999875

>PRK06647 DNA polymerase III subunits gamma and tau; Validated

Probab=85.65  E-value=17  Score=35.76  Aligned_cols=18  Identities=28%  Similarity=0.372  Sum_probs=15.2

Q ss_pred             cEEEEcCCCCchHHHHHH
Q 043110           75 DVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~l   92 (316)
                      -.++.||.|+|||.++..
T Consensus        40 ayLf~Gp~G~GKTt~Ar~   57 (563)
T PRK06647         40 AYIFSGPRGVGKTSSARA   57 (563)
T ss_pred             EEEEECCCCCCHHHHHHH
Confidence            379999999999988644

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	316
3ly5_A	262	Ddx18 Dead-Domain Length = 262		1e-36
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		8e-32
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		2e-28
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		3e-26
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		7e-26
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		8e-26
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		1e-24
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		3e-24
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		3e-24
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		4e-24
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		2e-22
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		1e-21
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		2e-21
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		2e-21
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		6e-21
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		2e-20
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		9e-19
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		5e-17
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		6e-17
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		6e-17
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		3e-16
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		3e-16
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		4e-16
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		4e-16
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		6e-16
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		6e-16
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		1e-15
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-15
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		2e-15
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		3e-15
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		3e-15
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		1e-14
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		2e-14
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		7e-14
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		1e-13
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		2e-13
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		2e-13
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		1e-12
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		1e-12
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		4e-09
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		2e-08
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		2e-08
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		4e-08
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		5e-08
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		5e-08
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		5e-08
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		6e-08
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		7e-08
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		2e-06

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score =  150 bits (378), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 91/235 (38%), Positives = 144/235 (61%), Gaps = 31/235 (13%)
Query: 32  FASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYL 91
           FAS C  +L  ++TL  +  + +GF   T++Q ++I  +L GRD+L  A TG+GKT+A+L
Sbjct: 54  FASLC--NLVNENTL--KAIKEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFL 109
Query: 92  APIINHLQS--YSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL--HRFRWIVPGYVMG 147
            P +  +    + PR    +GT  L+L PT EL +  + +L++L+  H   +   G +MG
Sbjct: 110 IPAVELIVKLRFMPR----NGTGVLILSPTRELAMQTFGVLKELMTHHVHTY---GLIMG 162
Query: 148 GGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEI 207
           G NRS E  +L  GI+I+VATPG LLDH+++T  F++ NL+ ++ DEADRIL++GF +E+
Sbjct: 163 GSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEEL 222
Query: 208 EEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLET-PVLIG 261
           ++I+ +L +R               RQ +L SAT   KV  L +ISL+  P+ +G
Sbjct: 223 KQIIKLLPTR---------------RQTMLFSATQTRKVEDLARISLKKEPLYVG 262

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score =  134 bits (336), Expect = 8e-32,   Method: Compositional matrix adjust.
 Identities = 80/222 (36%), Positives = 123/222 (55%), Gaps = 23/222 (10%)
Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F  LG+   LC+   ++LG+  PTK+Q +AIP+ L GRD++  A TG+GKT A+  PI+N
Sbjct: 45  FKDLGVTDVLCEAC-DQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILN 103
Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            L     R+      FALVL PT EL   + E  + L      +    ++GG +   +  
Sbjct: 104 ALLETPQRL------FALVLTPTRELAFQISEQFEALGSSI-GVQSAVIVGGIDSMSQSL 156
Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS 216
            L K   I++ATPG L+DHL++T  F    L++++ DEADRIL + F  E+++IL ++  
Sbjct: 157 ALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVI-P 215
Query: 217 RNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPV 258
           R+              R+  L SAT+ +KV  L + +L+ PV
Sbjct: 216 RD--------------RKTFLFSATMTKKVQKLQRAALKNPV 243

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score =  122 bits (307), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 81/231 (35%), Positives = 122/231 (52%), Gaps = 24/231 (10%)
Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           FS   L       L+E   +   T++Q Q I + L G+DVL  A TG+GKT+A+L P++ 
Sbjct: 27  FSDFPLSKKTLKGLQEA-QYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLE 85
Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL--LHRFRWIVPGYVMGGGNRSKE 154
            L  Y  +   + G   L++ PT EL    +E+L+K+   H F     G ++GG +   E
Sbjct: 86  AL--YRLQWTSTDGLGVLIISPTRELAYQTFEVLRKVGKNHDFS---AGLIIGGKDLKHE 140
Query: 155 KARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDIL 214
             R+   I+ILV TPG LL H+  T SF  T+L+ ++ DEADRIL++GF   +  +++ L
Sbjct: 141 AERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENL 199
Query: 215 GSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK 265
                            KRQ LL SAT  + V  L ++SL+ P  + + EK
Sbjct: 200 PK---------------KRQTLLFSATQTKSVKDLARLSLKNPEYVWVHEK 235

>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 =  115 bits (289), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 77/218 (35%), Positives = 113/218 (51%), Gaps = 21/218 (9%)
Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F  L LD T+ + +     ++ PT +Q  AIP IL  RD++  A TG+GKT A+L PIIN
Sbjct: 25  FDELKLDPTIRNNIL-LASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIIN 83
Query: 97  HLQSYSPRIDRSSGTF---ALVLVPTSELCLLVYEILQK--LLHRFRWIVPGYVMGGGNR 151
           HL        R S T     L+L PT EL + +    QK  L    R  V   V GG + 
Sbjct: 84  HLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNTPLRSCV---VYGGADT 140
Query: 152 SKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEIL 211
             +   ++ G  +LVATPG L+D ++     L    ++I+ DEADR+L++GF  +I +I+
Sbjct: 141 HSQIREVQMGCHLLVATPGRLVDFIEKNKISLEF-CKYIVLDEADRMLDMGFEPQIRKII 199
Query: 212 DILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHL 249
           +           E N  S + RQ L+ SAT  +++  L
Sbjct: 200 E-----------ESNMPSGINRQTLMFSATFPKEIQKL 226

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score =  114 bits (285), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 76/231 (32%), Positives = 118/231 (51%), Gaps = 38/231 (16%)
Query: 53  RLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF 112
           R  F  PT +QAQ  PV LSG D++  A TG+GKT++YL P I H+ ++ P ++R  G  
Sbjct: 46  RQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHI-NHQPFLERGDGPI 104
Query: 113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL 172
            LVL PT EL   V ++  +     R +    + GG  +  +   L +G+ I +ATPG L
Sbjct: 105 CLVLAPTRELAQQVQQVAAEYCRACR-LKSTCIYGGAPKGPQIRDLERGVEICIATPGRL 163
Query: 173 LDHLKHTSSFLHTNLR---WIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVS 229
           +D L+       TNLR   +++ DEADR+L++GF  +I +I+D +               
Sbjct: 164 IDFLECGK----TNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQI--------------- 204
Query: 230 NVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNVHFGSLE 280
              RQ L+ SAT  ++V  L               + F +D  +++ G+LE
Sbjct: 205 RPDRQTLMWSATWPKEVRQLA--------------EDFLKDYIHINIGALE 241

>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 =  114 bits (285), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 73/213 (34%), Positives = 113/213 (53%), Gaps = 24/213 (11%)
Query: 53  RLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF 112
           R  F  PT +QAQ  PV LSG D++  A TG+GKT++YL P I H+ ++ P ++R  G  
Sbjct: 60  RQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHI-NHQPFLERGDGPI 118
Query: 113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL 172
            LVL PT EL   V ++  +     R +    + GG  +  +   L +G+ I +ATPG L
Sbjct: 119 CLVLAPTRELAQQVQQVAAEYCRACR-LKSTCIYGGAPKGPQIRDLERGVEICIATPGRL 177
Query: 173 LDHLKHTSSFLHTNLR---WIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVS 229
           +D L+       TNLR   +++ DEADR+L++GF  +I +I+D +               
Sbjct: 178 IDFLECGK----TNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQI--------------- 218
Query: 230 NVKRQNLLLSATLNEKVNHLTKISLETPVLIGL 262
              RQ L+ SAT  ++V  L +  L+  + I +
Sbjct: 219 RPDRQTLMWSATWPKEVRQLAEDFLKDYIHINI 251

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score =  110 bits (275), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 77/224 (34%), Positives = 109/224 (48%), Gaps = 23/224 (10%)
Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F    L   + + L  R G   PT +QA A+P+ L G+D++  A TGTGKT+A+  PI  
Sbjct: 3   FKDFPLKPEILEALHGR-GLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61
Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            L   +P  +R     ALVL PT EL L V   L  +    + +    V GG    K+K 
Sbjct: 62  RL---APSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVA---VYGGTGYGKQKE 115
Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS 216
            L +G   +VATPG  LD+L+     L + +   + DEAD +L +GF +E+E +L     
Sbjct: 116 ALLRGADAVVATPGRALDYLRQGVLDL-SRVEVAVLDEADEMLSMGFEEEVEALLS---- 170
Query: 217 RNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                       +   RQ LL SATL      L +  ++ PVLI
Sbjct: 171 -----------ATPPSRQTLLFSATLPSWAKRLAERYMKNPVLI 203

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score =  108 bits (271), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 76/224 (33%), Positives = 109/224 (48%), Gaps = 23/224 (10%)
Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F    L   + + L  R G   PT ++A A+P+ L G+D++  A TGTGKT+A+  PI  
Sbjct: 3   FKDFPLKPEILEALHGR-GLTTPTPIEAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61
Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            L   +P  +R     ALVL PT EL L V   L  +    + +    V GG    K+K 
Sbjct: 62  RL---APSQERGRKPRALVLTPTRELALQVASELTAVAPHLKVVA---VYGGTGYGKQKE 115
Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS 216
            L +G   +VATPG  LD+L+     L + +   + DEAD +L +GF +E+E +L     
Sbjct: 116 ALLRGADAVVATPGRALDYLRQGVLDL-SRVEVAVLDEADEMLSMGFEEEVEALLS---- 170
Query: 217 RNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                       +   RQ LL SATL      L +  ++ PVLI
Sbjct: 171 -----------ATPPSRQTLLFSATLPSWAKRLAERYMKNPVLI 203

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score =  108 bits (271), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 72/208 (34%), Positives = 114/208 (54%), Gaps = 18/208 (8%)
Query: 53  RLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF 112
           R+G   PT +Q+QA P+IL G D++V A TGTGKT++YL P   HL S     ++ +G  
Sbjct: 37  RVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGPG 96
Query: 113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL 172
            LVL PT EL L V     K  + ++ +    + GG NR+ +   + KG+ I++ATPG L
Sbjct: 97  MLVLTPTRELALHVEAECSK--YSYKGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRL 154
Query: 173 LDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVK 232
            D L+  +S    ++ +++ DEAD++L++ F  +I +IL  L  R               
Sbjct: 155 ND-LQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKIL--LDVRP-------------D 198
Query: 233 RQNLLLSATLNEKVNHLTKISLETPVLI 260
           RQ ++ SAT  + V  L    L+ P+++
Sbjct: 199 RQTVMTSATWPDTVRQLALSYLKDPMIV 226

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score =  108 bits (270), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 68/221 (30%), Positives = 116/221 (52%), Gaps = 29/221 (13%)
Query: 56  FEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSP----RIDRSSGT 111
           +  PT VQ  AIP+I   RD++  A TG+GKT A+L PI++ + S  P    R  + +G 
Sbjct: 35  YTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKENGR 94
Query: 112 F--------ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGIS 163
           +        +LVL PT EL + +YE  +K  +R R + P  V GG +  ++   L +G  
Sbjct: 95  YGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSR-VRPCVVYGGADIGQQIRDLERGCH 153
Query: 164 ILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEIL--DILGSRNIAS 221
           +LVATPG L+D ++     L    ++++ DEADR+L++GF  +I  I+  D +  + +  
Sbjct: 154 LLVATPGRLVDMMERGKIGLDF-CKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGV-- 210
Query: 222 IGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGL 262
                      R  ++ SAT  +++  L +  L+  + + +
Sbjct: 211 -----------RHTMMFSATFPKEIQMLARDFLDEYIFLAV 240

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score =  103 bits (256), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 65/228 (28%), Positives = 118/228 (51%), Gaps = 21/228 (9%)
Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F+S  L   + D +  + G++ PT +Q  +IPVI SGRD++  A TG+GKT A+L PI++
Sbjct: 58  FTSADLRDIIIDNV-NKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILS 116
Query: 97  HL--QSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE 154
            L    +   + R      +++ PT EL + ++   +K      ++  G V GG +   +
Sbjct: 117 KLLEDPHELELGRPQ---VVIVSPTRELAIQIFNEARKFAFE-SYLKIGIVYGGTSFRHQ 172
Query: 155 KARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDIL 214
              + +G  +++ATPG LLD +  T      + R+++ DEADR+L++GF +++  I+  +
Sbjct: 173 NECITRGCHVVIATPGRLLDFVDRT-FITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHV 231
Query: 215 GSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGL 262
             R              + Q L+ SAT  E++  +    L+  V + +
Sbjct: 232 TMRP-------------EHQTLMFSATFPEEIQRMAGEFLKNYVFVAI 266

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score =  100 bits (249), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 77/226 (34%), Positives = 116/226 (51%), Gaps = 20/226 (8%)
Query: 53  RLGFEAPTKVQAQAIPVILSGRD--VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSG 110
           R+ F   T VQ + I  ILS  D  V+  A TGTGKT A+L PI  HL   + + D    
Sbjct: 38  RMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHL--INTKFDSQYM 95
Query: 111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGY----VMGGGNRSKEKARLRK-GISIL 165
             A+++ PT +L L + E   K +H   + +  Y    ++GG +      ++ K   +I+
Sbjct: 96  VKAVIVAPTRDLALQI-EAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIV 154
Query: 166 VATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEG 225
           +ATPG L+D L+  S+     + + + DEADR+LE+GF  ++E I  IL  +N  S    
Sbjct: 155 IATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKS---- 210
Query: 226 NEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD--EKKFPE 269
               N+K   LL SATL++KV  L    +     + LD  +K  PE
Sbjct: 211 --ADNIK--TLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPE 252

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score =  100 bits (248), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 77/226 (34%), Positives = 116/226 (51%), Gaps = 20/226 (8%)
Query: 53  RLGFEAPTKVQAQAIPVILSGRD--VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSG 110
           R+ F   T VQ + I  ILS  D  V+  A TGTGKT A+L PI  HL   + + D    
Sbjct: 89  RMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHL--INTKFDSQYM 146
Query: 111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGY----VMGGGNRSKEKARLRK-GISIL 165
             A+++ PT +L L + E   K +H   + +  Y    ++GG +      ++ K   +I+
Sbjct: 147 VKAVIVAPTRDLALQI-EAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIV 205
Query: 166 VATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEG 225
           +ATPG L+D L+  S+     + + + DEADR+LE+GF  ++E I  IL  +N  S    
Sbjct: 206 IATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKS---- 261
Query: 226 NEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD--EKKFPE 269
               N+K   LL SATL++KV  L    +     + LD  +K  PE
Sbjct: 262 --ADNIK--TLLFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPE 303

>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 = 99.8 bits (247), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 72/205 (35%), Positives = 108/205 (52%), Gaps = 18/205 (8%)
Query: 53  RLGFEAPTKVQAQAIPVILSGRD--VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSG 110
           R+ F   T VQ + I  ILS  D  V+  A TGTGKT A+L PI  HL   + + D    
Sbjct: 38  RMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHL--INTKFDSQYM 95
Query: 111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGY----VMGGGNRSKEKARLRK-GISIL 165
             A+++ PT +L L + E   K +H   + +  Y    ++GG +      ++ K   +I+
Sbjct: 96  VKAVIVAPTRDLALQI-EAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIV 154
Query: 166 VATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEG 225
           +ATPG L+D L+  S+     + + + DEADR+LE+GF  ++E I  IL  +N  S    
Sbjct: 155 IATPGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKS---- 210
Query: 226 NEVSNVKRQNLLLSATLNEKVNHLT 250
               N+K   LL SATL++KV  L 
Sbjct: 211 --ADNIK--TLLFSATLDDKVQKLA 231

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 97.8 bits (242), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 71/211 (33%), Positives = 104/211 (49%), Gaps = 23/211 (10%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL 114
           GFE P+ +Q +AIPV ++GRD+L  A  GTGKT A++ P    L+   P++++     AL
Sbjct: 40  GFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPT---LEKVKPKLNKIQ---AL 93
Query: 115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLD 174
           ++VPT EL L   +++ + L +   I      GG N   +  RL + + ILV TPG +LD
Sbjct: 94  IMVPTRELALQTSQVV-RTLGKHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLD 152
Query: 175 HLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQ 234
                 + L ++    I DEAD++L   F   IE+IL  L   +               Q
Sbjct: 153 LASRKVADL-SDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTH---------------Q 196
Query: 235 NLLLSATLNEKVNHLTKISLETPVLIGLDEK 265
           +LL SAT    V       L  P  I L E+
Sbjct: 197 SLLFSATFPLTVKEFMVKHLHKPYEINLMEE 227

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 95.9 bits (237), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 66/204 (32%), Positives = 101/204 (49%), Gaps = 22/204 (10%)
Query: 54  LGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA 113
           +G+E P+ +Q ++IP+ LSGRD+L  A  GTGK+ AYL P++  L      I       A
Sbjct: 21  MGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLKKDNIQ------A 74
Query: 114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLL 173
           +V+VPT EL L V +I  ++             GG N   +  RL   + +++ATPG +L
Sbjct: 75  MVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRIL 134
Query: 174 DHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKR 233
           D +K   + +  +++ I+ DEAD++L   F + +E+I+  L                  R
Sbjct: 135 DLIKKGVAKVD-HVQMIVLDEADKLLSQDFVQIMEDIILTLPK---------------NR 178
Query: 234 QNLLLSATLNEKVNHLTKISLETP 257
           Q LL SAT    V       LE P
Sbjct: 179 QILLYSATFPLSVQKFMNSHLEKP 202

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 90.9 bits (224), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 55/177 (31%), Positives = 97/177 (54%), Gaps = 12/177 (6%)
Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGR-DVLVNAATGTGKTVAYLAPII 95
           F+ L L   + + +R + GFE PT +Q + IP+ L+   +++  A TG+GKT ++  P+I
Sbjct: 8   FNELNLSDNILNAIRNK-GFEKPTDIQXKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66
Query: 96  NHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK 155
                    ++ ++G  A++L PT EL + V + ++ L       +    + GG     +
Sbjct: 67  -------ELVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLKIAK--IYGGKAIYPQ 117
Query: 156 ARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILD 212
            +  K  +I+V TPG +LDH+   +  L  N+++ I DEAD  L  GF K++E+IL+
Sbjct: 118 IKALKNANIVVGTPGRILDHINRGTLNLK-NVKYFILDEADEXLNXGFIKDVEKILN 173

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 85.1 bits (209), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 68/207 (32%), Positives = 98/207 (47%), Gaps = 26/207 (12%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRS-SGTFA 113
           GFE P+ +Q +AI  I+ G DVL  A +GTGKT  +    I  LQ    RID S     A
Sbjct: 41  GFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFS---IAALQ----RIDTSVKAPQA 93
Query: 114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLL 173
           L+L PT EL L + +++  L   F   +  +   GG    E A   +   I+V TPG + 
Sbjct: 94  LMLAPTRELALQIQKVVMALA--FHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVF 151
Query: 174 DHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKR 233
           D+++    F    ++  I DEAD +L  GF ++I +I  +L                   
Sbjct: 152 DNIQR-RRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTT--------------- 195
Query: 234 QNLLLSATLNEKVNHLTKISLETPVLI 260
           Q +LLSAT+   V  +T   +  PV I
Sbjct: 196 QVVLLSATMPNDVLEVTTKFMRNPVRI 222

>pdb|1QDE|A Chain A, Crystal Structure Of The Atpase Domain Of Translation Initiation Factor 4a From Saccharomyces Cerevisiae-The Prototype Of The Dead Box Protein Family Length = 224

Iteration: 1
 Score = 84.7 bits (208), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 68/207 (32%), Positives = 98/207 (47%), Gaps = 26/207 (12%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRS-SGTFA 113
           GFE P+ +Q +AI  I+ G DVL  A +GTGKT  +    I  LQ    RID S     A
Sbjct: 33  GFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFS---IAALQ----RIDTSVKAPQA 85
Query: 114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLL 173
           L+L PT EL L + +++  L   F   +  +   GG    E A   +   I+V TPG + 
Sbjct: 86  LMLAPTRELALQIQKVVMALA--FHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVF 143
Query: 174 DHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKR 233
           D+++    F    ++  I DEAD +L  GF ++I +I  +L                   
Sbjct: 144 DNIQR-RRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTT--------------- 187
Query: 234 QNLLLSATLNEKVNHLTKISLETPVLI 260
           Q +LLSAT+   V  +T   +  PV I
Sbjct: 188 QVVLLSATMPNDVLEVTTKFMRNPVRI 214

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 84.7 bits (208), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 68/207 (32%), Positives = 98/207 (47%), Gaps = 26/207 (12%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRS-SGTFA 113
           GFE P+ +Q +AI  I+ G DVL  A +GTGKT  +    I  LQ    RID S     A
Sbjct: 40  GFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFS---IAALQ----RIDTSVKAPQA 92
Query: 114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLL 173
           L+L PT EL L + +++  L   F   +  +   GG    E A   +   I+V TPG + 
Sbjct: 93  LMLAPTRELALQIQKVVMAL--AFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVF 150
Query: 174 DHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKR 233
           D+++    F    ++  I DEAD +L  GF ++I +I  +L                   
Sbjct: 151 DNIQR-RRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTT--------------- 194
Query: 234 QNLLLSATLNEKVNHLTKISLETPVLI 260
           Q +LLSAT+   V  +T   +  PV I
Sbjct: 195 QVVLLSATMPNDVLEVTTKFMRNPVRI 221

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 82.4 bits (202), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 113/236 (47%), Gaps = 26/236 (11%)
Query: 26  ETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTG 85
           ET +E+  +  F ++GL   L   +    GFE P+ +Q +AI  I+ GRDV+  + +GTG
Sbjct: 7   ETSEEVDVTPTFDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTG 65
Query: 86  KTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYV 145
           KT  +   ++  L        +   T AL+L PT EL + + + L   L  +  +     
Sbjct: 66  KTATFSISVLQCLDI------QVRETQALILAPTRELAVQIQKGLLA-LGDYMNVQCHAC 118
Query: 146 MGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTN-LRWIIFDEADRILELGFG 204
           +GG N  ++  +L  G  ++  TPG + D ++  S  L T  ++ ++ DEAD +L  GF 
Sbjct: 119 IGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRS--LRTRAIKMLVLDEADEMLNKGFK 176
Query: 205 KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
           ++I ++   L                   Q +L+SATL  ++  +T   +  P+ I
Sbjct: 177 EQIYDVYRYLPPAT---------------QVVLISATLPHEILEMTNKFMTDPIRI 217

>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 = 82.0 bits (201), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 113/236 (47%), Gaps = 26/236 (11%)
Query: 26  ETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTG 85
           ET +E+  +  F ++GL   L   +    GFE P+ +Q +AI  I+ GRDV+  + +GTG
Sbjct: 29  ETSEEVDVTPTFDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTG 87
Query: 86  KTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYV 145
           KT  +   ++  L        +   T AL+L PT EL + + + L   L  +  +     
Sbjct: 88  KTATFSISVLQCLDI------QVRETQALILAPTRELAVQIQKGLLA-LGDYMNVQCHAC 140
Query: 146 MGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTN-LRWIIFDEADRILELGFG 204
           +GG N  ++  +L  G  ++  TPG + D ++  S  L T  ++ ++ DEAD +L  GF 
Sbjct: 141 IGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRS--LRTRAIKMLVLDEADEMLNKGFK 198
Query: 205 KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
           ++I ++   L                   Q +L+SATL  ++  +T   +  P+ I
Sbjct: 199 EQIYDVYRYLPPAT---------------QVVLISATLPHEILEMTNKFMTDPIRI 239

>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 = 82.0 bits (201), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 113/236 (47%), Gaps = 26/236 (11%)
Query: 26  ETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTG 85
           ET +E+  +  F ++GL   L   +    GFE P+ +Q +AI  I+ GRDV+  + +GTG
Sbjct: 29  ETSEEVDVTPTFDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTG 87
Query: 86  KTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYV 145
           KT  +   ++  L        +   T AL+L PT EL + + + L   L  +  +     
Sbjct: 88  KTATFSISVLQCLDI------QVRETQALILAPTRELAVQIQKGLLA-LGDYMNVQCHAC 140
Query: 146 MGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTN-LRWIIFDEADRILELGFG 204
           +GG N  ++  +L  G  ++  TPG + D ++  S  L T  ++ ++ DEAD +L  GF 
Sbjct: 141 IGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRS--LRTRAIKMLVLDEADEMLNKGFK 198
Query: 205 KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
           ++I ++   L                   Q +L+SATL  ++  +T   +  P+ I
Sbjct: 199 EQIYDVYRYLPPAT---------------QVVLISATLPHEILEMTNKFMTDPIRI 239

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 82.0 bits (201), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 113/236 (47%), Gaps = 26/236 (11%)
Query: 26  ETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTG 85
           ET +E+  +  F ++GL   L   +    GFE P+ +Q +AI  I+ GRDV+  + +GTG
Sbjct: 28  ETSEEVDVTPTFDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTG 86
Query: 86  KTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYV 145
           KT  +   ++  L        +   T AL+L PT EL + + + L   L  +  +     
Sbjct: 87  KTATFSISVLQCLDI------QVRETQALILAPTRELAVQIQKGLLA-LGDYMNVQCHAC 139
Query: 146 MGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTN-LRWIIFDEADRILELGFG 204
           +GG N  ++  +L  G  ++  TPG + D ++  S  L T  ++ ++ DEAD +L  GF 
Sbjct: 140 IGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRS--LRTRAIKMLVLDEADEMLNKGFK 197
Query: 205 KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
           ++I ++   L                   Q +L+SATL  ++  +T   +  P+ I
Sbjct: 198 EQIYDVYRYLPPAT---------------QVVLISATLPHEILEMTNKFMTDPIRI 238

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 81.6 bits (200), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 62/210 (29%), Positives = 100/210 (47%), Gaps = 25/210 (11%)
Query: 54  LGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA 113
           L F  PT++Q + IP  L G   +  + TGTGKT AYL PI   ++     +       A
Sbjct: 22  LRFYKPTEIQERIIPGALRGESXVGQSQTGTGKTHAYLLPIXEKIKPERAEVQ------A 75
Query: 114 LVLVPTSELCLLVY-EILQ--KLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPG 170
           ++  PT EL   +Y E L+  K   + R IV   ++GG ++ K   +L     I++ TPG
Sbjct: 76  VITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKLNVQPHIVIGTPG 135
Query: 171 HLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSN 230
            + D ++  +  +HT    ++ DEAD  L+ GF  ++++I     +R    +        
Sbjct: 136 RINDFIREQALDVHTA-HILVVDEADLXLDXGFITDVDQI----AARXPKDL-------- 182
Query: 231 VKRQNLLLSATLNEKVNHLTKISLETPVLI 260
              Q L+ SAT+ EK+    K   E P  +
Sbjct: 183 ---QXLVFSATIPEKLKPFLKKYXENPTFV 209

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 81.3 bits (199), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 66/210 (31%), Positives = 103/210 (49%), Gaps = 31/210 (14%)
Query: 42  LDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSY 101
           ++  +   +RE +GF+  T+VQ++ IP++L G++V+V A TG+GKT AY  PI+      
Sbjct: 1   MNEKIEQAIRE-MGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPIL------ 53
Query: 102 SPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKG 161
                   G  +LV+ PT EL   V   ++  + R+       V GG     +  R+R  
Sbjct: 54  ------ELGMKSLVVTPTRELTRQVASHIRD-IGRYMDTKVAEVYGGMPYKAQINRVRNA 106
Query: 162 ISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIAS 221
             I+VATPG LLD L        ++   +I DEAD + E+GF  +I+ IL    +R I  
Sbjct: 107 -DIVVATPGRLLD-LWSKGVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITG 164
Query: 222 IGEGNEVSNVKRQNLLLSATLNEKVNHLTK 251
                          L SAT+ E++  + K
Sbjct: 165 ---------------LFSATIPEEIRKVVK 179

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/207 (32%), Positives = 94/207 (45%), Gaps = 26/207 (12%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRS-SGTFA 113
           GFE P+ +Q +AI  I+ G DVL  A +GTGKT  +    I  LQ    RID S     A
Sbjct: 40  GFEEPSAIQQRAIXPIIEGHDVLAQAQSGTGKTGTFS---IAALQ----RIDTSVKAPQA 92
Query: 114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLL 173
           L L PT EL L + +++  L   F   +  +   GG    E A   +   I+V TPG + 
Sbjct: 93  LXLAPTRELALQIQKVVXALA--FHXDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVF 150
Query: 174 DHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKR 233
           D+++    F    ++  I DEAD  L  GF ++I +I  +L                   
Sbjct: 151 DNIQR-RRFRTDKIKXFILDEADEXLSSGFKEQIYQIFTLLPPTT--------------- 194
Query: 234 QNLLLSATLNEKVNHLTKISLETPVLI 260
           Q +LLSAT    V  +T      PV I
Sbjct: 195 QVVLLSATXPNDVLEVTTKFXRNPVRI 221

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 64/225 (28%), Positives = 107/225 (47%), Gaps = 26/225 (11%)
Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F ++GL   L   +    GFE P+ +Q +AI  I+ GRDV+  + +GTGKT  +   ++ 
Sbjct: 3   FDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            L        +   T AL+L PT EL + V + L   L  +  +     +GG N  ++  
Sbjct: 62  CLDI------QVRETQALILAPTRELAVQVQKGLLA-LGDYMNVQSHACIGGTNVGEDIR 114
Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTN-LRWIIFDEADRILELGFGKEIEEILDILG 215
           +L  G  ++  TPG + D ++  S  L T  ++ ++ DEAD +L  GF ++I ++   L 
Sbjct: 115 KLDYGQHVVAGTPGRVFDMIRRRS--LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLP 172
Query: 216 SRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                             Q +L+SATL  +V  +T   +  P+ I
Sbjct: 173 PAT---------------QVVLISATLPHEVLEMTNKFMTDPIRI 202

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/210 (30%), Positives = 96/210 (45%), Gaps = 30/210 (14%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL 114
           GFE P+ +Q +AI   + G DV+  A +GTGKT  +   I+  L+           T AL
Sbjct: 49  GFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEI------EFKETQAL 102
Query: 115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLR-KGISILVATPGHLL 173
           VL PT EL   + +++   L  +        +GG N   E  +L+ +   I+V TPG + 
Sbjct: 103 VLAPTRELAQQIQKVILA-LGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVF 161
Query: 174 DHLKHTSSFLHTNLRWI---IFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSN 230
           D L       + + +WI   + DEAD +L  GF  +I EI   L               N
Sbjct: 162 DMLNRR----YLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKL---------------N 202
Query: 231 VKRQNLLLSATLNEKVNHLTKISLETPVLI 260
              Q +LLSAT+   V  +TK  +  P+ I
Sbjct: 203 TSIQVVLLSATMPTDVLEVTKKFMRDPIRI 232

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 79.3 bits (194), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 62/210 (29%), Positives = 102/210 (48%), Gaps = 19/210 (9%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL 114
           GF+ PT +Q QAIPV+L GR++L +A TG+GKT+A+  PI+  L+  +     + G  AL
Sbjct: 48  GFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPA-----NKGFRAL 102
Query: 115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLD 174
           ++ PT EL   ++  L K+     + +           K   +  K   ILV TP  L+ 
Sbjct: 103 IISPTRELASQIHRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIY 162
Query: 175 HLKHTSSFLH-TNLRWIIFDEADRILELGFGKEIEEILDILGSRN-IASIGEGNEVSNVK 232
            LK     +   ++ W++ DE+D++ E G            G R+ +ASI        V+
Sbjct: 163 LLKQDPPGIDLASVEWLVVDESDKLFEDG----------KTGFRDQLASIFLACTSHKVR 212
Query: 233 RQNLLLSATLNEKVNHLTKISLETPVLIGL 262
           R   + SAT    V    K++L+  + + +
Sbjct: 213 RA--MFSATFAYDVEQWCKLNLDNVISVSI 240

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 79.0 bits (193), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 63/225 (28%), Positives = 107/225 (47%), Gaps = 26/225 (11%)
Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F ++GL   L   +    GFE P+ +Q +AI  I+ GRDV+  + +GTGKT  +   ++ 
Sbjct: 3   FDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSVSVLQ 61
Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            L        +   T AL+L PT EL + V + L   L  +  +     +GG N  ++  
Sbjct: 62  CLDI------QVRETQALILAPTRELAVQVQKGLLA-LGDYMNVQCHACIGGTNVGEDIR 114
Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTN-LRWIIFDEADRILELGFGKEIEEILDILG 215
           +L  G  ++  TPG + D ++  S  L T  ++ ++ DEAD +L  GF ++I ++   L 
Sbjct: 115 KLDYGQHVVAGTPGRVFDMIRRRS--LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLP 172
Query: 216 SRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                             Q +L+SATL  ++  +T   +  P+ I
Sbjct: 173 PAT---------------QVVLISATLPHEILEMTNKFMTDPIRI 202

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 77.4 bits (189), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/208 (30%), Positives = 98/208 (47%), Gaps = 26/208 (12%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL 114
           GFE P+ +Q +AI   + G DV+  A +GTGKT  +   I+  ++     +D  + T AL
Sbjct: 59  GFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIE-----LDLKA-TQAL 112
Query: 115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLR-KGISILVATPGHLL 173
           VL PT EL   + +++   L  +        +GG N   E  +L+ +   I+V TPG + 
Sbjct: 113 VLAPTRELAQQIQKVVMA-LGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVF 171
Query: 174 DHLKHTSSFLHTN-LRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVK 232
           D L     +L    ++  + DEAD +L  GF  +I +I   L S                
Sbjct: 172 DMLNR--RYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNT-------------- 215
Query: 233 RQNLLLSATLNEKVNHLTKISLETPVLI 260
            Q +LLSAT+   V  +TK  +  P+ I
Sbjct: 216 -QVVLLSATMPSDVLEVTKKFMRDPIRI 242

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 76.3 bits (186), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 63/208 (30%), Positives = 98/208 (47%), Gaps = 26/208 (12%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL 114
           GFE P+ +Q +AI   + G DV+  A +GTGKT  +   I+  ++     +D  + T AL
Sbjct: 33  GFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIE-----LDLKA-TQAL 86
Query: 115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLR-KGISILVATPGHLL 173
           VL PT EL   + +++   L  +        +GG N   E  +L+ +   I+V TPG + 
Sbjct: 87  VLAPTRELAQQIQKVVMA-LGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVF 145
Query: 174 DHLKHTSSFLHTN-LRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVK 232
           D L     +L    ++  + DEAD +L  GF  +I +I   L S                
Sbjct: 146 DMLNR--RYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNT-------------- 189
Query: 233 RQNLLLSATLNEKVNHLTKISLETPVLI 260
            Q +LLSAT+   V  +TK  +  P+ I
Sbjct: 190 -QVVLLSATMPSDVLEVTKKFMRDPIRI 216

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 74.3 bits (181), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 58/217 (26%), Positives = 106/217 (48%), Gaps = 32/217 (14%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL 114
           GFE P++VQ + IP  + G DVL  A +G GKT  ++   +  L+  + ++        L
Sbjct: 26  GFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVS------VL 79
Query: 115 VLVPTSELCLLVYEILQKLLHRFRWIVP----GYVMGGGNRSKEKARLRKGI-SILVATP 169
           V+  T EL   +     K   RF   +P        GG +  K++  L+K    I+V TP
Sbjct: 80  VMCHTRELAFQI----SKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTP 135
Query: 170 GHLLDHLKHTSSFLHTNLRWIIFDEADRILE-LGFGKEIEEILDILGSRNIASIGEGNEV 228
           G +L  L    S    +++  I DEAD++LE L   ++++EI                 +
Sbjct: 136 GRIL-ALARNKSLNLKHIKHFILDEADKMLEQLDMRRDVQEIF---------------RM 179
Query: 229 SNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK 265
           +  ++Q ++ SATL++++  + +  ++ P+ I +D++
Sbjct: 180 TPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDE 216

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score = 73.6 bits (179), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 71/234 (30%), Positives = 113/234 (48%), Gaps = 37/234 (15%)
Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F SL L   + + LR   GFE P+ VQ +AIP+   G D++V A +GTGKT  +    ++
Sbjct: 26  FESLLLSRPVLEGLRAA-GFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALD 84
Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            L      +  +  T  L+L PT E+ + ++ ++  +  +   +     +GG   S++K 
Sbjct: 85  SL------VLENLSTQILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKT 138
Query: 157 RLRKGISILVATPGHL-----LDHLKHTSSFLHTNLRWIIFDEADRILELG-FGKEIEEI 210
           RL+K   I V +PG +     LD+L   S      +R  I DEAD++LE G F ++I  I
Sbjct: 139 RLKK-CHIAVGSPGRIKQLIELDYLNPGS------IRLFILDEADKLLEEGSFQEQINWI 191
Query: 211 LDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKV-NHLTKISLETPVLIGLD 263
              L +                +Q L +SAT  E + N LTK  +  P  + L+
Sbjct: 192 YSSLPA---------------SKQMLAVSATYPEFLANALTKY-MRDPTFVRLN 229

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 57/217 (26%), Positives = 105/217 (48%), Gaps = 32/217 (14%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL 114
           GFE P++VQ + IP  + G DVL  A +G GKT  ++   +  L+  + ++        L
Sbjct: 27  GFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVS------VL 80
Query: 115 VLVPTSELCLLVYEILQKLLHRFRWIVP----GYVMGGGNRSKEKARLRKGI-SILVATP 169
           V+  T EL   +     K   RF   +P        GG +  K++  L+K    I+V TP
Sbjct: 81  VMCHTRELAFQI----SKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTP 136
Query: 170 GHLLDHLKHTSSFLHTNLRWIIFDEADRILE-LGFGKEIEEILDILGSRNIASIGEGNEV 228
           G +L  L    S    +++  I DE D++LE L   ++++EI                 +
Sbjct: 137 GRIL-ALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIF---------------RM 180
Query: 229 SNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK 265
           +  ++Q ++ SATL++++  + +  ++ P+ I +D++
Sbjct: 181 TPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDE 217

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 73.2 bits (178), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 57/217 (26%), Positives = 105/217 (48%), Gaps = 32/217 (14%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL 114
           GFE P++VQ + IP  + G DVL  A +G GKT  ++   +  L+  + ++        L
Sbjct: 27  GFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVS------VL 80
Query: 115 VLVPTSELCLLVYEILQKLLHRFRWIVP----GYVMGGGNRSKEKARLRKGIS-ILVATP 169
           V+  T EL   +     K   RF   +P        GG +  K++  L+K    I+V TP
Sbjct: 81  VMCHTRELAFQI----SKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTP 136
Query: 170 GHLLDHLKHTSSFLHTNLRWIIFDEADRILE-LGFGKEIEEILDILGSRNIASIGEGNEV 228
           G +L  L    S    +++  I DE D++LE L   ++++EI                 +
Sbjct: 137 GRIL-ALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIF---------------RM 180
Query: 229 SNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK 265
           +  ++Q ++ SATL++++  + +  ++ P+ I +D++
Sbjct: 181 TPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDE 217

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 58/207 (28%), Positives = 91/207 (43%), Gaps = 24/207 (11%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL 114
           GFE P+ +Q +AI   + G DV+  A +GTG T  +   I+  ++     +D  + T AL
Sbjct: 34  GFEXPSAIQQRAILPCIXGYDVIAQAQSGTGXTATFAISILQQIE-----LDLXA-TQAL 87
Query: 115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLD 174
           VL PT EL   +  ++  L           + G   R++ +    +   I+V TPG + D
Sbjct: 88  VLAPTRELAQQIQXVVMALGDYMGASCHACIGGTNVRAEVQXLQMEAPHIIVGTPGRVFD 147
Query: 175 HLKHTSSFLH-TNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKR 233
            L     +L    +   + DEAD +L  GF  +I +I   L S                 
Sbjct: 148 MLNR--RYLSPXYIXMFVLDEADEMLSRGFXDQIYDIFQXLNSNT--------------- 190
Query: 234 QNLLLSATLNEKVNHLTKISLETPVLI 260
           Q +LLSAT+   V  +T   +  P+ I
Sbjct: 191 QVVLLSATMPSDVLEVTXXFMRDPIRI 217

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score = 70.5 bits (171), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 56/211 (26%), Positives = 102/211 (48%), Gaps = 30/211 (14%)
Query: 55  GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL 114
           GFE P++VQ + IP  + G DVL  A +G GKT  ++   +  L+  + ++        L
Sbjct: 33  GFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPVTGQVS------VL 86
Query: 115 VLVPTSELCLLV---YEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGIS-ILVATPG 170
           V+  T EL   +   YE   K +   +  V     GG +  K++  L+K    I+V TPG
Sbjct: 87  VMCHTRELAFQISKEYERFSKYMPNVKVAV---FFGGLSIKKDEEVLKKNCPHIVVGTPG 143
Query: 171 HLLDHLKHTSSFLHTNLRWIIFDEADRILE-LGFGKEIEEILDILGSRNIASIGEGNEVS 229
            +L  L    S    +++  I DE D++LE L   ++++EI                 ++
Sbjct: 144 RILA-LARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIF---------------RMT 187
Query: 230 NVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
             ++Q ++ SATL++++  + +  ++ P+ I
Sbjct: 188 PHEKQVMMFSATLSKEIRPVCRKFMQDPMEI 218

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 58.9 bits (141), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 57/231 (24%), Positives = 106/231 (45%), Gaps = 45/231 (19%)
Query: 31  IFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTV 88
           ++++  F  LGL   L   +   + F+ P+K+Q +A+P++L    R+++  + +GTGKT 
Sbjct: 18  LYSAKSFDELGLAPELLKGIYA-MKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTA 76
Query: 89  AYLAPIINHL--QSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVM 146
           A+   ++  +  +  SP+        A+ L P+ EL     E++Q+ + +F  I    ++
Sbjct: 77  AFSLTMLTRVNPEDASPQ--------AICLAPSRELARQTLEVVQE-MGKFTKITSQLIV 127
Query: 147 GGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKE 206
                S EK + +    ++V TPG +LD ++     L   ++  + DEAD +L+      
Sbjct: 128 PD---SFEKNK-QINAQVIVGTPGTVLDLMRRKLMQLQ-KIKIFVLDEADNMLD------ 176
Query: 207 IEEILDILGSRNIASIGEGNEVSNVKR------QNLLLSATLNEKVNHLTK 251
                           G G++   VKR      Q +L SAT  + V    K
Sbjct: 177 --------------QQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAK 213

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/225 (25%), Positives = 102/225 (45%), Gaps = 45/225 (20%)
Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYLAPI 94
           F  LGL   L   +   + F+ P+K+Q +A+P++L    R+++  + +GTGKT A+   +
Sbjct: 7   FDELGLAPELLKGIYA-MKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 95  INHL--QSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS 152
           +  +  +  SP+        A+ L P+ EL     E++Q+ + +F  I    ++     S
Sbjct: 66  LTRVNPEDASPQ--------AICLAPSRELARQTLEVVQE-MGKFTKITSQLIVPD---S 113
Query: 153 KEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILD 212
            EK + +    ++V TPG +LD ++     L   ++  + DEAD +L+            
Sbjct: 114 FEKNK-QINAQVIVGTPGTVLDLMRRKLMQLQ-KIKIFVLDEADNMLD------------ 159
Query: 213 ILGSRNIASIGEGNEVSNVKR------QNLLLSATLNEKVNHLTK 251
                     G G++   VKR      Q +L SAT  + V    K
Sbjct: 160 --------QQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAK 196

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/225 (25%), Positives = 102/225 (45%), Gaps = 45/225 (20%)
Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYLAPI 94
           F  LGL   L   +   + F+ P+K+Q +A+P++L    R+++  + +GTGKT A+   +
Sbjct: 7   FDELGLAPELLKGIYA-MKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTM 65
Query: 95  INHL--QSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS 152
           +  +  +  SP+        A+ L P+ EL     E++Q+ + +F  I    ++     S
Sbjct: 66  LTRVNPEDASPQ--------AICLAPSRELARQTLEVVQE-MGKFTKITSQLIVPD---S 113
Query: 153 KEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILD 212
            EK + +    ++V TPG +LD ++     L   ++  + DEAD +L+            
Sbjct: 114 FEKNK-QINAQVIVGTPGTVLDLMRRKLMQLQ-KIKIFVLDEADNMLD------------ 159
Query: 213 ILGSRNIASIGEGNEVSNVKR------QNLLLSATLNEKVNHLTK 251
                     G G++   VKR      Q +L SAT  + V    K
Sbjct: 160 --------QQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAK 196

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 55.5 bits (132), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 48/217 (22%), Positives = 99/217 (45%), Gaps = 37/217 (17%)
Query: 54  LGFEAPTKVQAQAIPVILS--GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT 111
           +GF  P+K+Q  A+P++L+   ++++  + +GTGKT A++  +++ ++        +   
Sbjct: 43  MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEP------ANKYP 96
Query: 112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGH 171
             L L PT EL L   ++++++   +  +   Y +  GN+ +   ++ +   I++ TPG 
Sbjct: 97  QCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAV-RGNKLERGQKISE--QIVIGTPGT 153
Query: 172 LLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNV 231
           +LD            ++  + DEAD +                    IA+ G  ++   +
Sbjct: 154 VLDWCSKLKFIDPKKIKVFVLDEADVM--------------------IATQGHQDQSIRI 193
Query: 232 KR------QNLLLSATLNEKVNHLTKISLETPVLIGL 262
           +R      Q LL SAT  + V    +  +  P +I L
Sbjct: 194 QRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 230

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 49/219 (22%), Positives = 101/219 (46%), Gaps = 41/219 (18%)
Query: 54  LGFEAPTKVQAQAIPVILS--GRDVLVNAATGTGKTVAYLAPIINHLQSYS--PRIDRSS 109
           +GF  P+K+Q  A+P++L+   ++++  + +GTGKT A++  +++ ++  +  P+     
Sbjct: 80  MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQ----- 134
Query: 110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATP 169
               L L PT EL L   ++++++   +  +   Y +  GN+ +   ++ +   I++ TP
Sbjct: 135 ---CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAV-RGNKLERGQKISE--QIVIGTP 188
Query: 170 GHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVS 229
           G +LD            ++  + DEAD +                    IA+ G  ++  
Sbjct: 189 GTVLDWCSKLKFIDPKKIKVFVLDEADVM--------------------IATQGHQDQSI 228
Query: 230 NVKR------QNLLLSATLNEKVNHLTKISLETPVLIGL 262
            ++R      Q LL SAT  + V    +  +  P +I L
Sbjct: 229 RIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 267

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 49/219 (22%), Positives = 101/219 (46%), Gaps = 41/219 (18%)
Query: 54  LGFEAPTKVQAQAIPVILS--GRDVLVNAATGTGKTVAYLAPIINHLQSYS--PRIDRSS 109
           +GF  P+K+Q  A+P++L+   ++++  + +GTGKT A++  +++ ++  +  P+     
Sbjct: 43  MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQ----- 97
Query: 110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATP 169
               L L PT EL L   ++++++   +  +   Y +  GN+ +   ++ +   I++ TP
Sbjct: 98  ---CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAV-RGNKLERGQKISE--QIVIGTP 151
Query: 170 GHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVS 229
           G +LD            ++  + DEAD +                    IA+ G  ++  
Sbjct: 152 GTVLDWCSKLKFIDPKKIKVFVLDEADVM--------------------IATQGHQDQSI 191
Query: 230 NVKR------QNLLLSATLNEKVNHLTKISLETPVLIGL 262
            ++R      Q LL SAT  + V    +  +  P +I L
Sbjct: 192 RIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 230

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 48/217 (22%), Positives = 99/217 (45%), Gaps = 37/217 (17%)
Query: 54  LGFEAPTKVQAQAIPVILS--GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT 111
           +GF  P+K+Q  A+P++L+   ++++  + +GTGKT A++  +++ ++  +         
Sbjct: 59  MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQ----- 113
Query: 112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGH 171
             L L PT EL L   ++++++   +  +   Y +  GN+ +   ++ +   I++ TPG 
Sbjct: 114 -CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAV-RGNKLERGQKISE--QIVIGTPGT 169
Query: 172 LLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNV 231
           +LD            ++  + DEAD +                    IA+ G  ++   +
Sbjct: 170 VLDWCSKLKFIDPKKIKVFVLDEADVM--------------------IATQGHQDQSIRI 209
Query: 232 KR------QNLLLSATLNEKVNHLTKISLETPVLIGL 262
           +R      Q LL SAT  + V    +  +  P +I L
Sbjct: 210 QRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 246

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 54.7 bits (130), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 49/219 (22%), Positives = 101/219 (46%), Gaps = 41/219 (18%)
Query: 54  LGFEAPTKVQAQAIPVILS--GRDVLVNAATGTGKTVAYLAPIINHLQSYS--PRIDRSS 109
           +GF  P+K+Q  A+P++L+   ++++  + +GTGKT A++  +++ ++  +  P+     
Sbjct: 110 MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQ----- 164
Query: 110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATP 169
               L L PT EL L   ++++++   +  +   Y +  GN+ +   ++ +   I++ TP
Sbjct: 165 ---CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAV-RGNKLERGQKISE--QIVIGTP 218
Query: 170 GHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVS 229
           G +LD            ++  + DEAD +                    IA+ G  ++  
Sbjct: 219 GTVLDWCSKLKFIDPKKIKVFVLDEADVM--------------------IATQGHQDQSI 258
Query: 230 NVKR------QNLLLSATLNEKVNHLTKISLETPVLIGL 262
            ++R      Q LL SAT  + V    +  +  P +I L
Sbjct: 259 RIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 297

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 54.7 bits (130), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 48/217 (22%), Positives = 99/217 (45%), Gaps = 37/217 (17%)
Query: 54  LGFEAPTKVQAQAIPVILS--GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT 111
           +GF  P+K+Q  A+P++L+   ++++  + +GTGKT A++  +++ ++  +         
Sbjct: 110 MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPANKYPQ----- 164
Query: 112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGH 171
             L L PT EL L   ++++++   +  +   Y +  GN+ +   ++ +   I++ TPG 
Sbjct: 165 -CLCLSPTYELALQTGKVIEQMGKFYPELKLAYAV-RGNKLERGQKISE--QIVIGTPGT 220
Query: 172 LLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNV 231
           +LD            ++  + DEAD +                    IA+ G  ++   +
Sbjct: 221 VLDWCSKLKFIDPKKIKVFVLDEADVM--------------------IATQGHQDQSIRI 260
Query: 232 KR------QNLLLSATLNEKVNHLTKISLETPVLIGL 262
           +R      Q LL SAT  + V    +  +  P +I L
Sbjct: 261 QRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKL 297

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	316
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	9e-74
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	3e-73
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	7e-66
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	7e-65
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	1e-63
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	2e-54
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	4e-53
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	7e-53
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	8e-53
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	1e-52
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	3e-52
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-49
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	8e-49
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	4e-48
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-47
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	2e-44
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	7e-44
3bor_A	237	Human initiation factor 4A-II; translation initiat	2e-43
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	6e-43
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	2e-42
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	4e-42
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	6e-42
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	2e-41
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	4e-41
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	4e-40
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	2e-39
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	7e-39
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	4e-38
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	1e-37
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	3e-37
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	4e-37
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-12
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	3e-12
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	7e-10
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	1e-09
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	1e-09
3b6e_A	216	Interferon-induced helicase C domain-containing P;	2e-09
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	2e-09
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	2e-08
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	3e-07
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	9e-07
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	5e-06
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	2e-05
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	3e-05
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	7e-05
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	7e-05
1yks_A	440	Genome polyprotein [contains: flavivirin protease	2e-04
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	3e-04
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	5e-04

>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 =  226 bits (579), Expect = 9e-74
 Identities = 88/261 (33%), Positives = 146/261 (55%), Gaps = 22/261 (8%)

Query: 4   QPLNSQTISKKKKRNDKMSKKKETVKEIFASCCFSSLG--LDSTLCDQLRERLGFEAPTK 61
           Q +N+       +   ++      +   F    F+SL   ++      ++E +GF   T+
Sbjct: 21  QSMNNVEKPDNDEDESEVPSLPLGLTGAFEDTSFASLCNLVNENTLKAIKE-MGFTNMTE 79

Query: 62  VQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE 121
           +Q ++I  +L GRD+L  A TG+GKT+A+L P +  +     R    +GT  L+L PT E
Sbjct: 80  IQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELI--VKLRFMPRNGTGVLILSPTRE 137

Query: 122 LCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSS 181
           L +  + +L++L+        G +MGG NRS E  +L  GI+I+VATPG LLDH+++T  
Sbjct: 138 LAMQTFGVLKELM-THHVHTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPG 196

Query: 182 FLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSAT 241
           F++ NL+ ++ DEADRIL++GF +E+++I+ +L +               +RQ +L SAT
Sbjct: 197 FMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPT---------------RRQTMLFSAT 241

Query: 242 LNEKVNHLTKISLE-TPVLIG 261
              KV  L +ISL+  P+ +G
Sbjct: 242 QTRKVEDLARISLKKEPLYVG 262

>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 =  224 bits (574), Expect = 3e-73
 Identities = 82/258 (31%), Positives = 133/258 (51%), Gaps = 25/258 (9%)

Query: 10  TISKKKKRNDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPV 69
           ++  +++   ++ +  E +  +     FS   L       L+E   +   T++Q Q I +
Sbjct: 1   SMQVERESISRLMQNYEKI-NVNEITRFSDFPLSKKTLKGLQE-AQYRLVTEIQKQTIGL 58

Query: 70  ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI 129
            L G+DVL  A TG+GKT+A+L P++  L  Y  +   + G   L++ PT EL    +E+
Sbjct: 59  ALQGKDVLGAAKTGSGKTLAFLVPVLEAL--YRLQWTSTDGLGVLIISPTRELAYQTFEV 116

Query: 130 LQKLL--HRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNL 187
           L+K+   H F     G ++GG +   E  R+   I+ILV TPG LL H+  T SF  T+L
Sbjct: 117 LRKVGKNHDFSA---GLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDL 172

Query: 188 RWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVN 247
           + ++ DEADRIL++GF   +  +++ L                 KRQ LL SAT  + V 
Sbjct: 173 QMLVLDEADRILDMGFADTMNAVIENLPK---------------KRQTLLFSATQTKSVK 217

Query: 248 HLTKISLETPVLIGLDEK 265
            L ++SL+ P  + + EK
Sbjct: 218 DLARLSLKNPEYVWVHEK 235

>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 =  215 bits (549), Expect = 7e-66
 Identities = 72/260 (27%), Positives = 117/260 (45%), Gaps = 17/260 (6%)

Query: 7   NSQTISKKKKRNDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQA 66
           +     K          K++  KE+          LD  +   +   + F   T VQ + 
Sbjct: 44  DEVHFDKTTFSKLIHVPKEDNSKEVTLDSLLEEGVLDKEIHKAITR-MEFPGLTPVQQKT 102

Query: 67  IPVILSG--RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCL 124
           I  ILS    DV+  A TGTGKT A+L PI  HL   + + D      A+++ PT +L L
Sbjct: 103 IKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHL--INTKFDSQYMVKAVIVAPTRDLAL 160

Query: 125 LVYEILQKLLHRFRWIVP---GYVMGGGNRSKEKARLRK-GISILVATPGHLLDHLKHTS 180
            +   ++K+      +       ++GG +      ++ K   +I++ATPG L+D L+  S
Sbjct: 161 QIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYS 220

Query: 181 SFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSA 240
           +     + + + DEADR+LE+GF  ++E I  IL  +        N  S    + LL SA
Sbjct: 221 NKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEK--------NSKSADNIKTLLFSA 272

Query: 241 TLNEKVNHLTKISLETPVLI 260
           TL++KV  L    +     +
Sbjct: 273 TLDDKVQKLANNIMNKKECL 292

>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 =  213 bits (543), Expect = 7e-65
 Identities = 73/244 (29%), Positives = 118/244 (48%), Gaps = 19/244 (7%)

Query: 24  KKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG--RDVLVNAA 81
           K++  KE+          LD  +   +   + F   T VQ + I  ILS    DV+  A 
Sbjct: 10  KEDNSKEVTLDSLLEEGVLDKEIHKAITR-MEFPGLTPVQQKTIKPILSSEDHDVIARAK 68

Query: 82  TGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIV 141
           TGTGKT A+L PI  HL   + + D      A+++ PT +L L +   ++K+ H   + +
Sbjct: 69  TGTGKTFAFLIPIFQHL--INTKFDSQYMVKAVIVAPTRDLALQIEAEVKKI-HDMNYGL 125

Query: 142 PGY----VMGGGNRSKEKARLRK-GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEAD 196
             Y    ++GG +      ++ K   +I++ATPG L+D L+  S+     + + + DEAD
Sbjct: 126 KKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFVDYKVLDEAD 185

Query: 197 RILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLET 256
           R+LE+GF  ++E I  IL  +        N  S    + LL SATL++KV  L    +  
Sbjct: 186 RLLEIGFRDDLETISGILNEK--------NSKSADNIKTLLFSATLDDKVQKLANNIMNK 237

Query: 257 PVLI 260
              +
Sbjct: 238 KECL 241

>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 =  200 bits (512), Expect = 1e-63
 Identities = 82/255 (32%), Positives = 132/255 (51%), Gaps = 27/255 (10%)

Query: 8   SQTISKKKKRNDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAI 67
                +  + +D  ++  + + E   +  F  LG+   LC+   + LG+  PTK+Q +AI
Sbjct: 16  ENLYFQSMEEHDSPTEASQPIVEEEETKTFKDLGVTDVLCEACDQ-LGWTKPTKIQIEAI 74

Query: 68  PVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY 127
           P+ L GRD++  A TG+GKT A+  PI+N L   +P+       FALVL PT EL   + 
Sbjct: 75  PLALQGRDIIGLAETGSGKTGAFALPILNAL-LETPQ-----RLFALVLTPTRELAFQIS 128

Query: 128 EILQKL--LHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHT 185
           E  + L      +  V   ++GG +   +   L K   I++ATPG L+DHL++T  F   
Sbjct: 129 EQFEALGSSIGVQSAV---IVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLR 185

Query: 186 NLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEK 245
            L++++ DEADRIL + F  E+++IL ++                  R+  L SAT+ +K
Sbjct: 186 ALKYLVMDEADRILNMDFETEVDKILKVIPR---------------DRKTFLFSATMTKK 230

Query: 246 VNHLTKISLETPVLI 260
           V  L + +L+ PV  
Sbjct: 231 VQKLQRAALKNPVKC 245

>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 =  176 bits (450), Expect = 2e-54
 Identities = 74/227 (32%), Positives = 114/227 (50%), Gaps = 17/227 (7%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F  L LD T+ + +     ++ PT +Q  AIP IL  RD++  A TG+GKT A+L PIIN
Sbjct: 25  FDELKLDPTIRNNIL-LASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIIN 83

Query: 97  HL---QSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSK 153
           HL        R  +++    L+L PT EL + +    QK       +    V GG +   
Sbjct: 84  HLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHS 142

Query: 154 EKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDI 213
           +   ++ G  +LVATPG L+D ++     L    ++I+ DEADR+L++GF  +I +I   
Sbjct: 143 QIREVQMGCHLLVATPGRLVDFIEKNKISLE-FCKYIVLDEADRMLDMGFEPQIRKI--- 198

Query: 214 LGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                   I E N  S + RQ L+ SAT  +++  L    L   + +
Sbjct: 199 --------IEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFM 237

>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 =  173 bits (440), Expect = 4e-53
 Identities = 73/228 (32%), Positives = 115/228 (50%), Gaps = 31/228 (13%)

Query: 39  SLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHL 98
           +      L   +  R+G   PT +Q+QA P+IL G D++V A TGTGKT++YL P   HL
Sbjct: 24  AFQQYPDLLKSII-RVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHL 82

Query: 99  QSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHR-FRWIVPGYVMGGGNRSKEKAR 157
            S     ++ +G   LVL PT EL L V     K  ++  + I    + GG NR+ +   
Sbjct: 83  DSQPISREQRNGPGMLVLTPTRELALHVEAECSKYSYKGLKSIC---IYGGRNRNGQIED 139

Query: 158 LRKGISILVATPGHLLDHLKHTSSFLHTNLR---WIIFDEADRILELGFGKEIEEILDIL 214
           + KG+ I++ATPG L D   +       NLR   +++ DEAD++L++ F  +I +I    
Sbjct: 140 ISKGVDIIIATPGRLNDLQMNN----SVNLRSITYLVIDEADKMLDMEFEPQIRKI---- 191

Query: 215 GSRNIASIGEGNEVSNV--KRQNLLLSATLNEKVNHLTKISLETPVLI 260
                        + +V   RQ ++ SAT  + V  L    L+ P+++
Sbjct: 192 -------------LLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIV 226

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} Length = 242

 Score =  172 bits (439), Expect = 7e-53
 Identities = 74/229 (32%), Positives = 114/229 (49%), Gaps = 29/229 (12%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F      + + D +  R  F  PT +QAQ  PV LSG D++  A TG+GKT++YL P I 
Sbjct: 31  FYEANFPANVMDVIA-RQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIV 89

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
           H+    P ++R  G   LVL PT EL   V ++  +       +    + GG  +  +  
Sbjct: 90  HINH-QPFLERGDGPICLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIR 147

Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTNLR---WIIFDEADRILELGFGKEIEEILDI 213
            L +G+ I +ATPG L+D L+       TNLR   +++ DEADR+L++GF  +I +I   
Sbjct: 148 DLERGVEICIATPGRLIDFLECG----KTNLRRTTYLVLDEADRMLDMGFEPQIRKI--- 200

Query: 214 LGSRNIASIGEGNEVSNVK--RQNLLLSATLNEKVNHLTKISLETPVLI 260
                         V  ++  RQ L+ SAT  ++V  L +  L+  + I
Sbjct: 201 --------------VDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHI 235

>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 =  172 bits (439), Expect = 8e-53
 Identities = 60/230 (26%), Positives = 104/230 (45%), Gaps = 26/230 (11%)

Query: 36  CFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPII 95
                 ++S L   + +  GF+ PT +Q QAIPV+L GR++L +A TG+GKT+A+  PI+
Sbjct: 30  LDQEYKINSRLLQNILD-AGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPIL 88

Query: 96  NHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK 155
             L+        + G  AL++ PT EL   ++  L K+           +      +K+ 
Sbjct: 89  MQLKQ-----PANKGFRALIISPTRELASQIHRELIKISEG-TGFRIHMIHKAAVAAKKF 142

Query: 156 AR-LRKGISILVATPGHLLDHLKHTSSFLH-TNLRWIIFDEADRILE---LGFGKEIEEI 210
                K   ILV TP  L+  LK     +   ++ W++ DE+D++ E    GF  ++  I
Sbjct: 143 GPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASI 202

Query: 211 LDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                             ++ K +  + SAT    V    K++L+  + +
Sbjct: 203 F--------------LACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISV 238

>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 =  171 bits (435), Expect = 1e-52
 Identities = 77/224 (34%), Positives = 108/224 (48%), Gaps = 23/224 (10%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F    L   + + L    G   PT +QA A+P+ L G+D++  A TGTGKT+A+  PI  
Sbjct: 3   FKDFPLKPEILEALHG-RGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAE 61

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            L   +P  +R     ALVL PT EL L V   L  +    + +V  Y  GG    K+K 
Sbjct: 62  RL---APSQERGRKPRALVLTPTRELALQVASELTAVAPHLK-VVAVY--GGTGYGKQKE 115

Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS 216
            L +G   +VATPG  LD+L+     L + +   + DEAD +L +GF +E+E +L     
Sbjct: 116 ALLRGADAVVATPGRALDYLRQGVLDL-SRVEVAVLDEADEMLSMGFEEEVEALLSATPP 174

Query: 217 RNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                           RQ LL SATL      L +  ++ PVLI
Sbjct: 175 ---------------SRQTLLFSATLPSWAKRLAERYMKNPVLI 203

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  170 bits (433), Expect = 3e-52
 Identities = 60/232 (25%), Positives = 108/232 (46%), Gaps = 26/232 (11%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F+       + + ++  L F  PT++Q + IP  L G  ++  + TGTGKT AYL PI+ 
Sbjct: 6   FTRFPFQPFIIEAIKT-LRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIME 64

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL---LHRFRWIVPGYVMGGGNRSK 153
            ++     +       A++  PT EL   +Y    K+     + R IV   ++GG ++ K
Sbjct: 65  KIKPERAEVQ------AVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQK 118

Query: 154 EKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDI 213
              +L     I++ TPG + D ++  +  +H     ++ DEAD +L++GF  ++++I   
Sbjct: 119 ALEKLNVQPHIVIGTPGRINDFIREQALDVH-TAHILVVDEADLMLDMGFITDVDQIAAR 177

Query: 214 LGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK 265
           +                   Q L+ SAT+ EK+    K  +E P  + + E 
Sbjct: 178 M---------------PKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLEH 214

>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 =  169 bits (430), Expect = 2e-49
 Identities = 64/227 (28%), Positives = 113/227 (49%), Gaps = 23/227 (10%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F+S  L   + D +  + G++ PT +Q  +IPVI SGRD++  A TG+GKT A+L PI++
Sbjct: 58  FTSADLRDIIIDNVN-KSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILS 116

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            L    P          +++ PT EL + ++   +K      ++  G V GG +   +  
Sbjct: 117 KLLE-DPHELELGRPQVVIVSPTRELAIQIFNEARKFAFES-YLKIGIVYGGTSFRHQNE 174

Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTNLR---WIIFDEADRILELGFGKEIEEILDI 213
            + +G  +++ATPG LLD +  T            +++ DEADR+L++GF +++  I+  
Sbjct: 175 CITRGCHVVIATPGRLLDFVDRT----FITFEDTRFVVLDEADRMLDMGFSEDMRRIMTH 230

Query: 214 LGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
           +  R              + Q L+ SAT  E++  +    L+  V +
Sbjct: 231 VTMRP-------------EHQTLMFSATFPEEIQRMAGEFLKNYVFV 264

>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 =  161 bits (409), Expect = 8e-49
 Identities = 71/227 (31%), Positives = 111/227 (48%), Gaps = 29/227 (12%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F    L   L   + E +G+E P+ +Q ++IP+ LSGRD+L  A  GTGK+ AYL P++ 
Sbjct: 5   FEDYCLKRELLMGIFE-MGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL---LHRFRWIVPGYVMGGGNRSK 153
            L      I       A+V+VPT EL L V +I  ++   +   + ++     GG N   
Sbjct: 64  RLDLKKDNIQ------AMVIVPTRELALQVSQICIQVSKHMGGAK-VMATT--GGTNLRD 114

Query: 154 EKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDI 213
           +  RL   + +++ATPG +LD +K   + +  +++ I+ DEAD++L   F + +E+I+  
Sbjct: 115 DIMRLDDTVHVVIATPGRILDLIKKGVAKV-DHVQMIVLDEADKLLSQDFVQIMEDIILT 173

Query: 214 LGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
           L                  RQ LL SAT    V       LE P  I
Sbjct: 174 LPK---------------NRQILLYSATFPLSVQKFMNSHLEKPYEI 205

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  165 bits (420), Expect = 4e-48
 Identities = 65/239 (27%), Positives = 111/239 (46%), Gaps = 32/239 (13%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           FS + +   +   +     +  PT VQ  AIP+I   RD++  A TG+GKT A+L PI++
Sbjct: 17  FSDVEMGEIIMGNIE-LTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILS 75

Query: 97  HL------------QSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGY 144
            +            +       R     +LVL PT EL + +YE  +K  +R   + P  
Sbjct: 76  QIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRS-RVRPCV 134

Query: 145 VMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLR---WIIFDEADRILEL 201
           V GG +  ++   L +G  +LVATPG L+D ++         L    +++ DEADR+L++
Sbjct: 135 VYGGADIGQQIRDLERGCHLLVATPGRLVDMMERG----KIGLDFCKYLVLDEADRMLDM 190

Query: 202 GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
           GF  +I  I++                    R  ++ SAT  +++  L +  L+  + +
Sbjct: 191 GFEPQIRRIVEQDTMP-----------PKGVRHTMMFSATFPKEIQMLARDFLDEYIFL 238

>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 =  163 bits (414), Expect = 1e-47
 Identities = 66/227 (29%), Positives = 114/227 (50%), Gaps = 31/227 (13%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGR-DVLVNAATGTGKTVAYLAPII 95
           F+ L L   + + +R   GFE PT +Q + IP+ L+   +++  A TG+GKT ++  P+I
Sbjct: 8   FNELNLSDNILNAIRN-KGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 66

Query: 96  NHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL--LHRFRWIVPGYVMGGGNRSK 153
                    ++ ++G  A++L PT EL + V + ++ L      + I   Y  GG     
Sbjct: 67  E-------LVNENNGIEAIILTPTRELAIQVADEIESLKGNKNLK-IAKIY--GGKAIYP 116

Query: 154 EKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDI 213
           +   L+   +I+V TPG +LDH+   +  L  N+++ I DEAD +L +GF K++E+IL  
Sbjct: 117 QIKALKNA-NIVVGTPGRILDHINRGTLNL-KNVKYFILDEADEMLNMGFIKDVEKIL-- 172

Query: 214 LGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                           N  ++ LL SAT+  ++ +L K  +     I
Sbjct: 173 -------------NACNKDKRILLFSATMPREILNLAKKYMGDYSFI 206

>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 =  155 bits (394), Expect = 2e-44
 Identities = 69/255 (27%), Positives = 116/255 (45%), Gaps = 36/255 (14%)

Query: 12  SKKKKRNDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLR--ERLGFEAPTKVQAQAIPV 69
            +  K  D    + ET +E+  +  F ++GL   L   LR     GFE P+ +Q +AI  
Sbjct: 14  KRLLKEEDMTKVEFETSEEVDVTPTFDTMGLREDL---LRGIYAYGFEKPSAIQQRAIKQ 70

Query: 70  ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSS-GTFALVLVPTSELCLLVYE 128
           I+ GRDV+  + +GTGKT  +   ++         +D     T AL+L PT EL + + +
Sbjct: 71  IIKGRDVIAQSQSGTGKTATFSISVLQ-------CLDIQVRETQALILAPTRELAVQIQK 123

Query: 129 ILQKLLH--RFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHT- 185
            L  L      +        GG N  ++  +L  G  ++  TPG + D ++  S  L T 
Sbjct: 124 GLLALGDYMNVQ-CHACI--GGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRRRS--LRTR 178

Query: 186 NLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEK 245
            ++ ++ DEAD +L  GF ++I ++   L                   Q +L+SATL  +
Sbjct: 179 AIKMLVLDEADEMLNKGFKEQIYDVYRYL---------------PPATQVVLISATLPHE 223

Query: 246 VNHLTKISLETPVLI 260
           +  +T   +  P+ I
Sbjct: 224 ILEMTNKFMTDPIRI 238

>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 =  153 bits (390), Expect = 7e-44
 Identities = 74/250 (29%), Positives = 108/250 (43%), Gaps = 32/250 (12%)

Query: 19  DKMSKKKETVKEIFASCCFSSLGLDSTLCDQLR--ERLGFEAPTKVQAQAIPVILSGRDV 76
           D   +  + +     +  F    L   L   L      GFE P+ +Q +AIPV ++GRD+
Sbjct: 7   DTRPQTDDVLNTKGNT--FEDFYLKREL---LMGIFEAGFEKPSPIQEEAIPVAITGRDI 61

Query: 77  LVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSG-TFALVLVPTSELCLLVYEILQKLLH 135
           L  A  GTGKT A++ P +        ++        AL++VPT EL L   ++++ L  
Sbjct: 62  LARAKNGTGKTAAFVIPTLE-------KVKPKLNKIQALIMVPTRELALQTSQVVRTLG- 113

Query: 136 RFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEA 195
           +   I      GG N   +  RL + + ILV TPG +LD      + L ++    I DEA
Sbjct: 114 KHCGISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASRKVADL-SDCSLFIMDEA 172

Query: 196 DRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLE 255
           D++L   F   IE+IL  L                   Q+LL SAT    V       L 
Sbjct: 173 DKMLSRDFKTIIEQILSFL---------------PPTHQSLLFSATFPLTVKEFMVKHLH 217

Query: 256 TPVLIGLDEK 265
            P  I L E+
Sbjct: 218 KPYEINLMEE 227

>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 =  148 bits (375), Expect = 2e-43
 Identities = 72/260 (27%), Positives = 111/260 (42%), Gaps = 36/260 (13%)

Query: 7   NSQTISKKKKRNDKMSKKKET-VKEIFASCCFSSLGLDSTLCDQLR--ERLGFEAPTKVQ 63
           +    S  ++         E+   EI  +  F  + L  +L   LR     GFE P+ +Q
Sbjct: 3   HHHHHSSGRENLYFQGGVIESNWNEIVDN--FDDMNLKESL---LRGIYAYGFEKPSAIQ 57

Query: 64  AQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSS-GTFALVLVPTSEL 122
            +AI   + G DV+  A +GTGKT  +   I+        +++     T ALVL PT EL
Sbjct: 58  QRAIIPCIKGYDVIAQAQSGTGKTATFAISILQ-------QLEIEFKETQALVLAPTREL 110

Query: 123 CLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLR-KGISILVATPGHLLDHLKHTSS 181
              + +++  L   +        +GG N   E  +L+ +   I+V TPG + D L     
Sbjct: 111 AQQIQKVILALG-DYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNRRY- 168

Query: 182 FLHT-NLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSA 240
            L    ++  + DEAD +L  GF  +I EI   L               N   Q +LLSA
Sbjct: 169 -LSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKL---------------NTSIQVVLLSA 212

Query: 241 TLNEKVNHLTKISLETPVLI 260
           T+   V  +TK  +  P+ I
Sbjct: 213 TMPTDVLEVTKKFMRDPIRI 232

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A Length = 224

 Score =  146 bits (371), Expect = 6e-43
 Identities = 71/235 (30%), Positives = 102/235 (43%), Gaps = 47/235 (20%)

Query: 37  FSSLGLDSTLCDQLR--ERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPI 94
           F  + LD  L   LR     GFE P+ +Q +AI  I+ G DVL  A +GTGKT  +    
Sbjct: 16  FDDMELDENL---LRGVFGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAA 72

Query: 95  INHLQSYSPRIDRSS-GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMG------ 147
           +        RID S     AL+L PT EL L + +++  L          + M       
Sbjct: 73  LQ-------RIDTSVKAPQALMLAPTRELALQIQKVVMAL---------AFHMDIKVHAC 116

Query: 148 -GGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHT-NLRWIIFDEADRILELGFGK 205
            GG    E A   +   I+V TPG + D+++       T  ++  I DEAD +L  GF +
Sbjct: 117 IGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRR--FRTDKIKMFILDEADEMLSSGFKE 174

Query: 206 EIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
           +I +I  +L                   Q +LLSAT+   V  +T   +  PV I
Sbjct: 175 QIYQIFTLL---------------PPTTQVVLLSATMPNDVLEVTTKFMRNPVRI 214

>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 =  148 bits (376), Expect = 2e-42
 Identities = 61/211 (28%), Positives = 98/211 (46%), Gaps = 34/211 (16%)

Query: 52  ERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT 111
             +GF+  T+VQ++ IP++L G++V+V A TG+GKT AY  PI+        +       
Sbjct: 10  REMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL----GMK------- 58

Query: 112 FALVLVPTSELCLLVYEILQKLLH--RFRWIVPGYVMGGGNRSKEKARLRKGISILVATP 169
            +LV+ PT EL   V   ++ +      +      V GG     +  R+R    I+VATP
Sbjct: 59  -SLVVTPTRELTRQVASHIRDIGRYMDTKVAE---VYGGMPYKAQINRVR-NADIVVATP 113

Query: 170 GHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVS 229
           G LLD        L ++   +I DEAD + E+GF  +I+ IL                  
Sbjct: 114 GRLLDLWSKGVIDL-SSFEIVIIDEADLMFEMGFIDDIKIILAQT--------------- 157

Query: 230 NVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
           + ++   L SAT+ E++  + K  +     I
Sbjct: 158 SNRKITGLFSATIPEEIRKVVKDFITNYEEI 188

>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 =  144 bits (365), Expect = 4e-42
 Identities = 55/230 (23%), Positives = 109/230 (47%), Gaps = 33/230 (14%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F    L   L   + +  GFE P++VQ + IP  + G DVL  A +G GKT  ++   + 
Sbjct: 16  FRDFLLKPELLRAIVD-CGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 74

Query: 97  HLQSYSPRIDRSSG-TFALVLVPTSELCLLVYEILQKL---LHRFRWIVPGYVMGGGNRS 152
                  +++  +G    LV+  T EL   + +  ++    +   + +   +  GG +  
Sbjct: 75  -------QLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVK-VAVFF--GGLSIK 124

Query: 153 KEKARLRKGIS-ILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE-LGFGKEIEEI 210
           K++  L+K    I+V TPG +L   ++ S  L  +++  I DE D++LE L   ++++EI
Sbjct: 125 KDEEVLKKNCPHIVVGTPGRILALARNKSLNL-KHIKHFILDECDKMLEQLDMRRDVQEI 183

Query: 211 LDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
             +                  ++Q ++ SATL++++  + +  ++ P+ I
Sbjct: 184 FRMT---------------PHEKQVMMFSATLSKEIRPVCRKFMQDPMEI 218

>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 =  148 bits (377), Expect = 6e-42
 Identities = 72/270 (26%), Positives = 109/270 (40%), Gaps = 42/270 (15%)

Query: 3   AQPLNSQTISKKKKRNDKMSKKKETVKEIFASCC-----FSSLGLDSTLCDQLR--ERLG 55
                  + S+  +  D      E    I ++       F  + L  +L   LR     G
Sbjct: 3   LGSPEFMSASQDSRSRDNGPDGMEPEGVIESNWNEIVDSFDDMNLSESL---LRGIYAYG 59

Query: 56  FEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSS-GTFAL 114
           FE P+ +Q +AI   + G DV+  A +GTGKT  +   I+        +I+     T AL
Sbjct: 60  FEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQ-------QIELDLKATQAL 112

Query: 115 VLVPTSELCLLVYEILQKLLH--RFRWIVPGYVMGGGNRSKEKARLR-KGISILVATPGH 171
           VL PT EL   + +++  L               GG N   E  +L+ +   I+V TPG 
Sbjct: 113 VLAPTRELAQQIQKVVMALGDYMGAS-CHACI--GGTNVRAEVQKLQMEAPHIIVGTPGR 169

Query: 172 LLDHLKHTSSFLHT-NLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSN 230
           + D L      L    ++  + DEAD +L  GF  +I +I   L               N
Sbjct: 170 VFDMLNRRY--LSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKL---------------N 212

Query: 231 VKRQNLLLSATLNEKVNHLTKISLETPVLI 260
              Q +LLSAT+   V  +TK  +  P+ I
Sbjct: 213 SNTQVVLLSATMPSDVLEVTKKFMRDPIRI 242

>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 =  147 bits (373), Expect = 2e-41
 Identities = 72/258 (27%), Positives = 108/258 (41%), Gaps = 53/258 (20%)

Query: 14  KKKRNDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLR--ERLGFEAPTKVQAQAIPVIL 71
             + +   +   + V +      F  + LD  L   LR     GFE P+ +Q +AI  I+
Sbjct: 6   DIEESQIQTNYDKVVYK------FDDMELDENL---LRGVFGYGFEEPSAIQQRAIMPII 56

Query: 72  SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSS-GTFALVLVPTSELCLLVYEIL 130
            G DVL  A +GTGKT  +    +        RID S     AL+L PT EL L + +++
Sbjct: 57  EGHDVLAQAQSGTGKTGTFSIAALQ-------RIDTSVKAPQALMLAPTRELALQIQKVV 109

Query: 131 QKLLHRFRWIVPGYVMG-------GGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFL 183
             L          + M        GG    E A   +   I+V TPG + D+++      
Sbjct: 110 MAL---------AFHMDIKVHACIGGTSFVEDAEGLRDAQIVVGTPGRVFDNIQRRR--F 158

Query: 184 HT-NLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATL 242
            T  ++  I DEAD +L  GF ++I +I  +L                   Q +LLSAT+
Sbjct: 159 RTDKIKMFILDEADEMLSSGFKEQIYQIFTLL---------------PPTTQVVLLSATM 203

Query: 243 NEKVNHLTKISLETPVLI 260
              V  +T   +  PV I
Sbjct: 204 PNDVLEVTTKFMRNPVRI 221

>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 =  141 bits (359), Expect = 4e-41
 Identities = 64/257 (24%), Positives = 112/257 (43%), Gaps = 33/257 (12%)

Query: 12  SKKKKRNDKMSKKKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVIL 71
           S +  ++    + +     +     F SL L   + + LR   GFE P+ VQ +AIP+  
Sbjct: 1   SMRTAQDLSSPRTRTGDVLLAEPADFESLLLSRPVLEGLRA-AGFERPSPVQLKAIPLGR 59

Query: 72  SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ 131
            G D++V A +GTGKT  +    ++ L   +           L+L PT E+ + ++ ++ 
Sbjct: 60  CGLDLIVQAKSGTGKTCVFSTIALDSLVLENLSTQ------ILILAPTREIAVQIHSVIT 113

Query: 132 KL---LHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHT-NL 187
            +   +            GG   S++K RL K   I V +PG +   ++     L+  ++
Sbjct: 114 AIGIKMEGLE-CHVFI--GGTPLSQDKTRL-KKCHIAVGSPGRIKQLIELDY--LNPGSI 167

Query: 188 RWIIFDEADRILELG-FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKV 246
           R  I DEAD++LE G F ++I  I   L +                +Q L +SAT  E +
Sbjct: 168 RLFILDEADKLLEEGSFQEQINWIYSSLPA---------------SKQMLAVSATYPEFL 212

Query: 247 NHLTKISLETPVLIGLD 263
            +     +  P  + L+
Sbjct: 213 ANALTKYMRDPTFVRLN 229

>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 =  143 bits (363), Expect = 4e-40
 Identities = 56/236 (23%), Positives = 113/236 (47%), Gaps = 33/236 (13%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F    L   L   + +  GFE P++VQ + IP  + G DVL  A +G GKT  ++   + 
Sbjct: 10  FRDFLLKPELLRAIVD-CGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 68

Query: 97  HLQSYSPRIDRSSG-TFALVLVPTSELCLLVYEILQKL---LHRFRWIVPGYVMGGGNRS 152
                  +++  +G    LV+  T EL   + +  ++    +   + +   +  GG +  
Sbjct: 69  -------QLEPVTGQVSVLVMCHTRELAFQISKEYERFSKYMPNVK-VAVFF--GGLSIK 118

Query: 153 KEKARLRKGIS-ILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE-LGFGKEIEEI 210
           K++  L+K    I+V TPG +L   ++ S  L  +++  I DE D++LE L   ++++EI
Sbjct: 119 KDEEVLKKNCPHIVVGTPGRILALARNKSLNL-KHIKHFILDECDKMLEQLDMRRDVQEI 177

Query: 211 LDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK 266
             +                  ++Q ++ SATL++++  + +  ++ P+ I +D++ 
Sbjct: 178 FRMT---------------PHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDET 218

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  142 bits (360), Expect = 2e-39
 Identities = 29/247 (11%), Positives = 69/247 (27%), Gaps = 37/247 (14%)

Query: 52  ERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT 111
           ++   +  T  Q      I+ G+   + A TG GKT   +   +   +    +       
Sbjct: 15  KKKFGKDLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLARKG-KK------- 66

Query: 112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRK----GISILVA 167
            + ++ PT  L     E LQKL      +          + +++   +        ILV 
Sbjct: 67  -SALVFPTVTLVKQTLERLQKLAD--EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVF 123

Query: 168 TPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNE 227
           +   +  + +  S        ++  D+ D +L+     +   ++  +             
Sbjct: 124 STQFVSKNREKLSQ---KRFDFVFVDDVDAVLKASRNIDTLLMMVGI------------- 167

Query: 228 VSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNVHFGSLESDVKEEV 287
               +      S     K+    K      +++             +        +   V
Sbjct: 168 --PEEIIRKAFSTIKQGKIYERPKNLKPGILVV----SSATAKPRGIRPLLFRDLLNFTV 221

Query: 288 EHPNTTL 294
               +  
Sbjct: 222 GRLVSVA 228

>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 =  138 bits (349), Expect = 7e-39
 Identities = 49/228 (21%), Positives = 98/228 (42%), Gaps = 30/228 (13%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYLAPI 94
           F  L L   L   +   +GF  P+K+Q  A+P++L+   ++++  + +GTGKT A++  +
Sbjct: 94  FEELRLKPQLLQGVYA-MGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAM 152

Query: 95  INHLQSYSPRIDRSS-GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSK 153
           ++       +++ ++     L L PT EL L   ++++++   +  +   Y + G    +
Sbjct: 153 LS-------QVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLER 205

Query: 154 EKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE-LGFGKEIEEILD 212
                +    I++ TPG +LD            ++  + DEAD ++   G   +   I  
Sbjct: 206 ---GQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQR 262

Query: 213 ILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
           +L                   Q LL SAT  + V    +  +  P +I
Sbjct: 263 MLPR---------------NCQMLLFSATFEDSVWKFAQKVVPDPNVI 295

>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 =  138 bits (350), Expect = 4e-38
 Identities = 50/230 (21%), Positives = 99/230 (43%), Gaps = 34/230 (14%)

Query: 37  FSSLGLDSTLCDQLR--ERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYLA 92
           F  L L   L   L+    +GF  P+K+Q  A+P++L+   ++++  + +GTGKT A++ 
Sbjct: 27  FEELRLKPQL---LQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 83

Query: 93  PIINHLQSYSPRIDRSS-GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR 151
            +++       +++ ++     L L PT EL L   ++++++   +  +   Y + G   
Sbjct: 84  AMLS-------QVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKL 136

Query: 152 SKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL-GFGKEIEEI 210
            +     +    I++ TPG +LD            ++  + DEAD ++   G   +   I
Sbjct: 137 ER---GQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRI 193

Query: 211 LDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
             +L                   Q LL SAT  + V    +  +  P +I
Sbjct: 194 QRMLPR---------------NCQMLLFSATFEDSVWKFAQKVVPDPNVI 228

>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 =  135 bits (343), Expect = 3e-37
 Identities = 51/231 (22%), Positives = 98/231 (42%), Gaps = 39/231 (16%)

Query: 37  FSSLGLDSTLCDQLR--ERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYLA 92
           F  LGL   L   L+    + F+ P+K+Q +A+P++L    R+++  + +GTGKT A+  
Sbjct: 7   FDELGLAPEL---LKGIYAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSL 63

Query: 93  PIINHLQSYSPRIDRSS-GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR 151
            ++        R++       A+ L P+ EL     E++Q++  +F  I    ++     
Sbjct: 64  TMLT-------RVNPEDASPQAICLAPSRELARQTLEVVQEMG-KFTKITSQLIVPDSFE 115

Query: 152 SKEKARLRKGISILVATPGHLLDHLKHTSSFLHT-NLRWIIFDEADRILE-LGFGKEIEE 209
             ++        ++V TPG +LD ++     +    ++  + DEAD +L+  G G +   
Sbjct: 116 KNKQ----INAQVIVGTPGTVLDLMRRKL--MQLQKIKIFVLDEADNMLDQQGLGDQCIR 169

Query: 210 ILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
           +   L                   Q +L SAT  + V    K  +     +
Sbjct: 170 VKRFL---------------PKDTQLVLFSATFADAVRQYAKKIVPNANTL 205

>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 =  137 bits (347), Expect = 4e-37
 Identities = 50/230 (21%), Positives = 99/230 (43%), Gaps = 34/230 (14%)

Query: 37  FSSLGLDSTLCDQLR--ERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYLA 92
           F  L L   L   L+    +GF  P+K+Q  A+P++L+   ++++  + +GTGKT A++ 
Sbjct: 94  FEELRLKPQL---LQGVYAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVL 150

Query: 93  PIINHLQSYSPRIDRSS-GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR 151
            +++       +++ ++     L L PT EL L   ++++++   +  +   Y + G   
Sbjct: 151 AMLS-------QVEPANKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKL 203

Query: 152 SKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL-GFGKEIEEI 210
            +     +    I++ TPG +LD            ++  + DEAD ++   G   +   I
Sbjct: 204 ER---GQKISEQIVIGTPGTVLDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRI 260

Query: 211 LDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
             +L                   Q LL SAT  + V    +  +  P +I
Sbjct: 261 QRMLPR---------------NCQMLLFSATFEDSVWKFAQKVVPDPNVI 295

>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 = 67.2 bits (163), Expect = 2e-12
 Identities = 58/358 (16%), Positives = 113/358 (31%), Gaps = 136/358 (37%)

Query: 48  DQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDR 107
            +LR+ L      +++          ++VL++   G+GKT   +A  ++   SY  +   
Sbjct: 138 LKLRQAL-----LELR--------PAKNVLIDGVLGSGKTW--VA--LDVCLSYKVQCKM 180

Query: 108 SSGTFALVL--VPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKAR---LRKGI 162
               F L L    + E  L   E+LQKLL++   I P +     + S  K R   ++  +
Sbjct: 181 DFKIFWLNLKNCNSPETVL---EMLQKLLYQ---IDPNWTSRSDHSSNIKLRIHSIQAEL 234

Query: 163 SILVATPGH-----LLDHLKHTSSFLHTNLRWII--FDEADRIL---------------- 199
             L+ +  +     +L ++++               F+ + +IL                
Sbjct: 235 RRLLKSKPYENCLLVLLNVQN---------AKAWNAFNLSCKILLTTRFKQVTDFLSAAT 285

Query: 200 ---------ELGFGK-EIEEIL-DILGSRN--------------IASIGEG-----NEVS 229
                     +     E++ +L   L  R               ++ I E          
Sbjct: 286 TTHISLDHHSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWD 345

Query: 230 NVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK-------FPEDKSNVHFGSLE-- 280
           N K  N        +K+  + + SL   VL   + +K       FP   +++    L   
Sbjct: 346 NWKHVN-------CDKLTTIIESSLN--VLEPAEYRKMFDRLSVFPPS-AHIPTILLSLI 395

Query: 281 --SDVKEEVE--------------HPNTTLSS-----------STEDFMLPAKLVQRY 311
               +K +V                P  +  S              ++ L   +V  Y
Sbjct: 396 WFDVIKSDVMVVVNKLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHY 453

>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 = 66.0 bits (160), Expect = 3e-12
 Identities = 37/238 (15%), Positives = 82/238 (34%), Gaps = 12/238 (5%)

Query: 59  PTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVP 118
           P   Q           + L+   TG GKT+  +      L  Y  ++        L+L P
Sbjct: 10  PRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKYGGKV--------LMLAP 60

Query: 119 TSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKH 178
           T  L L   E  ++L +     +    + G    +E+++      ++VATP  + + L  
Sbjct: 61  TKPLVLQHAESFRRLFNLPPEKI--VALTGEKSPEERSKAWARAKVIVATPQTIENDLLA 118

Query: 179 TSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLL 238
                  ++  I+FDEA R +       I           +      +  S  ++   ++
Sbjct: 119 -GRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVI 177

Query: 239 SATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNVHFGSLESDVKEEVEHPNTTLSS 296
           +    E + + ++ S +    +     ++        +  +   ++E +      L+ 
Sbjct: 178 NNLGIEHIEYRSENSPDVRPYVKGIRFEWVRVDLPEIYKEVRKLLREMLRDALKPLAE 235

>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 = 58.8 bits (141), Expect = 7e-10
 Identities = 27/136 (19%), Positives = 53/136 (38%), Gaps = 7/136 (5%)

Query: 63  QAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSEL 122
           Q +     ++G++ L+ A TG+GKT   +    +H Q     +        + L     +
Sbjct: 253 QIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQ----NMPAGRKAKVVFLATKVPV 308

Query: 123 CLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK-ARLRKGISILVATPGHLLDHLKHTSS 181
                 + +    R  + V G  + G N S     ++ +   I+V TP  L++  +  + 
Sbjct: 309 YEQQKNVFKHHFERQGYSVQG--ISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTL 366

Query: 182 FLHTNLRWIIFDEADR 197
              +    +IFDE   
Sbjct: 367 TSLSIFTLMIFDECHN 382

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A* Length = 696

 Score = 58.5 bits (140), Expect = 1e-09
 Identities = 26/136 (19%), Positives = 52/136 (38%), Gaps = 5/136 (3%)

Query: 63  QAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSEL 122
           Q +     + G++ ++ A TG GKT   L    +HL+    +  +      +       +
Sbjct: 18  QLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLK----KFPQGQKGKVVFFANQIPV 73

Query: 123 CLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSF 182
                 +  K   R  + V G   G    +    ++ +   I++ TP  L+++LK  +  
Sbjct: 74  YEQNKSVFSKYFERHGYRVTGI-SGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIP 132

Query: 183 LHTNLRWIIFDEADRI 198
             +    +IFDE    
Sbjct: 133 SLSIFTLMIFDECHNT 148

>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 = 58.0 bits (139), Expect = 1e-09
 Identities = 25/135 (18%), Positives = 52/135 (38%), Gaps = 5/135 (3%)

Query: 63  QAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSEL 122
           Q +     ++G++ L+ A TG+GKT   +    +H Q     +        + L     +
Sbjct: 12  QIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQ----NMPAGRKAKVVFLATKVPV 67

Query: 123 CLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSF 182
                 + +    R  + V G + G    +    ++ +   I+V TP  L++  +  +  
Sbjct: 68  YEQQKNVFKHHFERQGYSVQG-ISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLT 126

Query: 183 LHTNLRWIIFDEADR 197
             +    +IFDE   
Sbjct: 127 SLSIFTLMIFDECHN 141

>3b6e_A Interferon-induced helicase C domain-containing P; DECH, DEXD/H RNA-binding helicase, innate immunity, IFIH1, S genomics; 1.60A {Homo sapiens} Length = 216

 Score = 56.0 bits (135), Expect = 2e-09
 Identities = 29/140 (20%), Positives = 55/140 (39%), Gaps = 13/140 (9%)

Query: 63  QAQAIPVILSGRDVLVNAATGTGKT-VAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE 121
           Q +     L G+++++   TG+GKT VA      +HL     +   S     +VLV    
Sbjct: 38  QMEVAQPALEGKNIIICLPTGSGKTRVAVYI-AKDHLDK---KKKASEPGKVIVLVNKVL 93

Query: 122 LCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK-ARLRKGISILVATPGHLLDHLKHTS 180
           L   ++    +   +  + V    + G  + K     + K   I+++T   L + L +  
Sbjct: 94  LVEQLFRKEFQPFLKKWYRV--IGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLE 151

Query: 181 SFLH-----TNLRWIIFDEA 195
           +        ++   II DE 
Sbjct: 152 NGEDAGVQLSDFSLIIIDEC 171

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus} Length = 555

 Score = 57.2 bits (137), Expect = 2e-09
 Identities = 21/135 (15%), Positives = 47/135 (34%), Gaps = 5/135 (3%)

Query: 63  QAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSEL 122
           Q +       G++ ++ A TG GKT   L    +HL+    +         +       +
Sbjct: 9   QLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLK----KFPCGQKGKVVFFANQIPV 64

Query: 123 CLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSF 182
                 +  +   R  + +        +    +  +     I++ TP  L+++L + +  
Sbjct: 65  YEQQATVFSRYFERLGYNIASISGATSDSVSVQHIIEDN-DIIILTPQILVNNLNNGAIP 123

Query: 183 LHTNLRWIIFDEADR 197
             +    +IFDE   
Sbjct: 124 SLSVFTLMIFDECHN 138

>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 = 55.0 bits (131), Expect = 2e-08
 Identities = 25/135 (18%), Positives = 52/135 (38%), Gaps = 5/135 (3%)

Query: 63  QAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSEL 122
           Q +     ++G++ L+ A TG+GKT   +    +H Q     +        + L     +
Sbjct: 253 QIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQ----NMPAGRKAKVVFLATKVPV 308

Query: 123 CLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSF 182
                 + +    R  + V G + G    +    ++ +   I+V TP  L++  +  +  
Sbjct: 309 YEQQKNVFKHHFERQGYSVQG-ISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLT 367

Query: 183 LHTNLRWIIFDEADR 197
             +    +IFDE   
Sbjct: 368 SLSIFTLMIFDECHN 382

>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 = 51.0 bits (122), Expect = 3e-07
 Identities = 49/207 (23%), Positives = 84/207 (40%), Gaps = 33/207 (15%)

Query: 38  SSLGLDSTLCDQLRERLGFEAPTKVQAQAIP-VILSGRDVLVNAATGTGKT-VAYLAPII 95
             L +D  +   L+ER G E+    QA+A+   IL G++ L++  T +GKT +A +A ++
Sbjct: 4   DELRVDERIKSTLKER-GIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIA-MV 61

Query: 96  NHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK 155
           + +         + G  A+ +VP   L    ++  Q    +    V       G+   + 
Sbjct: 62  HRI--------LTQGGKAVYIVPLKALAEEKFQEFQD-WEKIGLRVAMAT---GDYDSKD 109

Query: 156 ARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILG 215
             L K   I++AT     D L    S    +++ ++ DE   I     G  +E IL  + 
Sbjct: 110 EWLGKY-DIIIATAEK-FDSLLRHGSSWIKDVKILVADEIHLIGSRDRGATLEVILAHM- 166

Query: 216 SRNIASIGEGNEVSNVKRQNLLLSATL 242
                 IG              LSAT+
Sbjct: 167 LGKAQIIG--------------LSATI 179

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus} Length = 715

 Score = 49.3 bits (118), Expect = 9e-07
 Identities = 34/161 (21%), Positives = 64/161 (39%), Gaps = 22/161 (13%)

Query: 38  SSLGLDSTLCDQLRERLGFEAPTKVQAQAIP-VILSGRDVLVNAATGTGKT-VAYLAPII 95
             L L S + + +++R G +     Q +A+   +L G  +L+ + TG+GKT +A +  II
Sbjct: 11  EDLKLPSNVIEIIKKR-GIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMG-II 68

Query: 96  NHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGG--GNRSK 153
           + L     +        A+ + P   L    Y   +           G+ +    G+   
Sbjct: 69  SFLLKNGGK--------AIYVTPLRALTNEKYLTFKDWEL------IGFKVAMTSGDYDT 114

Query: 154 EKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE 194
           + A L+    I++ T    LD L          + + + DE
Sbjct: 115 DDAWLKNY-DIIITTYEK-LDSLWRHRPEWLNEVNYFVLDE 153

>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 = 46.7 bits (111), Expect = 5e-06
 Identities = 32/154 (20%), Positives = 55/154 (35%), Gaps = 16/154 (10%)

Query: 41  GLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQS 100
            + S     L+E  G E     QA+A+  + SG+++L+   T  GKT+     ++     
Sbjct: 9   SISSYAVGILKEE-GIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREA-- 65

Query: 101 YSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRK 160
                    G  +L +VP   L    YE  +K   +    +       G+       L  
Sbjct: 66  -------IKGGKSLYVVPLRALAGEKYESFKK-WEKIGLRIGIST---GDYESRDEHLGD 114

Query: 161 GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE 194
              I+V T     D L    +     +  ++ DE
Sbjct: 115 C-DIIVTTSEK-ADSLIRNRASWIKAVSCLVVDE 146

>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 = 45.4 bits (108), Expect = 2e-05
 Identities = 35/157 (22%), Positives = 56/157 (35%), Gaps = 33/157 (21%)

Query: 70  ILSGRDVLVNAATGTGKTV------AYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC 123
           IL        A TG GKT        +LA                 G    V+ PTS L 
Sbjct: 68  ILRKESFAATAPTGVGKTSFGLAMSLFLA---------------LKGKRCYVIFPTSLLV 112

Query: 124 LLVYEILQKLLHRFRWIVPGYVMG--GGNRSKEKARLRKGI---SILVATPGHLLDHLKH 178
           +   E ++K   +        +    G    +EK    + +    I++ T   L  H + 
Sbjct: 113 IQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYRE 172

Query: 179 TSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILG 215
              F      +I  D+ D IL+    K ++++L +LG
Sbjct: 173 LGHF-----DFIFVDDVDAILKA--SKNVDKLLHLLG 202

>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 Length = 451

 Score = 44.5 bits (105), Expect = 3e-05
 Identities = 28/164 (17%), Positives = 49/164 (29%), Gaps = 28/164 (17%)

Query: 57  EAPTKVQAQAIPVILS-GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALV 115
            A  +   +    I    R  +++   G GKT   L  I+        R         L+
Sbjct: 2   SAMGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALLRRLRT--------LI 53

Query: 116 LVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDH 175
           L PT  +   + E L+      R+  P        R            + +         
Sbjct: 54  LAPTRVVAAEMEEALRG--LPIRYQTPAVKSDHTGREI----------VDLMCHATFTTR 101

Query: 176 LKHTSSFLHTNLRWIIFDEA-----DRILELGFGKEIEEILDIL 214
           L  +S+ +  N   I+ DEA       +   G+     E+ +  
Sbjct: 102 L-LSSTRV-PNYNLIVMDEAHFTDPCSVAARGYISTRVEMGEAA 143

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae} Length = 1010

 Score = 43.6 bits (102), Expect = 7e-05
 Identities = 41/156 (26%), Positives = 60/156 (38%), Gaps = 24/156 (15%)

Query: 63  QAQAIPVILSGRDVLVNAATGTGKT-VAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE 121
           Q  AI  I  G  VLV+A T  GKT VA  A  I        R+           + TS 
Sbjct: 91  QDTAISCIDRGESVLVSAHTSAGKTVVAEYA--IAQSLKNKQRV-----------IYTSP 137

Query: 122 LCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSS 181
           +  L  +  ++LL  F  +  G + G    + +          LV T   L   L   S 
Sbjct: 138 IKALSNQKYRELLAEFGDV--GLMTGDITINPDA-------GCLVMTTEILRSMLYRGSE 188

Query: 182 FLHTNLRWIIFDEADRILELGFGKEIEEILDILGSR 217
            +   + W+IFDE   + +   G   EE + +L  +
Sbjct: 189 VMR-EVAWVIFDEVHYMRDKERGVVWEETIILLPDK 223

>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} Length = 1108

 Score = 43.7 bits (102), Expect = 7e-05
 Identities = 40/150 (26%), Positives = 57/150 (38%), Gaps = 24/150 (16%)

Query: 63  QAQAIPVILSGRDVLVNAATGTGKT-VAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE 121
           Q  AI  I  G  VLV+A T  GKT VA  A  I        R+           + TS 
Sbjct: 189 QDTAISCIDRGESVLVSAHTSAGKTVVAEYA--IAQSLKNKQRV-----------IYTSP 235

Query: 122 LCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSS 181
           +  L  +  ++LL  F  +  G + G    + +          LV T   L   L   S 
Sbjct: 236 IKALSNQKYRELLAEFGDV--GLMTGDITINPDA-------GCLVMTTEILRSMLYRGSE 286

Query: 182 FLHTNLRWIIFDEADRILELGFGKEIEEIL 211
            +   + W+IFDE   + +   G   EE +
Sbjct: 287 VMR-EVAWVIFDEVHYMRDKERGVVWEETI 315

>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* Length = 440

 Score = 41.4 bits (97), Expect = 2e-04
 Identities = 25/149 (16%), Positives = 41/149 (27%), Gaps = 27/149 (18%)

Query: 69  VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE 128
           ++  G   +++   G GKT  +L  I+        R         LVL PT  +   + E
Sbjct: 4   MLKKGMTTVLDFHPGAGKTRRFLPQILAECARRRLRT--------LVLAPTRVVLSEMKE 55

Query: 129 ILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLR 188
                   F  +   +           A       I        L +     + +  N  
Sbjct: 56  -------AFHGLDVKFHTQA-----FSAHGSGREVIDAMCHA-TLTYRMLEPTRV-VNWE 101

Query: 189 WIIFDE-----ADRILELGFGKEIEEILD 212
            II DE        I   G+        +
Sbjct: 102 VIIMDEAHFLDPASIAARGWAAHRARANE 130

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4a92_A* 1cu1_A 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A 8ohm_A 2f55_A 1jr6_A 1onb_A Length = 666

 Score = 41.5 bits (97), Expect = 3e-04
 Identities = 24/136 (17%), Positives = 40/136 (29%), Gaps = 27/136 (19%)

Query: 61  KVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTS 120
              +    V  S +   ++A TG+GK+      +     +   ++        LVL P+ 
Sbjct: 220 TDNSSPPAVPQSFQVAHLHAPTGSGKS----TKVPAAYAAQGYKV--------LVLNPSV 267

Query: 121 ELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTS 180
              L     + K       I P    G    +        G  +  +T G  L     + 
Sbjct: 268 AATLGFGAYMSKAHG----IDPNIRTGVRTITT-------GAPVTYSTYGKFLADGGCSG 316

Query: 181 SFLHTNLRWIIFDEAD 196
                    II DE  
Sbjct: 317 G----AYDIIICDECH 328

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A* Length = 620

 Score = 40.8 bits (96), Expect = 5e-04
 Identities = 11/59 (18%), Positives = 21/59 (35%)

Query: 69  VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY 127
            +     V + + TG+GKT+  L   + +      ++     T +       EL  L  
Sbjct: 18  SLQKSYGVALESPTGSGKTIMALKSALQYSSERKLKVLYLVRTNSQEEQVIKELRSLSS 76

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	316
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	100.0
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	100.0
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	100.0
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	100.0
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	100.0
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	100.0
3bor_A	237	Human initiation factor 4A-II; translation initiat	100.0
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	100.0
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	100.0
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	100.0
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	100.0
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	100.0
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	100.0
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	100.0
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	100.0
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	100.0
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	100.0
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	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
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	100.0
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	100.0
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	100.0
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	100.0
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	100.0
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.98
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.96
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.96
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.96
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.95
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.95
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.95
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.95
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.95
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.94
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.94
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.94
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.94
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.93
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.93
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.93
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.93
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.93
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.93
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.93
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.92
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.92
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.92
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.91
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.91
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.9
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.89
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.89
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.89
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.89
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.87
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.86
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.85
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.84
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.83
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.81
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.8
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.8
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.8
3h1t_A	590	Type I site-specific restriction-modification syst	99.78
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.77
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.77
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.75
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.74
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	99.72
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.65
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.62
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	99.61
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	99.53
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	99.46
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	99.44
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	99.43
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.33
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	99.12
3upu_A	459	ATP-dependent DNA helicase DDA; RECA-like domain,	98.28
4b3f_X	646	DNA-binding protein smubp-2; hydrolase, helicase;	98.25
3e1s_A	574	Exodeoxyribonuclease V, subunit RECD; alpha and be	98.24
2gk6_A	624	Regulator of nonsense transcripts 1; UPF1, helicas	98.18
2xzl_A	802	ATP-dependent helicase NAM7; hydrolase-RNA complex	98.14
2wjy_A	800	Regulator of nonsense transcripts 1; nonsense medi	98.03
2o0j_A	385	Terminase, DNA packaging protein GP17; nucleotide-	97.58
3cpe_A	592	Terminase, DNA packaging protein GP17; large termi	97.37
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	97.11
3lfu_A	647	DNA helicase II; SF1 helicase, ATP-binding, DNA da	97.07
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	97.0
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	96.93
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	96.69
1pjr_A	724	PCRA; DNA repair, DNA replication, SOS response, h	96.69
2zpa_A	671	Uncharacterized protein YPFI; RNA modification enz	96.68
1uaa_A	673	REP helicase, protein (ATP-dependent DNA helicase	96.67
2b8t_A	223	Thymidine kinase; deoxyribonucleoside kinase, zinc	96.58
2orw_A	184	Thymidine kinase; TMTK, TP4A, transferase; HET: 4T	96.48
1l8q_A	324	Chromosomal replication initiator protein DNAA; AA	96.4
3te6_A	318	Regulatory protein SIR3; heterochromatin, gene sil	96.38
3u4q_A	1232	ATP-dependent helicase/nuclease subunit A; helicas	96.36
1xx6_A	191	Thymidine kinase; NESG, northeast structural genom	96.29
2j9r_A	214	Thymidine kinase; TK1, DNK, lasso, transferase, AT	96.09
3u61_B	324	DNA polymerase accessory protein 44; AAA+, ATP hyd	96.09
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	96.04
3h4m_A	285	Proteasome-activating nucleotidase; ATPase, PAN, A	96.02
1w4r_A	195	Thymidine kinase; type II, human, cytosolic, phosp	96.01
3bos_A	242	Putative DNA replication factor; P-loop containing	96.01
2chg_A	226	Replication factor C small subunit; DNA-binding pr	95.93
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	95.7
1d2n_A	272	N-ethylmaleimide-sensitive fusion protein; hexamer	95.66
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	95.57
2p65_A	187	Hypothetical protein PF08_0063; CLPB, malaria, str	95.46
2orv_A	234	Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2	95.44
3kl4_A	433	SRP54, signal recognition 54 kDa protein; signal r	95.43
2v1u_A	387	Cell division control protein 6 homolog; DNA repli	95.4
3syl_A	309	Protein CBBX; photosynthesis, rubisco activase, AA	95.26
1a5t_A	334	Delta prime, HOLB; zinc finger, DNA replication; 2	95.24
1sxj_E	354	Activator 1 40 kDa subunit; clamp loader, processi	95.22
1g5t_A	196	COB(I)alamin adenosyltransferase; P-loop protein,	95.15
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	95.08
2dr3_A	247	UPF0273 protein PH0284; RECA superfamily ATPase, h	94.98
3eie_A	322	Vacuolar protein sorting-associated protein 4; AAA	94.94
3e2i_A	219	Thymidine kinase; Zn-binding, ATP-binding, DNA syn	94.86
1njg_A	250	DNA polymerase III subunit gamma; rossman-like fol	94.81
2qby_B	384	CDC6 homolog 3, cell division control protein 6 ho	94.58
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	94.55
2qby_A	386	CDC6 homolog 1, cell division control protein 6 ho	94.37
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	94.33
1sxj_D	353	Activator 1 41 kDa subunit; clamp loader, processi	94.25
2qz4_A	262	Paraplegin; AAA+, SPG7, protease, ADP, structural	94.25
3dm5_A	443	SRP54, signal recognition 54 kDa protein; protein-	94.15
1iqp_A	327	RFCS; clamp loader, extended AAA-ATPase domain, co	94.14
2q6t_A	444	DNAB replication FORK helicase; hydrolase; 2.90A {	94.14
1fnn_A	389	CDC6P, cell division control protein 6; ORC1, AAA	94.13
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	94.04
4b4t_J	405	26S protease regulatory subunit 8 homolog; hydrola	94.04
3vfd_A	389	Spastin; ATPase, microtubule severing, hydrolase;	94.02
2r6a_A	454	DNAB helicase, replicative helicase; replication,	93.98
1sxj_C	340	Activator 1 40 kDa subunit; clamp loader, processi	93.64
1n0w_A	243	DNA repair protein RAD51 homolog 1; DNA repair, ho	93.54
2qp9_X	355	Vacuolar protein sorting-associated protein 4; ATP	93.4
3pvs_A	447	Replication-associated recombination protein A; ma	93.39
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	93.31
1sxj_B	323	Activator 1 37 kDa subunit; clamp loader, processi	92.97
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	92.58
3hu3_A	489	Transitional endoplasmic reticulum ATPase; VCP, tr	92.24
3cmu_A	2050	Protein RECA, recombinase A; homologous recombinat	92.21
1cr0_A	296	DNA primase/helicase; RECA-type protein fold, tran	92.0
4a1f_A	338	DNAB helicase, replicative DNA helicase; hydrolase	91.47
1w5s_A	412	Origin recognition complex subunit 2 ORC2; replica	91.28
2zr9_A	349	Protein RECA, recombinase A; recombination, RECA m	91.13
3bh0_A	315	DNAB-like replicative helicase; ATPase, replicatio	91.11
3m6a_A	543	ATP-dependent protease LA 1; alpha, beta, ATP-bind	91.06
3co5_A	143	Putative two-component system transcriptional RES	90.76
2l8b_A	189	Protein TRAI, DNA helicase I; RECD, hydrolase; NMR	90.68
3n70_A	145	Transport activator; sigma-54, ntpase, PSI, MCSG,	90.63
1jr3_A	373	DNA polymerase III subunit gamma; processivity, pr	90.07
2z43_A	324	DNA repair and recombination protein RADA; archaea	90.04
3lda_A	400	DNA repair protein RAD51; DNA binding protein, ATP	89.22
3hr8_A	356	Protein RECA; alpha and beta proteins (A/B, A+B),	89.13
1xp8_A	366	RECA protein, recombinase A; recombination, radior	88.89
4b4t_M	434	26S protease regulatory subunit 6A; hydrolase, AAA	88.48
3nwn_A	359	Kinesin-like protein KIF9; motor domain, ADP, stru	88.27
3io5_A	333	Recombination and repair protein; storage dimer, i	88.14
1e9r_A	437	Conjugal transfer protein TRWB; coupling protein,	87.98
1v5w_A	343	DMC1, meiotic recombination protein DMC1/LIM15 hom	87.87
1bg2_A	325	Kinesin; motor protein, ATPase, microtubule associ	87.54
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	87.11
2i1q_A	322	DNA repair and recombination protein RADA; ATPase,	87.04
3dc4_A	344	Kinesin-like protein NOD; catalytic domain, ATPase	86.75
2vvg_A	350	Kinesin-2; motor protein, nucleotide-binding, micr	86.63
2y65_A	365	Kinesin, kinesin heavy chain; motor protein; HET:	86.61
3lre_A	355	Kinesin-like protein KIF18A; motor protein, nucleo	86.59
1goj_A	355	Kinesin, kinesin heavy chain; motor protein, ATPas	86.49
4a14_A	344	Kinesin, kinesin-like protein KIF7; motor protein,	86.46
2h58_A	330	Kinesin-like protein KIFC3 variant; motor domain,	86.4
3b6u_A	372	Kinesin-like protein KIF3B; structural genomics co	86.27
2zfi_A	366	Kinesin-like protein KIF1A, kinesin heavy chain is	86.26
1v8k_A	410	Kinesin-like protein KIF2C; microtubule destabiliz	86.2
1qvr_A	854	CLPB protein; coiled coil, AAA ATPase, chaperone;	86.18
4etp_A	403	Kinesin-like protein KAR3; kinesin motor protein,	86.17
2nr8_A	358	Kinesin-like protein KIF9; motor domain, ADP, stru	86.11
3gbj_A	354	KIF13B protein; kinesin, motor domain, ADP, struct	86.07
3hws_A	363	ATP-dependent CLP protease ATP-binding subunit CL;	86.03
3t0q_A	349	AGR253WP; kinesin, alpha and beta proteins, P-loop	85.94
1t5c_A	349	CENP-E protein, centromeric protein E; kinesin mot	85.89
1x88_A	359	Kinesin-like protein KIF11; switch II, motor domai	85.88
2qgz_A	308	Helicase loader, putative primosome component; str	85.8
2heh_A	387	KIF2C protein; kinesin, motor domain, ADP, structu	85.65
3nbx_X	500	ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structu	85.55
3cmw_A	1706	Protein RECA, recombinase A; homologous recombinat	85.39
3cob_A	369	Kinesin heavy chain-like protein; motor, switch II	85.33
1f9v_A	347	Kinesin-like protein KAR3; kinesin-related protein	85.27
3u06_A	412	Protein claret segregational; motor domain, stalk	85.16
2x8a_A	274	Nuclear valosin-containing protein-like; nuclear p	85.11
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	85.1
2wbe_C	373	Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mit	85.1
1u0j_A	267	DNA replication protein; AAA+ protein, P-loop atpa	84.8
2owm_A	443	Nckin3-434, related to kinesin-like protein KIF1C;	84.7
3hjh_A	483	Transcription-repair-coupling factor; MFD, mutatio	84.68
3bfn_A	388	Kinesin-like protein KIF22; limited proteolysis, s	84.67
1w36_B	1180	RECB, exodeoxyribonuclease V beta chain; recombina	84.61
4ag6_A	392	VIRB4 ATPase, type IV secretory pathway VIRB4 comp	84.3
2rep_A	376	Kinesin-like protein KIFC1; structural genomics co	83.96
3cf0_A	301	Transitional endoplasmic reticulum ATPase; AAA, P9	83.49
2zts_A	251	Putative uncharacterized protein PH0186; KAIC like	83.4
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	83.37
2fna_A	357	Conserved hypothetical protein; structural genomic	83.34
1xwi_A	322	SKD1 protein; VPS4B, AAA ATPase, protein transport	83.16
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	83.09
1ls1_A	295	Signal recognition particle protein; FFH, SRP54, S	82.76
1tue_A	212	Replication protein E1; helicase, replication, E1E	82.27
3b85_A	208	Phosphate starvation-inducible protein; PHOH2, ATP	82.03
4b4t_H	467	26S protease regulatory subunit 7 homolog; hydrola	82.0
1ofh_A	310	ATP-dependent HSL protease ATP-binding subunit HSL	81.88
2bjv_A	265	PSP operon transcriptional activator; AAA, transcr	81.85
1kgd_A	180	CASK, peripheral plasma membrane CASK; maguk, guan	81.63
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	81.55
4b4t_L	437	26S protease subunit RPT4; hydrolase, AAA-atpases,	81.4
2oap_1	511	GSPE-2, type II secretion system protein; hexameri	81.3
2r44_A	331	Uncharacterized protein; putative ATPase, structur	81.04
1lv7_A	257	FTSH; alpha/beta domain, four helix bundle, hydrol	80.65
2gza_A	361	Type IV secretion system protein VIRB11; ATPase, h	80.4
4b4t_K	428	26S protease regulatory subunit 6B homolog; hydrol	80.29
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	80.21
1lvg_A	198	Guanylate kinase, GMP kinase; transferase; HET: AD	80.05

>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=100.00  E-value=1.5e-41  Score=295.33  Aligned_cols=214  Identities=33%  Similarity=0.538  Sum_probs=191.3

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ...+|+++++++.+.+.+ .++||..|+++|.++++.+++|+|+++++|||+|||++|++|++..+..... .....+++
T Consensus        27 ~~~~f~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~~~~g~~~l~~apTGsGKT~~~~l~~l~~l~~~~~-~~~~~~~~  104 (242)
T 3fe2_A           27 PVLNFYEANFPANVMDVI-ARQNFTEPTAIQAQGWPVALSGLDMVGVAQTGSGKTLSYLLPAIVHINHQPF-LERGDGPI  104 (242)
T ss_dssp             CCSSTTTTTCCHHHHHHH-HTTTCCSCCHHHHHHHHHHHHTCCEEEEECTTSCHHHHHHHHHHHHHHTSCC-CCTTCCCS
T ss_pred             ccCCHhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCCEEEECCCcCHHHHHHHHHHHHHHHhccc-cccCCCCE
Confidence            446799999999999999 6789999999999999999999999999999999999999999999875332 22345778


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      +||++||++|+.|+++.++.++...+ ......+||.....+...+..+++|+|+||+++.+++.. ....+.+++++|+
T Consensus       105 ~lil~Pt~~L~~Q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~-~~~~~~~~~~lVi  182 (242)
T 3fe2_A          105 CLVLAPTRELAQQVQQVAAEYCRACR-LKSTCIYGGAPKGPQIRDLERGVEICIATPGRLIDFLEC-GKTNLRRTTYLVL  182 (242)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHHHTT-CCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHH-TSCCCTTCCEEEE
T ss_pred             EEEEeCcHHHHHHHHHHHHHHHhhcC-ceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHc-CCCCcccccEEEE
Confidence            99999999999999999999987754 566778889888888888888999999999999999976 4456789999999


Q ss_pred             ecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          193 DEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       193 DEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                      ||||++++++|...+..+++.++.               .+|+++||||+|+.+.++++.++++|+.|.++..
T Consensus       183 DEah~l~~~~~~~~~~~i~~~~~~---------------~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  240 (242)
T 3fe2_A          183 DEADRMLDMGFEPQIRKIVDQIRP---------------DRQTLMWSATWPKEVRQLAEDFLKDYIHINIGAL  240 (242)
T ss_dssp             TTHHHHHHTTCHHHHHHHHTTSCS---------------SCEEEEEESCCCHHHHHHHHHHCSSCEEEEECC-
T ss_pred             eCHHHHhhhCcHHHHHHHHHhCCc---------------cceEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            999999999999999999988876               8899999999999999999999999999998765

>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=100.00  E-value=8.8e-42  Score=305.81  Aligned_cols=210  Identities=24%  Similarity=0.430  Sum_probs=183.4

Q ss_pred             cccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC--CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCC
Q 043110           30 EIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDR  107 (316)
Q Consensus        30 ~~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g--~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~  107 (316)
                      +.....+|++++|++.+++.| ..+||..|+++|.++||.++.|  +|++++||||||||++|++|+++.+...      
T Consensus        87 p~~~~~~f~~l~l~~~l~~~l-~~~g~~~pt~iQ~~ai~~il~~~~~~~l~~a~TGsGKT~a~~lp~l~~l~~~------  159 (300)
T 3fmo_B           87 PLYSVKSFEELRLKPQLLQGV-YAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA------  159 (300)
T ss_dssp             CCCCCCCSGGGTCCHHHHHHH-HHTTCCSCCHHHHHHHHHHTSSSCCCEEEECCTTSSHHHHHHHHHHHHCCTT------
T ss_pred             CcCCcCCHhhcCCCHHHHHHH-HHcCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCCccHHHHHHHHHhhhcc------
Confidence            344567899999999999999 6789999999999999999987  9999999999999999999999988542      


Q ss_pred             CCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCce
Q 043110          108 SSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNL  187 (316)
Q Consensus       108 ~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l  187 (316)
                      ..++++||++||++||.|+++.++.++.........+..++.......   ..+++|+||||++|.+++.+.+.+.+.++
T Consensus       160 ~~~~~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~IlV~TP~~l~~~l~~~~~~~l~~l  236 (300)
T 3fmo_B          160 NKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKI  236 (300)
T ss_dssp             SCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC---CCCCSEEEECHHHHHHHHTTTCCCCGGGC
T ss_pred             CCCceEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh---cCCCCEEEECHHHHHHHHHhcCCCChhhc
Confidence            346679999999999999999999998776556667777766543221   45689999999999999987666777899


Q ss_pred             eEEEEecchhhhc-CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCC
Q 043110          188 RWIIFDEADRILE-LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDE  264 (316)
Q Consensus       188 ~~lViDEad~l~~-~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~  264 (316)
                      ++|||||||+|++ .+|...+..|+..++.               .+|+++||||+++.+..+++.++++|+.|.+..
T Consensus       237 ~~lVlDEad~l~~~~~~~~~~~~i~~~~~~---------------~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~~  299 (300)
T 3fmo_B          237 KVFVLDEADVMIATQGHQDQSIRIQRMLPR---------------NCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR  299 (300)
T ss_dssp             SEEEETTHHHHHHSTTHHHHHHHHHTTSCT---------------TCEEEEEESCCCHHHHHHHHHHSSSCEEEEECC
T ss_pred             eEEEEeCHHHHhhccCcHHHHHHHHHhCCC---------------CCEEEEEeccCCHHHHHHHHHHCCCCeEEEecC
Confidence            9999999999998 6899999999988876               899999999999999999999999999998754

>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=100.00  E-value=1.1e-40  Score=287.04  Aligned_cols=211  Identities=34%  Similarity=0.518  Sum_probs=177.1

Q ss_pred             ccCCccc-CCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCe
Q 043110           33 ASCCFSS-LGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGT  111 (316)
Q Consensus        33 ~~~~f~~-~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~  111 (316)
                      ...+|++ ++++++++++| .++||.+|+++|.++++.+++|+|+++++|||+|||++|++|++..+...........++
T Consensus        17 p~~~f~~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~~~~~~~~l~~apTGsGKT~~~~l~~~~~l~~~~~~~~~~~~~   95 (228)
T 3iuy_A           17 PTCRFKDAFQQYPDLLKSI-IRVGILKPTPIQSQAWPIILQGIDLIVVAQTGTGKTLSYLMPGFIHLDSQPISREQRNGP   95 (228)
T ss_dssp             CCCSHHHHHTTCHHHHHHH-HHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHC---------CCC
T ss_pred             ChhhHhhhhccCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhccchhhccCCC
Confidence            3467888 79999999999 667999999999999999999999999999999999999999999886543333334577


Q ss_pred             eEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEE
Q 043110          112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWII  191 (316)
Q Consensus       112 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lV  191 (316)
                      ++||++||++|+.|+++.++.+..  .........||.....+...+.++++|+|+||+++.+++.. ....+.+++++|
T Consensus        96 ~~lil~Pt~~L~~q~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~Tp~~l~~~~~~-~~~~~~~~~~lV  172 (228)
T 3iuy_A           96 GMLVLTPTRELALHVEAECSKYSY--KGLKSICIYGGRNRNGQIEDISKGVDIIIATPGRLNDLQMN-NSVNLRSITYLV  172 (228)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHHCC--TTCCEEEECC------CHHHHHSCCSEEEECHHHHHHHHHT-TCCCCTTCCEEE
T ss_pred             cEEEEeCCHHHHHHHHHHHHHhcc--cCceEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHc-CCcCcccceEEE
Confidence            899999999999999999998762  34566777888887777778888999999999999998876 455678899999


Q ss_pred             EecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEc
Q 043110          192 FDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGL  262 (316)
Q Consensus       192 iDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~  262 (316)
                      +||||++++++|...+..++..++.               .+|++++|||+|+.+.++++.++++|+.|.+
T Consensus       173 iDEah~~~~~~~~~~~~~i~~~~~~---------------~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~v  228 (228)
T 3iuy_A          173 IDEADKMLDMEFEPQIRKILLDVRP---------------DRQTVMTSATWPDTVRQLALSYLKDPMIVYV  228 (228)
T ss_dssp             ECCHHHHHHTTCHHHHHHHHHHSCS---------------SCEEEEEESCCCHHHHHHHHTTCSSCEEEEC
T ss_pred             EECHHHHhccchHHHHHHHHHhCCc---------------CCeEEEEEeeCCHHHHHHHHHHCCCCEEEeC
Confidence            9999999999999999999999876               8899999999999999999999999998864

>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=100.00  E-value=3.4e-40  Score=287.95  Aligned_cols=208  Identities=38%  Similarity=0.657  Sum_probs=187.0

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ...+|+++++++.+.+.| +++||..|+++|.++++.+++|+|+++.+|||+|||++|++|+++.+....      .+.+
T Consensus        41 ~~~~f~~l~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~il~~l~~~~------~~~~  113 (249)
T 3ber_A           41 ETKTFKDLGVTDVLCEAC-DQLGWTKPTKIQIEAIPLALQGRDIIGLAETGSGKTGAFALPILNALLETP------QRLF  113 (249)
T ss_dssp             HHCCTGGGTCCHHHHHHH-HHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHSC------CSSC
T ss_pred             ccCCHHHcCCCHHHHHHH-HHcCCCCCCHHHHHHHHHHhCCCCEEEEcCCCCCchhHhHHHHHHHHhcCC------CCce
Confidence            446799999999999999 778999999999999999999999999999999999999999999887632      3567


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      +||++||++|+.|+++.++.++...+ .....+.||.....+...+..+++|+|+||+++.+++.+...+.+.+++++|+
T Consensus       114 ~lil~Ptr~L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~lVi  192 (249)
T 3ber_A          114 ALVLTPTRELAFQISEQFEALGSSIG-VQSAVIVGGIDSMSQSLALAKKPHIIIATPGRLIDHLENTKGFNLRALKYLVM  192 (249)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHGGGT-CCEEEECTTSCHHHHHHHHHTCCSEEEECHHHHHHHHHHSTTCCCTTCCEEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhccCC-eeEEEEECCCChHHHHHHhcCCCCEEEECHHHHHHHHHcCCCcCccccCEEEE
Confidence            99999999999999999999887654 55667788888877777888899999999999999998756666788999999


Q ss_pred             ecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcC
Q 043110          193 DEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD  263 (316)
Q Consensus       193 DEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~  263 (316)
                      ||||++++++|...+..++..++.               .+|++++|||+++.+.++++.++++|+.|.++
T Consensus       193 DEah~l~~~~~~~~l~~i~~~~~~---------------~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~v~  248 (249)
T 3ber_A          193 DEADRILNMDFETEVDKILKVIPR---------------DRKTFLFSATMTKKVQKLQRAALKNPVKCAVS  248 (249)
T ss_dssp             CSHHHHHHTTCHHHHHHHHHSSCS---------------SSEEEEEESSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             cChhhhhccChHHHHHHHHHhCCC---------------CCeEEEEeccCCHHHHHHHHHHCCCCEEEEec
Confidence            999999999999999999988876               78999999999999999999999999998764

>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=100.00  E-value=9.2e-40  Score=276.72  Aligned_cols=203  Identities=34%  Similarity=0.504  Sum_probs=183.0

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      .+|+++++++++++.| ..+||..|+++|.++++.+++|+|+++.+|||+|||++|++|+++.+...      ..++++|
T Consensus         3 ~~f~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~------~~~~~~l   75 (206)
T 1vec_A            3 NEFEDYCLKRELLMGI-FEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK------KDNIQAM   75 (206)
T ss_dssp             SSGGGSCCCHHHHHHH-HTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT------SCSCCEE
T ss_pred             CChhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHccCCCEEEECCCCCchHHHHHHHHHHHhccc------CCCeeEE
Confidence            5799999999999999 67899999999999999999999999999999999999999999887542      2356799


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      |++||++|+.|+++.++.+....+...+....|+.....+...+..+++|+|+||+++.+.+.+ ....+.+++++|+||
T Consensus        76 il~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~lViDE  154 (206)
T 1vec_A           76 VIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKK-GVAKVDHVQMIVLDE  154 (206)
T ss_dssp             EECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHT-TCSCCTTCCEEEEET
T ss_pred             EEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhcCCCCCEEEeCHHHHHHHHHc-CCcCcccCCEEEEEC
Confidence            9999999999999999999876655677788888888877777778899999999999998876 445667899999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEE
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI  260 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i  260 (316)
                      ||++.+.+|...+..++..++.               .+|++++|||+|+.+.++++.++++|+.|
T Consensus       155 ah~~~~~~~~~~l~~i~~~~~~---------------~~~~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          155 ADKLLSQDFVQIMEDIILTLPK---------------NRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             HHHHTSTTTHHHHHHHHHHSCT---------------TCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             hHHhHhhCcHHHHHHHHHhCCc---------------cceEEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence            9999999999999999999876               78999999999999999999999999876

>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=100.00  E-value=2e-39  Score=279.68  Aligned_cols=207  Identities=30%  Similarity=0.441  Sum_probs=180.4

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ...+|+++++++.+.+.| +++||..|+++|.++++.+++|+|+++.+|||+|||++|++|+++.+...      ..+.+
T Consensus        22 ~~~~f~~l~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~------~~~~~   94 (230)
T 2oxc_A           22 EPADFESLLLSRPVLEGL-RAAGFERPSPVQLKAIPLGRCGLDLIVQAKSGTGKTCVFSTIALDSLVLE------NLSTQ   94 (230)
T ss_dssp             --CCGGGGTCCHHHHHHH-HHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT------SCSCC
T ss_pred             CCCCHhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc------CCCce
Confidence            346799999999999999 67899999999999999999999999999999999999999999987542      23567


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      +||++||++|+.|+++.++.++.......+....||.....+...+ .+++|+|+||+++.+++.. ....+.+++++|+
T Consensus        95 ~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~Iiv~Tp~~l~~~~~~-~~~~~~~~~~lVi  172 (230)
T 2oxc_A           95 ILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL-KKCHIAVGSPGRIKQLIEL-DYLNPGSIRLFIL  172 (230)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT-TSCSEEEECHHHHHHHHHT-TSSCGGGCCEEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc-cCCCEEEECHHHHHHHHhc-CCcccccCCEEEe
Confidence            9999999999999999999988665456677777887776655544 4789999999999998876 4555678999999


Q ss_pred             ecchhhhcCC-cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcC
Q 043110          193 DEADRILELG-FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD  263 (316)
Q Consensus       193 DEad~l~~~~-~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~  263 (316)
                      ||||++++++ |...+..+++.++.               .+|++++|||+++.+.+++..++.+|+.|.++
T Consensus       173 DEah~~~~~~~~~~~~~~i~~~~~~---------------~~~~l~lSAT~~~~~~~~~~~~~~~p~~i~~~  229 (230)
T 2oxc_A          173 DEADKLLEEGSFQEQINWIYSSLPA---------------SKQMLAVSATYPEFLANALTKYMRDPTFVRLN  229 (230)
T ss_dssp             SSHHHHHSTTSSHHHHHHHHHHSCS---------------SCEEEEEESCCCHHHHHHHTTTCSSCEEECC-
T ss_pred             CCchHhhcCcchHHHHHHHHHhCCC---------------CCeEEEEEeccCHHHHHHHHHHcCCCeEEEcC
Confidence            9999999997 99999999999876               78999999999999999999999999998764

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=100.00  E-value=2.5e-39  Score=280.00  Aligned_cols=213  Identities=36%  Similarity=0.604  Sum_probs=182.8

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ...+|+++++++.+.+.| ..+||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+.....  ....+.+
T Consensus        23 ~~~~f~~~~l~~~l~~~l-~~~~~~~~~~~Q~~~i~~~~~~~~~li~a~TGsGKT~~~~~~~l~~l~~~~~--~~~~~~~   99 (236)
T 2pl3_A           23 EITRFSDFPLSKKTLKGL-QEAQYRLVTEIQKQTIGLALQGKDVLGAAKTGSGKTLAFLVPVLEALYRLQW--TSTDGLG   99 (236)
T ss_dssp             GCSBGGGSCCCHHHHHHH-HHTTCCBCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHTTC--CGGGCCC
T ss_pred             ccCCHhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCCEEEEeCCCCcHHHHHHHHHHHHHHhhcc--cccCCce
Confidence            346799999999999999 6789999999999999999999999999999999999999999998865322  1124677


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      +||++||++|+.|+++.++.++...+ ..+....|+.....+...+ .+++|+|+||+++.+++.......+.+++++|+
T Consensus       100 ~lil~Pt~~L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~-~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~lVi  177 (236)
T 2pl3_A          100 VLIISPTRELAYQTFEVLRKVGKNHD-FSAGLIIGGKDLKHEAERI-NNINILVCTPGRLLQHMDETVSFHATDLQMLVL  177 (236)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTSS-CCEEEECCC--CHHHHHHH-TTCSEEEECHHHHHHHHHHCSSCCCTTCCEEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhCCCC-eeEEEEECCCCHHHHHHhC-CCCCEEEECHHHHHHHHHhcCCcccccccEEEE
Confidence            99999999999999999999876543 4556677777766665555 578999999999999987755566788999999


Q ss_pred             ecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          193 DEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       193 DEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                      ||||++.+++|...+..++..++.               .+|++++|||+++.+.++++.++.+|+.|.++++
T Consensus       178 DEah~~~~~~~~~~~~~i~~~~~~---------------~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  235 (236)
T 2pl3_A          178 DEADRILDMGFADTMNAVIENLPK---------------KRQTLLFSATQTKSVKDLARLSLKNPEYVWVHEK  235 (236)
T ss_dssp             TTHHHHHHTTTHHHHHHHHHTSCT---------------TSEEEEEESSCCHHHHHHHHHSCSSCEEEECCC-
T ss_pred             eChHHHhcCCcHHHHHHHHHhCCC---------------CCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            999999999999999999998876               8899999999999999999999999999987653

>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=100.00  E-value=1.2e-39  Score=282.33  Aligned_cols=208  Identities=31%  Similarity=0.448  Sum_probs=171.6

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ...+|+++++++.+.+.| ..+||..|+++|.++++.+++|+|+++.+|||+|||++|++|+++.+...      ..+.+
T Consensus        28 ~~~~f~~l~l~~~l~~~l-~~~g~~~~~~~Q~~ai~~i~~~~~~li~apTGsGKT~~~~l~~l~~l~~~------~~~~~  100 (237)
T 3bor_A           28 IVDNFDDMNLKESLLRGI-YAYGFEKPSAIQQRAIIPCIKGYDVIAQAQSGTGKTATFAISILQQLEIE------FKETQ  100 (237)
T ss_dssp             CCCSGGGSCCCHHHHHHH-HHHTCCSCCHHHHHHHHHHHTTCCEEECCCSSHHHHHHHHHHHHHHCCTT------SCSCC
T ss_pred             ccCChhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHHhc------CCCce
Confidence            346799999999999999 67899999999999999999999999999999999999999999987542      23567


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcC-CcEEEeCcHHHHHHHhcCCccccCceeEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKG-ISILVATPGHLLDHLKHTSSFLHTNLRWII  191 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lV  191 (316)
                      +||++||++|+.|+++.++.++...+ ..+....||.....+...+..+ ++|+|+||+++.+++.. ....+.+++++|
T Consensus       101 ~lil~Pt~~L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~-~~~~~~~~~~lV  178 (237)
T 3bor_A          101 ALVLAPTRELAQQIQKVILALGDYMG-ATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNR-RYLSPKWIKMFV  178 (237)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTTT-CCEEEECC-------------CCCSEEEECHHHHHHHHHT-TSSCSTTCCEEE
T ss_pred             EEEEECcHHHHHHHHHHHHHHhhhcC-ceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHh-CCcCcccCcEEE
Confidence            99999999999999999999876543 4555667777766666666555 89999999999999876 445567899999


Q ss_pred             EecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCC
Q 043110          192 FDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDE  264 (316)
Q Consensus       192 iDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~  264 (316)
                      +||||++++++|...+..+++.++.               .+|++++|||+|+++.++++.++++|+.|.++.
T Consensus       179 iDEah~~~~~~~~~~l~~i~~~~~~---------------~~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v~~  236 (237)
T 3bor_A          179 LDEADEMLSRGFKDQIYEIFQKLNT---------------SIQVVLLSATMPTDVLEVTKKFMRDPIRILVKK  236 (237)
T ss_dssp             EESHHHHHHTTCHHHHHHHHHHSCT---------------TCEEEEECSSCCHHHHHHHHHHCSSCEEEC---
T ss_pred             ECCchHhhccCcHHHHHHHHHhCCC---------------CCeEEEEEEecCHHHHHHHHHHCCCCEEEEecC
Confidence            9999999999999999999998876               889999999999999999999999999997653

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=100.00  E-value=5.8e-40  Score=280.92  Aligned_cols=209  Identities=28%  Similarity=0.471  Sum_probs=180.3

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      ..+|+++++++.+.+.| +++||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+...      ..+.++
T Consensus         3 ~~~f~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~l~~l~~~------~~~~~~   75 (219)
T 1q0u_A            3 ETQFTRFPFQPFIIEAI-KTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPE------RAEVQA   75 (219)
T ss_dssp             -CCGGGSCCCHHHHHHH-HHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTT------SCSCCE
T ss_pred             CCCHhhCCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhC------cCCceE
Confidence            35799999999999999 77899999999999999999999999999999999999999999987542      235679


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcC---CceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEE
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFR---WIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWI  190 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~l  190 (316)
                      ||++||++|+.|+++.+++++....   ........||.........+..+++|+|+||+++.+++.. ....+.+++++
T Consensus        76 lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~-~~~~~~~~~~l  154 (219)
T 1q0u_A           76 VITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIRE-QALDVHTAHIL  154 (219)
T ss_dssp             EEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHT-TCCCGGGCCEE
T ss_pred             EEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHcCCCCCEEEeCHHHHHHHHHc-CCCCcCcceEE
Confidence            9999999999999999999986542   3455666777665555444556789999999999998876 44566789999


Q ss_pred             EEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          191 IFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       191 ViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                      |+||||++.+++|...+..++..++.               .+|++++|||+|+++.++++.++.+|+.|.+...
T Consensus       155 ViDEah~~~~~~~~~~l~~i~~~~~~---------------~~~~l~~SAT~~~~~~~~~~~~~~~p~~~~~~~~  214 (219)
T 1q0u_A          155 VVDEADLMLDMGFITDVDQIAARMPK---------------DLQMLVFSATIPEKLKPFLKKYMENPTFVHVLEH  214 (219)
T ss_dssp             EECSHHHHHHTTCHHHHHHHHHTSCT---------------TCEEEEEESCCCGGGHHHHHHHCSSCEEEECC--
T ss_pred             EEcCchHHhhhChHHHHHHHHHhCCc---------------ccEEEEEecCCCHHHHHHHHHHcCCCeEEEeecc
Confidence            99999999999999999999998876               7899999999999999999999999999987654

>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=100.00  E-value=2.6e-39  Score=284.51  Aligned_cols=210  Identities=40%  Similarity=0.705  Sum_probs=181.2

Q ss_pred             cccCCcccCC--CCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCC
Q 043110           32 FASCCFSSLG--LDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSS  109 (316)
Q Consensus        32 ~~~~~f~~~~--l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~  109 (316)
                      +...+|++++  +++.+++.| +.+||..|+++|.++++.++.|+|++++||||||||++|++|+++.+......  ...
T Consensus        49 ~~~~~f~~l~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~l~~l~~l~~~~~~--~~~  125 (262)
T 3ly5_A           49 FEDTSFASLCNLVNENTLKAI-KEMGFTNMTEIQHKSIRPLLEGRDLLAAAKTGSGKTLAFLIPAVELIVKLRFM--PRN  125 (262)
T ss_dssp             SGGGCC-----CCCHHHHHHH-HHTTCCBCCHHHHHHHHHHHHTCCCEECCCTTSCHHHHHHHHHHHHHHHTTCC--GGG
T ss_pred             cccCChhHhccccCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCcEEEEccCCCCchHHHHHHHHHHHHhcccc--ccC
Confidence            4556788887  999999999 67899999999999999999999999999999999999999999988763321  123


Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeE
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRW  189 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~  189 (316)
                      +.++||++||++|+.|+++.+++++.... .......|+.....+...+..+++|+|+||+++.+++.......+.++++
T Consensus       126 ~~~~lil~Pt~~La~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~  204 (262)
T 3ly5_A          126 GTGVLILSPTRELAMQTFGVLKELMTHHV-HTYGLIMGGSNRSAEAQKLGNGINIIVATPGRLLDHMQNTPGFMYKNLQC  204 (262)
T ss_dssp             CCCEEEECSSHHHHHHHHHHHHHHTTTCC-SCEEEECSSSCHHHHHHHHHHCCSEEEECHHHHHHHHHHCTTCCCTTCCE
T ss_pred             CceEEEEeCCHHHHHHHHHHHHHHHhhcC-ceEEEEECCCCHHHHHHHhcCCCCEEEEcHHHHHHHHHccCCcccccCCE
Confidence            66799999999999999999999987644 55667788888888888888889999999999999998766667789999


Q ss_pred             EEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCC-CEEE
Q 043110          190 IIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLET-PVLI  260 (316)
Q Consensus       190 lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~-p~~i  260 (316)
                      +|+||||++++++|...+..+++.++.               .+|+++||||+++.+.++++.++++ |++|
T Consensus       205 lViDEah~l~~~~~~~~l~~i~~~~~~---------------~~q~l~~SAT~~~~v~~~~~~~l~~~~~~v  261 (262)
T 3ly5_A          205 LVIDEADRILDVGFEEELKQIIKLLPT---------------RRQTMLFSATQTRKVEDLARISLKKEPLYV  261 (262)
T ss_dssp             EEECSHHHHHHTTCHHHHHHHHHHSCS---------------SSEEEEECSSCCHHHHHHHHHHCSSCCEEC
T ss_pred             EEEcChHHHhhhhHHHHHHHHHHhCCC---------------CCeEEEEEecCCHHHHHHHHHHcCCCCeee
Confidence            999999999999999999999999987               8899999999999999999999874 4544

>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=100.00  E-value=1.5e-39  Score=284.40  Aligned_cols=220  Identities=31%  Similarity=0.504  Sum_probs=185.8

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCC---CCCC
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRI---DRSS  109 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~---~~~~  109 (316)
                      ...+|+++++++.++++| .++||..|+++|.++++.+++|+|+++++|||+|||++|++|+++.+.......   ....
T Consensus        21 ~~~~f~~l~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~i~~~~~~l~~a~TGsGKT~~~~~~~l~~l~~~~~~~~~~~~~~   99 (253)
T 1wrb_A           21 VIENFDELKLDPTIRNNI-LLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTA   99 (253)
T ss_dssp             CCCSSGGGSCCCSTTTTT-TTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCB
T ss_pred             ccCCHhhCCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHHHhhccccccccccC
Confidence            345799999999999999 778999999999999999999999999999999999999999999987543211   1234


Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeE
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRW  189 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~  189 (316)
                      ++++||++||++|+.|+++.++.++...+ .......||.....+...+..+++|+|+||+++.+++.. ....+.++++
T Consensus       100 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~-~~~~~~~~~~  177 (253)
T 1wrb_A          100 YPKCLILAPTRELAIQILSESQKFSLNTP-LRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEK-NKISLEFCKY  177 (253)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSS-CCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHT-TSBCCTTCCE
T ss_pred             CceEEEEECCHHHHHHHHHHHHHHhccCC-ceEEEEECCCCHHHHHHHhCCCCCEEEECHHHHHHHHHc-CCCChhhCCE
Confidence            56899999999999999999999886543 556677888888888888888899999999999999876 4456688999


Q ss_pred             EEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCC
Q 043110          190 IIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK  266 (316)
Q Consensus       190 lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~  266 (316)
                      +|+||||++++++|...+..++..+..           .....+|++++|||+++++.++++.++.+|+.|.++...
T Consensus       178 lViDEah~~~~~~~~~~~~~i~~~~~~-----------~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~  243 (253)
T 1wrb_A          178 IVLDEADRMLDMGFEPQIRKIIEESNM-----------PSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRVG  243 (253)
T ss_dssp             EEEETHHHHHHTTCHHHHHHHHHSSCC-----------CCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC---
T ss_pred             EEEeCHHHHHhCchHHHHHHHHhhccC-----------CCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCCC
Confidence            999999999999999999999985432           011267999999999999999999999999999887654

>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=100.00  E-value=9.3e-39  Score=270.62  Aligned_cols=205  Identities=36%  Similarity=0.534  Sum_probs=181.5

Q ss_pred             CcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEE
Q 043110           36 CFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALV  115 (316)
Q Consensus        36 ~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~li  115 (316)
                      +|+++++++++.+.| +++||..|+++|.++++.+++|+|+++.+|||+|||++|++|+++.+.....   ...++++||
T Consensus         2 ~f~~~~l~~~l~~~l-~~~~~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~l~~~~~---~~~~~~~li   77 (207)
T 2gxq_A            2 EFKDFPLKPEILEAL-HGRGLTTPTPIQAAALPLALEGKDLIGQARTGTGKTLAFALPIAERLAPSQE---RGRKPRALV   77 (207)
T ss_dssp             CGGGSCCCHHHHHHH-HHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCCCC---TTCCCSEEE
T ss_pred             ChhhcCCCHHHHHHH-HHcCCCCCCHHHHHHHHHHcCCCCEEEECCCCChHHHHHHHHHHHHHhhccc---cCCCCcEEE
Confidence            699999999999999 6789999999999999999999999999999999999999999998864221   234678999


Q ss_pred             EeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecc
Q 043110          116 LVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEA  195 (316)
Q Consensus       116 l~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEa  195 (316)
                      ++|+++|+.|+++.++.++..   .......|+.....+...+..+++|+|+||+++.+++.. ....+.+++++|+|||
T Consensus        78 l~P~~~L~~q~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~iViDEa  153 (207)
T 2gxq_A           78 LTPTRELALQVASELTAVAPH---LKVVAVYGGTGYGKQKEALLRGADAVVATPGRALDYLRQ-GVLDLSRVEVAVLDEA  153 (207)
T ss_dssp             ECSSHHHHHHHHHHHHHHCTT---SCEEEECSSSCSHHHHHHHHHCCSEEEECHHHHHHHHHH-TSSCCTTCSEEEEESH
T ss_pred             EECCHHHHHHHHHHHHHHhhc---ceEEEEECCCChHHHHHHhhCCCCEEEECHHHHHHHHHc-CCcchhhceEEEEECh
Confidence            999999999999999988643   455677788887777777778899999999999999876 4556788999999999


Q ss_pred             hhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcC
Q 043110          196 DRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD  263 (316)
Q Consensus       196 d~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~  263 (316)
                      |++.+.+|...+..++..++.               .+|++++|||+++.+.++++.++.+|+.|.++
T Consensus       154 h~~~~~~~~~~~~~i~~~~~~---------------~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~~~  206 (207)
T 2gxq_A          154 DEMLSMGFEEEVEALLSATPP---------------SRQTLLFSATLPSWAKRLAERYMKNPVLINVI  206 (207)
T ss_dssp             HHHHHTTCHHHHHHHHHTSCT---------------TSEEEEECSSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             hHhhccchHHHHHHHHHhCCc---------------cCeEEEEEEecCHHHHHHHHHHcCCCeEEEcC
Confidence            999999999999999988776               78999999999999999999999999998764

>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=1.5e-38  Score=299.09  Aligned_cols=222  Identities=28%  Similarity=0.502  Sum_probs=192.6

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      ..+|++++|++.+++.| +++||.+|+|+|+++||.+++|+|++++||||||||++|++|+++.+...... ....++++
T Consensus        55 ~~~f~~~~l~~~l~~~l-~~~g~~~pt~iQ~~ai~~i~~g~d~i~~a~TGsGKT~a~~lpil~~l~~~~~~-~~~~~~~~  132 (434)
T 2db3_A           55 IQHFTSADLRDIIIDNV-NKSGYKIPTPIQKCSIPVISSGRDLMACAQTGSGKTAAFLLPILSKLLEDPHE-LELGRPQV  132 (434)
T ss_dssp             CCCGGGSCCCHHHHHHH-HHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCCC-CCTTCCSE
T ss_pred             cCChhhcCCCHHHHHHH-HHcCCCCCCHHHHHHHHHHhcCCCEEEECCCCCCchHHHHHHHHHHHHhcccc-cccCCccE
Confidence            45799999999999999 67899999999999999999999999999999999999999999998764322 22346789


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      ||++||++|+.|+++.+++++... ...+.+++||.....+...+..+++|+|+||++|.+++.+ ....+.+++++|+|
T Consensus       133 lil~PtreLa~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l~~~~~Ivv~Tp~~l~~~l~~-~~~~l~~~~~lVlD  210 (434)
T 2db3_A          133 VIVSPTRELAIQIFNEARKFAFES-YLKIGIVYGGTSFRHQNECITRGCHVVIATPGRLLDFVDR-TFITFEDTRFVVLD  210 (434)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTS-SCCCCEECTTSCHHHHHHHHTTCCSEEEECHHHHHHHHHT-TSCCCTTCCEEEEE
T ss_pred             EEEecCHHHHHHHHHHHHHHhccC-CcEEEEEECCCCHHHHHHHhhcCCCEEEEChHHHHHHHHh-CCcccccCCeEEEc
Confidence            999999999999999999988654 3566788899998888888888999999999999999986 44567899999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCCC
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKS  272 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~~  272 (316)
                      |||+|++++|...+..++..+..             .+.+|+++||||+|+.+..++..++.+|+.+.+..........
T Consensus       211 Eah~~~~~gf~~~~~~i~~~~~~-------------~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~i  276 (434)
T 2db3_A          211 EADRMLDMGFSEDMRRIMTHVTM-------------RPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIVGGACSDV  276 (434)
T ss_dssp             THHHHTSTTTHHHHHHHHHCTTS-------------CSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESSTTCCCTTE
T ss_pred             cHhhhhccCcHHHHHHHHHhcCC-------------CCCceEEEEeccCCHHHHHHHHHhccCCEEEEecccccccccc
Confidence            99999999999999999987532             1278999999999999999999999999999887654333333

>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=100.00  E-value=1.5e-38  Score=272.73  Aligned_cols=207  Identities=31%  Similarity=0.506  Sum_probs=171.4

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      .+|+++++++.+++.| .++||..|+++|.++++.+++|+|+++.+|||+|||++|++|+++.+...      ..+.++|
T Consensus        14 ~~f~~l~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~~~~~~~~lv~~pTGsGKT~~~~~~~l~~l~~~------~~~~~~l   86 (224)
T 1qde_A           14 YKFDDMELDENLLRGV-FGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS------VKAPQAL   86 (224)
T ss_dssp             CCGGGGTCCHHHHHHH-HHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCTT------CCSCCEE
T ss_pred             CChhhcCCCHHHHHHH-HHCCCCCCcHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHhcc------CCCceEE
Confidence            5799999999999999 67899999999999999999999999999999999999999999988542      2356799


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      |++|+++|+.|+++.++.++...+ .......|+.....+...+. .++|+|+||+++.+.+.+ ....+.+++++|+||
T Consensus        87 il~Pt~~L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~-~~~iiv~Tp~~l~~~~~~-~~~~~~~~~~iViDE  163 (224)
T 1qde_A           87 MLAPTRELALQIQKVVMALAFHMD-IKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQR-RRFRTDKIKMFILDE  163 (224)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTSC-CCEEEECC----------CT-TCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEET
T ss_pred             EEECCHHHHHHHHHHHHHHhcccC-ceEEEEeCCcchHHHHhcCC-CCCEEEECHHHHHHHHHh-CCcchhhCcEEEEcC
Confidence            999999999999999999876543 45566667766555544443 489999999999998876 455667899999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCC
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK  266 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~  266 (316)
                      ||++.+++|...+..++..++.               .+|++++|||+++++.++++.++.+|+.|.++.+.
T Consensus       164 ah~~~~~~~~~~l~~i~~~~~~---------------~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~~~  220 (224)
T 1qde_A          164 ADEMLSSGFKEQIYQIFTLLPP---------------TTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDE  220 (224)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCT---------------TCEEEEEESSCCHHHHHHHHHHCSSCEEEC-----
T ss_pred             hhHHhhhhhHHHHHHHHHhCCc---------------cCeEEEEEeecCHHHHHHHHHHCCCCEEEEecCCc
Confidence            9999999999999999998876               88999999999999999999999999999877653

>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=100.00  E-value=2.9e-38  Score=270.37  Aligned_cols=206  Identities=27%  Similarity=0.458  Sum_probs=179.1

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      ..+|+++++++.+.+.| .++||..|+++|.++++.+++|+|+++.+|||+|||++|++|++..+...      ..+.++
T Consensus        13 ~~~f~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~~~~~~~~li~~~TGsGKT~~~~~~~~~~~~~~------~~~~~~   85 (220)
T 1t6n_A           13 SSGFRDFLLKPELLRAI-VDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV------TGQVSV   85 (220)
T ss_dssp             -CCSTTSCCCHHHHHHH-HHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC------TTCCCE
T ss_pred             CCCHhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCchhhhhhHHHHHhhhcc------CCCEEE
Confidence            35799999999999999 67899999999999999999999999999999999999999999887542      234579


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhc-CCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRK-GISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      ||++||++|+.|+++.++++........+....|+.....+...+.. .++|+|+||+++.+++.. ....+.+++++|+
T Consensus        86 lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~lVi  164 (220)
T 1t6n_A           86 LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN-KSLNLKHIKHFIL  164 (220)
T ss_dssp             EEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT-TSSCCTTCCEEEE
T ss_pred             EEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHh-CCCCcccCCEEEE
Confidence            99999999999999999998876545677778888887766666654 479999999999998876 4556788999999


Q ss_pred             ecchhhhc-CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEc
Q 043110          193 DEADRILE-LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGL  262 (316)
Q Consensus       193 DEad~l~~-~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~  262 (316)
                      ||||++++ .+|...+..++..++.               .+|++++|||+++.+.++++.++.+|+.|.+
T Consensus       165 DEah~~~~~~~~~~~~~~i~~~~~~---------------~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~v  220 (220)
T 1t6n_A          165 DECDKMLEQLDMRRDVQEIFRMTPH---------------EKQVMMFSATLSKEIRPVCRKFMQDPMEIFV  220 (220)
T ss_dssp             ESHHHHHSSHHHHHHHHHHHHTSCS---------------SSEEEEEESCCCTTTHHHHHTTCSSCEEEEC
T ss_pred             cCHHHHhcccCcHHHHHHHHHhCCC---------------cCeEEEEEeecCHHHHHHHHHHcCCCeEEeC
Confidence            99999987 4788888888887765               7899999999999999999999999998853

>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=100.00  E-value=2.1e-38  Score=275.67  Aligned_cols=210  Identities=30%  Similarity=0.495  Sum_probs=170.2

Q ss_pred             CCcccC----CCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCC
Q 043110           35 CCFSSL----GLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSG  110 (316)
Q Consensus        35 ~~f~~~----~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~  110 (316)
                      .+|+++    ++++.+++.+ .++||..|+++|.++++.+++|+|+++.+|||+|||++|++|+++.+...     ...+
T Consensus        25 ~~f~~l~~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~~~~~~~~l~~a~TGsGKT~~~~l~~l~~l~~~-----~~~~   98 (245)
T 3dkp_A           25 ATFQQLDQEYKINSRLLQNI-LDAGFQMPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQP-----ANKG   98 (245)
T ss_dssp             SSHHHHHHHHCCCHHHHHHH-HHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHCSC-----CSSS
T ss_pred             cCHHHhhhccCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhCCCCEEEECCCCCcHHHHHHHHHHHHHhhc-----ccCC
Confidence            457766    8999999999 66899999999999999999999999999999999999999999988542     2346


Q ss_pred             eeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH-HHHHhcCCcEEEeCcHHHHHHHhcCC-ccccCcee
Q 043110          111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE-KARLRKGISILVATPGHLLDHLKHTS-SFLHTNLR  188 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~l~~~~~IlV~Tp~~l~~~l~~~~-~~~~~~l~  188 (316)
                      .++||++||++|+.|+++.++.++...+ .......++...... ......+++|+|+||+++.+++.... ...+.+++
T Consensus        99 ~~~lil~Pt~~L~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~  177 (245)
T 3dkp_A           99 FRALIISPTRELASQIHRELIKISEGTG-FRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVE  177 (245)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHHTTTSC-CCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCC
T ss_pred             ceEEEEeCCHHHHHHHHHHHHHHhcccC-ceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCc
Confidence            6799999999999999999999876544 333333332211111 11123468999999999999997753 45678899


Q ss_pred             EEEEecchhhhc---CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          189 WIIFDEADRILE---LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       189 ~lViDEad~l~~---~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                      ++|+||||++++   .+|...+..++..+...              +.|+++||||+|+++.++++.++++|+.|.++..
T Consensus       178 ~lViDEah~~~~~~~~~~~~~~~~i~~~~~~~--------------~~~~~~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  243 (245)
T 3dkp_A          178 WLVVDESDKLFEDGKTGFRDQLASIFLACTSH--------------KVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR  243 (245)
T ss_dssp             EEEESSHHHHHHHC--CHHHHHHHHHHHCCCT--------------TCEEEEEESSCCHHHHHHHHHHSSSCEEEEECC-
T ss_pred             EEEEeChHHhcccccccHHHHHHHHHHhcCCC--------------CcEEEEEeccCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            999999999998   47888888887766431              6899999999999999999999999999998764

>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=2.3e-35  Score=275.06  Aligned_cols=222  Identities=31%  Similarity=0.508  Sum_probs=184.9

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCC---------
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPR---------  104 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~---------  104 (316)
                      ..+|+++++++.+.++| +.+||..|+|+|+++||.++.|+|+++.+|||+|||++|++|+++.+......         
T Consensus        14 ~~~f~~~~l~~~l~~~l-~~~~~~~~~~~Q~~~i~~i~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~~~~~~~~~~~~~~   92 (417)
T 2i4i_A           14 IESFSDVEMGEIIMGNI-ELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILSQIYSDGPGEALRAMKEN   92 (417)
T ss_dssp             CSSGGGSCCCHHHHHHH-HHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHHHCCCHHHHHHHHC
T ss_pred             cCCHhhCCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHccCCCEEEEcCCCCHHHHHHHHHHHHHHHhccccchhhccccc
Confidence            35699999999999999 67899999999999999999999999999999999999999999988654321         


Q ss_pred             ---CCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCc
Q 043110          105 ---IDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSS  181 (316)
Q Consensus       105 ---~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~  181 (316)
                         .....++++||++||++|+.|+++.++.++...+ .......||.....+...+..+++|+|+||++|.+++.. ..
T Consensus        93 ~~~~~~~~~~~~lil~Pt~~L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~-~~  170 (417)
T 2i4i_A           93 GRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSR-VRPCVVYGGADIGQQIRDLERGCHLLVATPGRLVDMMER-GK  170 (417)
T ss_dssp             BTTBSCSBCCSEEEECSSHHHHHHHHHHHHHHHTTSS-CCEEEECSSSCHHHHHHHHTTCCSEEEECHHHHHHHHHT-TS
T ss_pred             cccccccCCccEEEECCcHHHHHHHHHHHHHHhCcCC-ceEEEEECCCCHHHHHHHhhCCCCEEEEChHHHHHHHHc-CC
Confidence               1122346799999999999999999999886543 566778888888888888888899999999999999886 44


Q ss_pred             cccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEE
Q 043110          182 FLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIG  261 (316)
Q Consensus       182 ~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~  261 (316)
                      ..+.+++++|+||||++++++|...+..++.....           .....+|++++|||+++.+..+...++.+|..+.
T Consensus       171 ~~~~~~~~iViDEah~~~~~~~~~~~~~i~~~~~~-----------~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~  239 (417)
T 2i4i_A          171 IGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTM-----------PPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLA  239 (417)
T ss_dssp             BCCTTCCEEEESSHHHHHHTTCHHHHHHHHTSSSC-----------CCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEE
T ss_pred             cChhhCcEEEEEChhHhhccCcHHHHHHHHHhccC-----------CCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEE
Confidence            56778999999999999999999999888864321           1122679999999999999999999999999888


Q ss_pred             cCCCCCCC
Q 043110          262 LDEKKFPE  269 (316)
Q Consensus       262 ~~~~~~~~  269 (316)
                      +.......
T Consensus       240 ~~~~~~~~  247 (417)
T 2i4i_A          240 VGRVGSTS  247 (417)
T ss_dssp             EC----CC
T ss_pred             eCCCCCCc
Confidence            76554333

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=100.00  E-value=1.5e-35  Score=275.95  Aligned_cols=217  Identities=28%  Similarity=0.476  Sum_probs=188.4

Q ss_pred             cccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCC
Q 043110           30 EIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSS  109 (316)
Q Consensus        30 ~~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~  109 (316)
                      +.....+|+++++++.+.+.| ..+||..|+|+|+++++.+++|+|+++.+|||+|||++|++|+++.+...      ..
T Consensus        32 ~~~~~~~f~~~~l~~~l~~~l-~~~g~~~~~~~Q~~ai~~i~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~------~~  104 (410)
T 2j0s_A           32 EVDVTPTFDTMGLREDLLRGI-YAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ------VR  104 (410)
T ss_dssp             TCCCCCSGGGGCCCHHHHHHH-HHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT------SC
T ss_pred             CccCCCCHhhcCCCHHHHHHH-HHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCCCchHHHHHHHHHHHhhc------cC
Confidence            334456899999999999999 67899999999999999999999999999999999999999999877431      23


Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeE
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRW  189 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~  189 (316)
                      +.++||++||++|+.|+++.++.++...+ ..+....||.....+...+..+++|+|+||+++.+++.. ....+..+++
T Consensus       105 ~~~~lil~Pt~~L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~ivv~Tp~~l~~~l~~-~~~~~~~~~~  182 (410)
T 2j0s_A          105 ETQALILAPTRELAVQIQKGLLALGDYMN-VQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRR-RSLRTRAIKM  182 (410)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHTTTTT-CCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHT-TSSCCTTCCE
T ss_pred             CceEEEEcCcHHHHHHHHHHHHHHhccCC-eEEEEEECCCCHHHHHHHhhcCCCEEEcCHHHHHHHHHh-CCccHhheeE
Confidence            56799999999999999999999886644 556677888888888888888899999999999999986 4556678999


Q ss_pred             EEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCC
Q 043110          190 IIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPE  269 (316)
Q Consensus       190 lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~  269 (316)
                      +|+||||++++++|...+..++..++.               ..|++++|||+++.+.++...++.+|..+.+.......
T Consensus       183 vViDEah~~~~~~~~~~~~~i~~~~~~---------------~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~  247 (410)
T 2j0s_A          183 LVLDEADEMLNKGFKEQIYDVYRYLPP---------------ATQVVLISATLPHEILEMTNKFMTDPIRILVKRDELTL  247 (410)
T ss_dssp             EEEETHHHHTSTTTHHHHHHHHTTSCT---------------TCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGGGCSC
T ss_pred             EEEccHHHHHhhhhHHHHHHHHHhCcc---------------CceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCccccC
Confidence            999999999999999999999887766               78999999999999999999999999988776655444


Q ss_pred             C
Q 043110          270 D  270 (316)
Q Consensus       270 ~  270 (316)
                      .
T Consensus       248 ~  248 (410)
T 2j0s_A          248 E  248 (410)
T ss_dssp             T
T ss_pred             C
Confidence            3

>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=4.5e-34  Score=265.64  Aligned_cols=220  Identities=23%  Similarity=0.412  Sum_probs=185.8

Q ss_pred             cccccccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC--CcEEEEcCCCCchHHHHHHHHHHHhhhcCC
Q 043110           26 ETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYLAPIINHLQSYSP  103 (316)
Q Consensus        26 ~~~~~~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g--~d~li~a~TGsGKT~~~~lp~l~~l~~~~~  103 (316)
                      ....+.....+|+++++++.+++.| .++||..|+|+|.++++.++.+  +++++.+|||+|||++|++|+++.+...  
T Consensus        16 ~~~~~~~~~~~f~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~~~~~~~~~~lv~apTGsGKT~~~~~~~~~~~~~~--   92 (412)
T 3fht_A           16 DPNSPLYSVKSFEELRLKPQLLQGV-YAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA--   92 (412)
T ss_dssp             CTTSTTCCSSCTGGGTCCHHHHHHH-HHTTCCSCCHHHHHHHHHHHSSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT--
T ss_pred             cCCCCccccCCHhhCCCCHHHHHHH-HHcCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCchHHHHHHHHHHHHhhhc--
Confidence            4445566778999999999999999 6789999999999999999987  8999999999999999999999887542  


Q ss_pred             CCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccc
Q 043110          104 RIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFL  183 (316)
Q Consensus       104 ~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~  183 (316)
                          ..++++||++|+++|+.|+++.++.+.............++.......   ...++|+|+||+++.+++.+.....
T Consensus        93 ----~~~~~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~ivv~T~~~l~~~~~~~~~~~  165 (412)
T 3fht_A           93 ----NKYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFID  165 (412)
T ss_dssp             ----SCSCCEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTTC---CCCCSEEEECHHHHHHHHTTSCSSC
T ss_pred             ----CCCCCEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhhh---cCCCCEEEECchHHHHHHHhcCCcC
Confidence                235579999999999999999999998766556666666665443221   3457999999999999997766677


Q ss_pred             cCceeEEEEecchhhhc-CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEc
Q 043110          184 HTNLRWIIFDEADRILE-LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGL  262 (316)
Q Consensus       184 ~~~l~~lViDEad~l~~-~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~  262 (316)
                      +.+++++|+||||++++ .++...+..+...++.               ..|++++|||+++.+..+...++.+|..+.+
T Consensus       166 ~~~~~~iViDEah~~~~~~~~~~~~~~~~~~~~~---------------~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~  230 (412)
T 3fht_A          166 PKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPR---------------NCQMLLFSATFEDSVWKFAQKVVPDPNVIKL  230 (412)
T ss_dssp             GGGCCEEEEETHHHHHSTTTTHHHHHHHHHTSCT---------------TCEEEEEESCCCHHHHHHHHHHSSSCEEECC
T ss_pred             hhhCcEEEEeCHHHHhhcCCcHHHHHHHHhhCCC---------------CceEEEEEeecCHHHHHHHHHhcCCCeEEee
Confidence            78999999999999997 6888888888888776               7899999999999999999999999999887


Q ss_pred             CCCCCCCC
Q 043110          263 DEKKFPED  270 (316)
Q Consensus       263 ~~~~~~~~  270 (316)
                      ........
T Consensus       231 ~~~~~~~~  238 (412)
T 3fht_A          231 KREEETLD  238 (412)
T ss_dssp             CGGGSSCT
T ss_pred             cccccccc
Confidence            76554443

>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=1.7e-34  Score=274.60  Aligned_cols=219  Identities=23%  Similarity=0.410  Sum_probs=178.3

Q ss_pred             ccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC--CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCC
Q 043110           31 IFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRS  108 (316)
Q Consensus        31 ~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g--~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~  108 (316)
                      .....+|++++|++.+++.| ..+||..|+|+|.+++|.++.|  +|++++||||||||++|++|+++.+...      .
T Consensus        88 ~~~~~~f~~~~l~~~l~~~l-~~~g~~~p~~~Q~~ai~~il~~~~~~~l~~a~TGsGKT~~~~l~il~~l~~~------~  160 (479)
T 3fmp_B           88 LYSVKSFEELRLKPQLLQGV-YAMGFNRPSKIQENALPLMLAEPPQNLIAQSQSGTGKTAAFVLAMLSQVEPA------N  160 (479)
T ss_dssp             CCCCCCSGGGTCCHHHHHHH-HHTTCCSCCHHHHHHHHHHTSBSCCEEEEECCSSSSHHHHHHHHHHTTCCTT------S
T ss_pred             ccCcCCHHHcCCCHHHHHHH-HHcCCCCCCHHHHHHHHHHHcCCCCcEEEEcCCCCchhHHHHHHHHHHHhhc------C
Confidence            34556899999999999999 6789999999999999999987  8999999999999999999999877542      2


Q ss_pred             CCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCcee
Q 043110          109 SGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLR  188 (316)
Q Consensus       109 ~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~  188 (316)
                      .++++||++||++|+.|+++.++.+..........+..++.......   ..+++|+|+||++|.+++.+...+.+.+++
T Consensus       161 ~~~~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~  237 (479)
T 3fmp_B          161 KYPQCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ---KISEQIVIGTPGTVLDWCSKLKFIDPKKIK  237 (479)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTTC---CCCCSEEEECHHHHHHHHTTSCCCCGGGCC
T ss_pred             CCCcEEEEeChHHHHHHHHHHHHHHHhhCCCceEEEEeCCccccccc---cCCCCEEEECchHHHHHHHhcCCcCcccCC
Confidence            35579999999999999999999998776556666666665432211   335789999999999999876677778999


Q ss_pred             EEEEecchhhhc-CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCC
Q 043110          189 WIIFDEADRILE-LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKF  267 (316)
Q Consensus       189 ~lViDEad~l~~-~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~  267 (316)
                      +||+||||++++ .+|...+..+...++.               .+|++++|||++..+..++..++.+|..+.+.....
T Consensus       238 ~iViDEah~~~~~~~~~~~~~~i~~~~~~---------------~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~~~  302 (479)
T 3fmp_B          238 VFVLDEADVMIATQGHQDQSIRIQRMLPR---------------NCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKREEE  302 (479)
T ss_dssp             EEEECCHHHHHTSTTHHHHHHHHHTTSCT---------------TSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC----
T ss_pred             EEEEECHHHHhhcCCcHHHHHHHHhhCCc---------------cceEEEEeCCCCHHHHHHHHHHcCCCeEEecccccc
Confidence            999999999997 5888888888877766               889999999999999999999999999998876654


Q ss_pred             CCCCCCc
Q 043110          268 PEDKSNV  274 (316)
Q Consensus       268 ~~~~~~~  274 (316)
                      .......
T Consensus       303 ~~~~~~~  309 (479)
T 3fmp_B          303 TLDTIKQ  309 (479)
T ss_dssp             -------
T ss_pred             CcCCceE
Confidence            4443333

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=100.00  E-value=1.3e-33  Score=262.80  Aligned_cols=219  Identities=29%  Similarity=0.443  Sum_probs=188.4

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      .+|+++++++.+.+.| .++||..|+++|+++++.++.|+|+++.+|||+|||++|++|+++.+...      ..+.++|
T Consensus        40 ~~f~~~~l~~~~~~~l-~~~~~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~------~~~~~~l  112 (414)
T 3eiq_A           40 DSFDDMNLSESLLRGI-YAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIELD------LKATQAL  112 (414)
T ss_dssp             CCGGGGCCCHHHHHHH-HHTTCCSCCHHHHHHHHHHHTTCCEEECCCSCSSSHHHHHHHHHHHCCTT------SCSCCEE
T ss_pred             cCHhhCCCCHHHHHHH-HHcCCCCCCHHHHHHhHHHhCCCCEEEECCCCCcccHHHHHHHHHHHhhc------CCceeEE
Confidence            6799999999999999 67899999999999999999999999999999999999999999887542      2356699


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHh-cCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLR-KGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      |++|+++|+.|+++.++.++...+ ..+....|+.....+...+. .+++|+|+||++|.+++.. ....+..++++|+|
T Consensus       113 il~P~~~L~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~-~~~~~~~~~~vViD  190 (414)
T 3eiq_A          113 VLAPTRELAQQIQKVVMALGDYMG-ASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNR-RYLSPKYIKMFVLD  190 (414)
T ss_dssp             EECSSHHHHHHHHHHHHHHGGGSC-CCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHH-TSSCSTTCCEEEEC
T ss_pred             EEeChHHHHHHHHHHHHHHhcccC-ceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHc-CCcccccCcEEEEE
Confidence            999999999999999999887654 55666778887777766665 6789999999999999876 44556789999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCCCC
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSN  273 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~~~  273 (316)
                      |||++.+++|...+..++..++.               ..|++++|||++..+..+...++.+|..+.+...........
T Consensus       191 Eah~~~~~~~~~~~~~~~~~~~~---------------~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  255 (414)
T 3eiq_A          191 EADEMLSRGFKDQIYDIFQKLNS---------------NTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKEELTLEGIR  255 (414)
T ss_dssp             SHHHHHHTTTHHHHHHHHTTSCT---------------TCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCCCCCTTSCC
T ss_pred             CHHHhhccCcHHHHHHHHHhCCC---------------CCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCCccCCCCce
Confidence            99999999999999999888776               889999999999999999999999999988776665554444


Q ss_pred             cccc
Q 043110          274 VHFG  277 (316)
Q Consensus       274 ~~~~  277 (316)
                      ..+.
T Consensus       256 ~~~~  259 (414)
T 3eiq_A          256 QFYI  259 (414)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            4333

>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=9e-34  Score=275.69  Aligned_cols=219  Identities=32%  Similarity=0.462  Sum_probs=181.1

Q ss_pred             CCcccCC----CCHHHHHHHHHHcCCCCCcHHHHHHHHHHh--CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCC
Q 043110           35 CCFSSLG----LDSTLCDQLRERLGFEAPTKVQAQAIPVIL--SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRS  108 (316)
Q Consensus        35 ~~f~~~~----l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il--~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~  108 (316)
                      .+|+++.    |+++++++| +++||..|+|+|.++|+.++  .|+|+++.||||+|||++|++|+++.+......  ..
T Consensus        17 ~~~~~l~~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~il~~~~~dvlv~apTGsGKTl~~~lpil~~l~~~~~~--~~   93 (579)
T 3sqw_A           17 VTLDSLLEEGVLDKEIHKAI-TRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD--SQ   93 (579)
T ss_dssp             CCHHHHHHTTSSCHHHHHHH-HTTTCSSCCHHHHHHHHHHHCSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTS--ST
T ss_pred             cCHHHHhhcCCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHHccCCCeEEEEcCCCcHHHHHHHHHHHHHHHhcccc--cc
Confidence            3455443    999999999 78999999999999999999  788999999999999999999999998774321  23


Q ss_pred             CCeeEEEEeCChHHHHHHHHHHHHHHhh---cCCceeEEeeCCCChHHHHHHHh-cCCcEEEeCcHHHHHHHhcCCcccc
Q 043110          109 SGTFALVLVPTSELCLLVYEILQKLLHR---FRWIVPGYVMGGGNRSKEKARLR-KGISILVATPGHLLDHLKHTSSFLH  184 (316)
Q Consensus       109 ~~~~~lil~Pt~~L~~Q~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~  184 (316)
                      .++++|||+||++|+.|+++.++.++..   .....+....||.....+...+. .+++|+|+||++|.+++.......+
T Consensus        94 ~~~~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~  173 (579)
T 3sqw_A           94 YMVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFF  173 (579)
T ss_dssp             TSCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHC
T ss_pred             CCCeEEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhcccccc
Confidence            4678999999999999999999998753   23345667788888777776664 4789999999999999876444566


Q ss_pred             CceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCC
Q 043110          185 TNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDE  264 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~  264 (316)
                      ..+++||+||||++++++|...+..|+..++...        ....+.+|+++||||+++.+..++..++.+|..+.+..
T Consensus       174 ~~~~~lViDEah~l~~~gf~~~~~~i~~~l~~~~--------~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~  245 (579)
T 3sqw_A          174 RFVDYKVLDEADRLLEIGFRDDLETISGILNEKN--------SKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDT  245 (579)
T ss_dssp             TTCCEEEEETHHHHTSTTTHHHHHHHHHHHHHHC--------SSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEES
T ss_pred             ccCCEEEEEChHHhhcCCCHHHHHHHHHHhhhhh--------cccccCceEEEEeccCChHHHHHHHHHcCCCceEEEee
Confidence            7899999999999999999999999999886521        11223679999999999999999999999988776543

>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=9.3e-34  Score=274.62  Aligned_cols=218  Identities=32%  Similarity=0.460  Sum_probs=180.0

Q ss_pred             CcccCC----CCHHHHHHHHHHcCCCCCcHHHHHHHHHHh--CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCC
Q 043110           36 CFSSLG----LDSTLCDQLRERLGFEAPTKVQAQAIPVIL--SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSS  109 (316)
Q Consensus        36 ~f~~~~----l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il--~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~  109 (316)
                      +|+++.    |++.+++.| .++||..|+|+|.++|+.++  .|+|++++||||+|||++|++|+++.+......  ...
T Consensus        69 ~~~~l~~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~~l~~~~~~~lv~apTGsGKTl~~~lpil~~l~~~~~~--~~~  145 (563)
T 3i5x_A           69 TLDSLLEEGVLDKEIHKAI-TRMEFPGLTPVQQKTIKPILSSEDHDVIARAKTGTGKTFAFLIPIFQHLINTKFD--SQY  145 (563)
T ss_dssp             CHHHHHHTTSSCHHHHHHH-HTTCCSSCCHHHHHHHHHHHSSSSEEEEEECCTTSCHHHHHHHHHHHHHHHTTTS--STT
T ss_pred             CHHHHhhcCCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhcCCCCeEEEECCCCCCccHHHHHHHHHHHHhcccc--ccC
Confidence            455553    999999999 77899999999999999999  678999999999999999999999998774432  234


Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhc---CCceeEEeeCCCChHHHHHHH-hcCCcEEEeCcHHHHHHHhcCCccccC
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRF---RWIVPGYVMGGGNRSKEKARL-RKGISILVATPGHLLDHLKHTSSFLHT  185 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~l-~~~~~IlV~Tp~~l~~~l~~~~~~~~~  185 (316)
                      ++++|||+||++|+.|+++.++.+....   ....+....||.....+...+ ..+++|+|+||++|.+++.+.....+.
T Consensus       146 ~~~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~  225 (563)
T 3i5x_A          146 MVKAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFR  225 (563)
T ss_dssp             SCCEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCT
T ss_pred             CeeEEEEcCcHHHHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccc
Confidence            5689999999999999999999986532   234566777888877776665 447899999999999998764444567


Q ss_pred             ceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCC
Q 043110          186 NLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDE  264 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~  264 (316)
                      .++++|+||||++++++|.+.+..++..++...        ....+.+|++++|||+++.+..++..++.+|..+.+..
T Consensus       226 ~~~~lViDEah~l~~~~f~~~~~~i~~~l~~~~--------~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~  296 (563)
T 3i5x_A          226 FVDYKVLDEADRLLEIGFRDDLETISGILNEKN--------SKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDT  296 (563)
T ss_dssp             TCCEEEEETHHHHTSTTTHHHHHHHHHHHHHHC--------SSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEES
T ss_pred             cceEEEEeCHHHHhccchHHHHHHHHHhhhhcc--------ccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEec
Confidence            899999999999999999999999999886421        11233679999999999999999999999987766543

>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=3.1e-33  Score=258.37  Aligned_cols=210  Identities=26%  Similarity=0.454  Sum_probs=180.5

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      ..+|+++++++.+.+.| +.+||..|+|+|.++++.++.|+|+++.+|||+|||++|++|++..+...      ..+.++
T Consensus         7 ~~~f~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~l~~~------~~~~~~   79 (391)
T 1xti_A            7 SSGFRDFLLKPELLRAI-VDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV------TGQVSV   79 (391)
T ss_dssp             --CGGGGCCCHHHHHHH-HHHSCCSCCHHHHHHHHHHTTTCCEEEECSSCSSHHHHHHHHHHHHCCCC------TTCCCE
T ss_pred             CCChhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhcCCcEEEECCCCCcHHHHHHHHHHHhhccc------CCCeeE
Confidence            46799999999999999 66899999999999999999999999999999999999999999887542      235579


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhc-CCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRK-GISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      ||++|+++|+.|+++.++++........+....|+.........+.. .++|+|+||+++..++.. ....+.+++++|+
T Consensus        80 lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~-~~~~~~~~~~vVi  158 (391)
T 1xti_A           80 LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN-KSLNLKHIKHFIL  158 (391)
T ss_dssp             EEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT-TSSCCTTCSEEEE
T ss_pred             EEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHc-CCccccccCEEEE
Confidence            99999999999999999999876656777788888887776666654 479999999999998876 4455678999999


Q ss_pred             ecchhhhcC-CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCC
Q 043110          193 DEADRILEL-GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKK  266 (316)
Q Consensus       193 DEad~l~~~-~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~  266 (316)
                      ||||++.++ ++...+..++..++.               ..|++++|||+++.+..+...++.+|..+.+....
T Consensus       159 DEaH~~~~~~~~~~~~~~~~~~~~~---------------~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~  218 (391)
T 1xti_A          159 DECDKMLEQLDMRRDVQEIFRMTPH---------------EKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDET  218 (391)
T ss_dssp             CSHHHHTSSHHHHHHHHHHHHTSCS---------------SSEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCC
T ss_pred             eCHHHHhhccchHHHHHHHHhhCCC---------------CceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCcc
Confidence            999999884 788888888877665               78999999999999999999999999988876553

>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=2.8e-33  Score=258.84  Aligned_cols=212  Identities=31%  Similarity=0.496  Sum_probs=179.4

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      .+|+++++++.+.+.| ..+||..|+|+|+++++.++.|+|+++.+|||+|||++|++|+++.+...      ..+.++|
T Consensus        21 ~~f~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~l~~~------~~~~~~l   93 (394)
T 1fuu_A           21 YKFDDMELDENLLRGV-FGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDTS------VKAPQAL   93 (394)
T ss_dssp             CSSGGGCCCHHHHHHH-HHHTCCSCCHHHHHHHHHHHHTCCEEECCCSSHHHHHHHHHHHHHHCCTT------CCSCCEE
T ss_pred             CChhhcCCCHHHHHHH-HHcCCCCCCHHHHHHHHHHhCCCCEEEECCCCChHHHHHHHHHHHHhhcc------CCCCCEE
Confidence            5799999999999999 66899999999999999999999999999999999999999999887542      2356799


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      |++|+++|+.|+++.+..++...+ ..+....|+.........+. +++|+|+||+++.+.+.. ....+.+++++|+||
T Consensus        94 il~P~~~L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~-~~~~~~~~~~vIiDE  170 (394)
T 1fuu_A           94 MLAPTRELALQIQKVVMALAFHMD-IKVHACIGGTSFVEDAEGLR-DAQIVVGTPGRVFDNIQR-RRFRTDKIKMFILDE  170 (394)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTSC-CCEEEECSSCCHHHHHHHHH-HCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEET
T ss_pred             EEcCCHHHHHHHHHHHHHHhccCC-eeEEEEeCCCchHHHHhhcC-CCCEEEECHHHHHHHHHh-CCcchhhCcEEEEEC
Confidence            999999999999999999876543 55666777777766555544 579999999999998876 445567899999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCC
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDK  271 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~  271 (316)
                      ||++.++++...+..++..++.               ..|++++|||+++.+..+...++.+|..+.+.........
T Consensus       171 ah~~~~~~~~~~~~~~~~~~~~---------------~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  232 (394)
T 1fuu_A          171 ADEMLSSGFKEQIYQIFTLLPP---------------TTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKDELTLEG  232 (394)
T ss_dssp             HHHHHHTTCHHHHHHHHHHSCT---------------TCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC-------
T ss_pred             hHHhhCCCcHHHHHHHHHhCCC---------------CceEEEEEEecCHHHHHHHHHhcCCCeEEEecCccccCCC
Confidence            9999999999999999998876               7899999999999999999999999998887766544433

>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=4.4e-33  Score=258.43  Aligned_cols=209  Identities=34%  Similarity=0.490  Sum_probs=179.7

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ...+|++++|++.+.+.| .++||..|+|+|+++++.+++|+++++.+|||+|||++|++|++..+...      ..+.+
T Consensus        19 ~~~~f~~~~l~~~l~~~l-~~~g~~~~~~~Q~~~i~~i~~~~~~li~a~TGsGKT~~~~~~~~~~~~~~------~~~~~   91 (400)
T 1s2m_A           19 KGNTFEDFYLKRELLMGI-FEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK------LNKIQ   91 (400)
T ss_dssp             --CCGGGGCCCHHHHHHH-HHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT------SCSCC
T ss_pred             ccCChhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhcCCCEEEECCCCcHHHHHHHHHHHHHHhhc------cCCcc
Confidence            456899999999999999 67899999999999999999999999999999999999999999887542      23557


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      +||++|+++|+.|+++.++.++...+ ..+....|+.....+...+..+++|+|+||+++.+++.. ....+.+++++|+
T Consensus        92 ~lil~P~~~L~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~Ivv~T~~~l~~~~~~-~~~~~~~~~~vIi  169 (400)
T 1s2m_A           92 ALIMVPTRELALQTSQVVRTLGKHCG-ISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASR-KVADLSDCSLFIM  169 (400)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTTT-CCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHT-TCSCCTTCCEEEE
T ss_pred             EEEEcCCHHHHHHHHHHHHHHhcccC-ceEEEEeCCcchHHHHHHhcCCCCEEEEchHHHHHHHHh-CCcccccCCEEEE
Confidence            99999999999999999999876543 556667788887777777777899999999999998876 4455678999999


Q ss_pred             ecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          193 DEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       193 DEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                      ||||++.+.+|...+..++..++.               ..|++++|||++..+..+...++.+|..+.....
T Consensus       170 DEaH~~~~~~~~~~~~~i~~~~~~---------------~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~~  227 (400)
T 1s2m_A          170 DEADKMLSRDFKTIIEQILSFLPP---------------THQSLLFSATFPLTVKEFMVKHLHKPYEINLMEE  227 (400)
T ss_dssp             ESHHHHSSHHHHHHHHHHHTTSCS---------------SCEEEEEESCCCHHHHHHHHHHCSSCEEESCCSS
T ss_pred             eCchHhhhhchHHHHHHHHHhCCc---------------CceEEEEEecCCHHHHHHHHHHcCCCeEEEeccc
Confidence            999999988888888888877665               7899999999999999999999999988766543

>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=5.5e-32  Score=249.90  Aligned_cols=209  Identities=24%  Similarity=0.443  Sum_probs=174.4

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC--CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g--~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      .+|++++|++.+.+.| .++||..|+|+|.++++.++.+  +++++++|||+|||++|++|++..+...      ..+.+
T Consensus         5 ~~f~~~~l~~~l~~~l-~~~~~~~~~~~Q~~~i~~~~~~~~~~~lv~a~TGsGKT~~~~~~~~~~~~~~------~~~~~   77 (395)
T 3pey_A            5 KSFDELGLAPELLKGI-YAMKFQKPSKIQERALPLLLHNPPRNMIAQSQSGTGKTAAFSLTMLTRVNPE------DASPQ   77 (395)
T ss_dssp             CSSTTSCCCHHHHHHH-HHTTCCSCCHHHHHHHHHHHCSSCCCEEEECCTTSCHHHHHHHHHHHHCCTT------CCSCC
T ss_pred             cCHhhCCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHHcCCCCeEEEECCCCCcHHHHHHHHHHHHhccC------CCCcc
Confidence            6899999999999999 6789999999999999999988  8999999999999999999999887542      23567


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      +||++|+++|+.|+++.++.++.... .......++......    ..+++|+|+||+++.+++.. ....+.+++++|+
T Consensus        78 ~lil~P~~~L~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~----~~~~~iiv~T~~~l~~~~~~-~~~~~~~~~~iIi  151 (395)
T 3pey_A           78 AICLAPSRELARQTLEVVQEMGKFTK-ITSQLIVPDSFEKNK----QINAQVIVGTPGTVLDLMRR-KLMQLQKIKIFVL  151 (395)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTSC-CCEEEESTTSSCTTS----CBCCSEEEECHHHHHHHHHT-TCBCCTTCCEEEE
T ss_pred             EEEECCCHHHHHHHHHHHHHHhcccC-eeEEEEecCchhhhc----cCCCCEEEEcHHHHHHHHHc-CCcccccCCEEEE
Confidence            99999999999999999999876544 344444444332211    23579999999999998876 4556778999999


Q ss_pred             ecchhhhc-CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCCCCCCCC
Q 043110          193 DEADRILE-LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEKKFPEDK  271 (316)
Q Consensus       193 DEad~l~~-~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~~~~~~~  271 (316)
                      ||||++.+ .++...+..+...++.               ..|++++|||+++.+..+...++.+|..+...........
T Consensus       152 DEah~~~~~~~~~~~~~~~~~~~~~---------------~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  216 (395)
T 3pey_A          152 DEADNMLDQQGLGDQCIRVKRFLPK---------------DTQLVLFSATFADAVRQYAKKIVPNANTLELQTNEVNVDA  216 (395)
T ss_dssp             ETHHHHHHSTTHHHHHHHHHHTSCT---------------TCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGGGCSCTT
T ss_pred             EChhhhcCccccHHHHHHHHHhCCC---------------CcEEEEEEecCCHHHHHHHHHhCCCCeEEEcccccccccc
Confidence            99999998 6888888888888776               7899999999999999999999999998877665544433

>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=1.1e-31  Score=245.49  Aligned_cols=205  Identities=30%  Similarity=0.524  Sum_probs=176.4

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC-CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG-RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g-~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ..+|+++++++.+.+.| +++||..|+|+|+++++.+++| +++++.+|||+|||++|++|++..+..       ..+.+
T Consensus         5 ~~~f~~~~l~~~~~~~l-~~~g~~~~~~~Q~~~i~~~~~~~~~~l~~~~TGsGKT~~~~~~~~~~~~~-------~~~~~   76 (367)
T 1hv8_A            5 YMNFNELNLSDNILNAI-RNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE-------NNGIE   76 (367)
T ss_dssp             CCCGGGSSCCHHHHHHH-HHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS-------SSSCC
T ss_pred             cCchhhcCCCHHHHHHH-HHcCCCCCCHHHHHHHHHHhCCCCCEEEECCCCChHHHHHHHHHHHHhcc-------cCCCc
Confidence            45799999999999999 6679999999999999999988 699999999999999999999987754       23567


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      +||++|+++|+.|+++.+..+.... ........|+.....+...+. +++|+|+||+++.+.+.. ....+.+++++|+
T Consensus        77 ~lil~P~~~L~~q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~-~~~iiv~T~~~l~~~~~~-~~~~~~~~~~iIi  153 (367)
T 1hv8_A           77 AIILTPTRELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALK-NANIVVGTPGRILDHINR-GTLNLKNVKYFIL  153 (367)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHH-TCSEEEECHHHHHHHHHT-TCSCTTSCCEEEE
T ss_pred             EEEEcCCHHHHHHHHHHHHHHhCCC-CceEEEEECCcchHHHHhhcC-CCCEEEecHHHHHHHHHc-CCcccccCCEEEE
Confidence            9999999999999999999987653 345566777777766665554 689999999999998876 4455678999999


Q ss_pred             ecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCC
Q 043110          193 DEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDE  264 (316)
Q Consensus       193 DEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~  264 (316)
                      ||||++.++++...+..++..++.               ..+++++|||++..+..+...++.++..+....
T Consensus       154 DEah~~~~~~~~~~~~~~~~~~~~---------------~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~  210 (367)
T 1hv8_A          154 DEADEMLNMGFIKDVEKILNACNK---------------DKRILLFSATMPREILNLAKKYMGDYSFIKAKI  210 (367)
T ss_dssp             ETHHHHHTTTTHHHHHHHHHTSCS---------------SCEEEEECSSCCHHHHHHHHHHCCSEEEEECCS
T ss_pred             eCchHhhhhchHHHHHHHHHhCCC---------------CceEEEEeeccCHHHHHHHHHHcCCCeEEEecC
Confidence            999999999999999999887765               789999999999999999999999888776544

>2z0m_A 337AA long hypothetical ATP-dependent RNA helicase DEAD; ATP-binding, hydrolase, nucleotide-binding, RNA binding protein, structural genomics; 1.90A {Sulfolobus tokodaii}

Probab=99.98  E-value=1.4e-30  Score=235.55  Aligned_cols=190  Identities=32%  Similarity=0.484  Sum_probs=165.1

Q ss_pred             CCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           42 LDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        42 l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      |++++.+.| +++||..|+|+|+++++.+++|+++++.+|||+|||++|++|+++.            +.++||++|+++
T Consensus         1 l~~~i~~~l-~~~g~~~l~~~Q~~~i~~i~~~~~~lv~~~TGsGKT~~~~~~~~~~------------~~~~liv~P~~~   67 (337)
T 2z0m_A            1 MNEKIEQAI-REMGFKNFTEVQSKTIPLMLQGKNVVVRAKTGSGKTAAYAIPILEL------------GMKSLVVTPTRE   67 (337)
T ss_dssp             CCHHHHHHH-HHTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHH------------TCCEEEECSSHH
T ss_pred             CCHHHHHHH-HHcCCCCCCHHHHHHHHHHhcCCCEEEEcCCCCcHHHHHHHHHHhh------------cCCEEEEeCCHH
Confidence            578999999 7799999999999999999999999999999999999999998763            234999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcC
Q 043110          122 LCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL  201 (316)
Q Consensus       122 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~  201 (316)
                      |+.|+++.+++++...+ .......|+.....+...+. .++|+|+||+++.+++.. ....+.+++++|+||||++.++
T Consensus        68 L~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~-~~~i~v~T~~~l~~~~~~-~~~~~~~~~~iViDEah~~~~~  144 (337)
T 2z0m_A           68 LTRQVASHIRDIGRYMD-TKVAEVYGGMPYKAQINRVR-NADIVVATPGRLLDLWSK-GVIDLSSFEIVIIDEADLMFEM  144 (337)
T ss_dssp             HHHHHHHHHHHHTTTSC-CCEEEECTTSCHHHHHHHHT-TCSEEEECHHHHHHHHHT-TSCCGGGCSEEEEESHHHHHHT
T ss_pred             HHHHHHHHHHHHhhhcC-CcEEEEECCcchHHHHhhcC-CCCEEEECHHHHHHHHHc-CCcchhhCcEEEEEChHHhhcc
Confidence            99999999999876544 45566777777766665554 489999999999998876 4455678999999999999999


Q ss_pred             CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEc
Q 043110          202 GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGL  262 (316)
Q Consensus       202 ~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~  262 (316)
                      ++...+..++..++.               ..+++++|||+++.+......++.++..+..
T Consensus       145 ~~~~~~~~~~~~~~~---------------~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~  190 (337)
T 2z0m_A          145 GFIDDIKIILAQTSN---------------RKITGLFSATIPEEIRKVVKDFITNYEEIEA  190 (337)
T ss_dssp             TCHHHHHHHHHHCTT---------------CSEEEEEESCCCHHHHHHHHHHSCSCEEEEC
T ss_pred             ccHHHHHHHHhhCCc---------------ccEEEEEeCcCCHHHHHHHHHhcCCceeeec
Confidence            999999999988876               7899999999999999999999998887753

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.96  E-value=1.1e-29  Score=237.12  Aligned_cols=185  Identities=18%  Similarity=0.186  Sum_probs=144.9

Q ss_pred             HHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           44 STLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        44 ~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      +++.+.+.+.+|| +|+|+|.++++.+++|+|+++.+|||+|||++|++|++..+.         .+.++||++||++|+
T Consensus         8 ~~~~~~l~~~~~~-~~~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~l~~~~~~~~---------~~~~~lil~Pt~~L~   77 (414)
T 3oiy_A            8 EDFRSFFKKKFGK-DLTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR---------KGKKSALVFPTVTLV   77 (414)
T ss_dssp             HHHHHHHHHHHSS-CCCHHHHHHHHHHTTTCCEECCSCSSSSHHHHHHHHHHHHHT---------TTCCEEEEESSHHHH
T ss_pred             HHHHHHHHHhcCC-CCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHhc---------CCCEEEEEECCHHHH
Confidence            3566777677888 599999999999999999999999999999999999888762         256799999999999


Q ss_pred             HHHHHHHHHHHhhcCCceeEEeeCCCCh---HHHHHHHhcC-CcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhh
Q 043110          124 LLVYEILQKLLHRFRWIVPGYVMGGGNR---SKEKARLRKG-ISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       124 ~Q~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~l~~~-~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~  199 (316)
                      .|+++.++.++.  ....+..+.|+...   ..+...+..+ ++|+|+||+++.+++..   ..+.+++++|+||||++.
T Consensus        78 ~q~~~~~~~~~~--~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~---~~~~~~~~iViDEaH~~~  152 (414)
T 3oiy_A           78 KQTLERLQKLAD--EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK---LSQKRFDFVFVDDVDAVL  152 (414)
T ss_dssp             HHHHHHHHHHCC--SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH---HTTCCCSEEEESCHHHHH
T ss_pred             HHHHHHHHHHcc--CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH---hccccccEEEEeChHhhh
Confidence            999999999875  34667778888877   5555666665 99999999999887764   445689999999998665


Q ss_pred             ----------c-CCcHHH-HHHHHHHhccCcccccCCCCccccccceEEEEeee-cchhHH
Q 043110          200 ----------E-LGFGKE-IEEILDILGSRNIASIGEGNEVSNVKRQNLLLSAT-LNEKVN  247 (316)
Q Consensus       200 ----------~-~~~~~~-i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT-~~~~v~  247 (316)
                                + .+|... +..++..++...    ........+.+|++++||| .|..+.
T Consensus       153 ~~~~~~d~~l~~~~~~~~~~~~i~~~~~~~~----~~~~l~~~~~~~~i~~SAT~~~~~~~  209 (414)
T 3oiy_A          153 KASRNIDTLLMMVGIPEEIIRKAFSTIKQGK----IYERPKNLKPGILVVSSATAKPRGIR  209 (414)
T ss_dssp             HCHHHHHHHHHHTTCCHHHHHHHHHHHHHTC----CCCCCTTCCCCEEEESSCCSSCCSST
T ss_pred             hccchhhhHHhhcCCcHHHHHHHHHhcccch----hhhhcccCCCceEEEEecCCCcchhH
Confidence                      3 678888 888988886100    0000001137899999999 666554

>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch repair, nucleotide-binding, DNA-binding, polymorphism, nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens} PDB: 2wwy_A*

Probab=99.96  E-value=1.8e-28  Score=237.86  Aligned_cols=198  Identities=20%  Similarity=0.248  Sum_probs=153.6

Q ss_pred             cccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCC
Q 043110           30 EIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSS  109 (316)
Q Consensus        30 ~~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~  109 (316)
                      .....+.++++++++.+.+.|.+.|||..|+|+|.++|+.+++|+|+++.+|||+|||++|++|++..            
T Consensus        16 ~~~~~w~~~~~~l~~~l~~~L~~~fg~~~~rp~Q~~~i~~il~g~d~lv~~pTGsGKTl~~~lpal~~------------   83 (591)
T 2v1x_A           16 SSPAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCS------------   83 (591)
T ss_dssp             CCGGGGCCSCSTTHHHHHHHHHHTSCCCSCCTTHHHHHHHHHTTCCEEEECCTTSCTTHHHHHHHHTS------------
T ss_pred             cchhccccccCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEEECCCChHHHHHHHHHHHc------------
Confidence            34455667789999999999976799999999999999999999999999999999999999999752            


Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHH---H---hcCCcEEEeCcHHHH------HHHh
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKAR---L---RKGISILVATPGHLL------DHLK  177 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---l---~~~~~IlV~Tp~~l~------~~l~  177 (316)
                      ..++|||+|+++|+.|+.+.+..++     +....+.++.........   +   ...++|+|+||++|.      +.+.
T Consensus        84 ~g~~lVisP~~~L~~q~~~~l~~~g-----i~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~  158 (591)
T 2v1x_A           84 DGFTLVICPLISLMEDQLMVLKQLG-----ISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLE  158 (591)
T ss_dssp             SSEEEEECSCHHHHHHHHHHHHHHT-----CCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHH
T ss_pred             CCcEEEEeCHHHHHHHHHHHHHhcC-----CcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHH
Confidence            2369999999999999999998862     445566666665543322   2   346899999999874      2232


Q ss_pred             cCCccccCceeEEEEecchhhhcCC--cHHHHHH--HHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHh
Q 043110          178 HTSSFLHTNLRWIIFDEADRILELG--FGKEIEE--ILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKIS  253 (316)
Q Consensus       178 ~~~~~~~~~l~~lViDEad~l~~~~--~~~~i~~--i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~  253 (316)
                      .  ...+..++++||||||++.++|  |.+.+..  ++.....               ..|++++|||+++.+...+..+
T Consensus       159 ~--~~~~~~i~~iViDEAH~is~~g~dfr~~~~~l~~l~~~~~---------------~~~ii~lSAT~~~~v~~~i~~~  221 (591)
T 2v1x_A          159 K--AYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFP---------------NASLIGLTATATNHVLTDAQKI  221 (591)
T ss_dssp             H--HHHTTCEEEEEEETGGGGSTTCTTCCGGGGGGGHHHHHCT---------------TSEEEEEESSCCHHHHHHHHHH
T ss_pred             h--hhhccCCcEEEEECcccccccccccHHHHHHHHHHHHhCC---------------CCcEEEEecCCCHHHHHHHHHH
Confidence            2  2345689999999999999987  7776654  2322222               6899999999999988877766


Q ss_pred             cC--CCEEEE
Q 043110          254 LE--TPVLIG  261 (316)
Q Consensus       254 l~--~p~~i~  261 (316)
                      +.  ++..+.
T Consensus       222 l~~~~~~~~~  231 (591)
T 2v1x_A          222 LCIEKCFTFT  231 (591)
T ss_dssp             TTCCSCEEEE
T ss_pred             hCCCCcEEEe
Confidence            65  444443

>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=99.95  E-value=1e-27  Score=238.55  Aligned_cols=186  Identities=24%  Similarity=0.294  Sum_probs=154.5

Q ss_pred             CcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           36 CFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPV-ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        36 ~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~-il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      +|++++|++.+.+.+ +.+||..|+++|.++++. +.+|+++++++|||||||++|.+|+++.+...        +.+++
T Consensus         2 ~f~~l~l~~~~~~~l-~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--------~~~~l   72 (720)
T 2zj8_A            2 RVDELRVDERIKSTL-KERGIESFYPPQAEALKSGILEGKNALISIPTASGKTLIAEIAMVHRILTQ--------GGKAV   72 (720)
T ss_dssp             BGGGCCSCHHHHHHH-HHTTCCBCCHHHHHHHTTTGGGTCEEEEECCGGGCHHHHHHHHHHHHHHHH--------CSEEE
T ss_pred             cHhhcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCccHHHHHHHHHHHHHHHhC--------CCEEE
Confidence            599999999999999 668999999999999998 88999999999999999999999999888742        45799


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      |++|+++|+.|+++.++.+.. .+ ..+....|+......   ....++|+|+||+++..++.+ ....+++++++|+||
T Consensus        73 ~i~P~raLa~q~~~~~~~l~~-~g-~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~~~~-~~~~l~~~~~vIiDE  146 (720)
T 2zj8_A           73 YIVPLKALAEEKFQEFQDWEK-IG-LRVAMATGDYDSKDE---WLGKYDIIIATAEKFDSLLRH-GSSWIKDVKILVADE  146 (720)
T ss_dssp             EECSSGGGHHHHHHHTGGGGG-GT-CCEEEECSCSSCCCG---GGGGCSEEEECHHHHHHHHHH-TCTTGGGEEEEEEET
T ss_pred             EEcCcHHHHHHHHHHHHHHHh-cC-CEEEEecCCCCcccc---ccCCCCEEEECHHHHHHHHHc-ChhhhhcCCEEEEEC
Confidence            999999999999999865543 22 455566665443221   124689999999999998876 334467899999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHH
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKI  252 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~  252 (316)
                      ||++.+++++..++.++..++.               ..|++++|||+++ ...+...
T Consensus       147 ~H~l~~~~r~~~~~~ll~~l~~---------------~~~ii~lSATl~n-~~~~~~~  188 (720)
T 2zj8_A          147 IHLIGSRDRGATLEVILAHMLG---------------KAQIIGLSATIGN-PEELAEW  188 (720)
T ss_dssp             GGGGGCTTTHHHHHHHHHHHBT---------------TBEEEEEECCCSC-HHHHHHH
T ss_pred             CcccCCCcccHHHHHHHHHhhc---------------CCeEEEEcCCcCC-HHHHHHH
Confidence            9999998999999999999975               7899999999985 4555543

>3l9o_A ATP-dependent RNA helicase DOB1; REC-A fold, winged-helix-turn-helix, antiparallel-coiled-COI domain, ATP-binding, helicase, hydrolase; 3.39A {Saccharomyces cerevisiae}

Probab=99.95  E-value=8.6e-28  Score=247.10  Aligned_cols=194  Identities=23%  Similarity=0.183  Sum_probs=160.0

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      ..|+.+++++.+...+... ++..|+++|.++++.+..|+|++++||||||||++|.+|++..+..         +.++|
T Consensus       162 ~~~~~~~l~~~~~~~~~~~-~~f~ltp~Q~~AI~~i~~g~dvLV~ApTGSGKTlva~l~i~~~l~~---------g~rvl  231 (1108)
T 3l9o_A          162 PNYDYTPIAEHKRVNEART-YPFTLDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN---------KQRVI  231 (1108)
T ss_dssp             SCCCSSTTTTTCCCSCSSC-CSSCCCHHHHHHHHHHTTTCCEEEECCSSSHHHHHHHHHHHHHHHT---------TCEEE
T ss_pred             CCcccCCCChhhhHHHHHh-CCCCCCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHHhc---------CCeEE
Confidence            4677788888777777344 4446999999999999999999999999999999999999998854         56799


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      |++||++|+.|+++.+..++.     .++++.|+...       ..+++|+|+||++|.+++.. ....+.++++|||||
T Consensus       232 vl~PtraLa~Q~~~~l~~~~~-----~VglltGd~~~-------~~~~~IlV~Tpe~L~~~L~~-~~~~l~~l~lVVIDE  298 (1108)
T 3l9o_A          232 YTSPIKALSNQKYRELLAEFG-----DVGLMTGDITI-------NPDAGCLVMTTEILRSMLYR-GSEVMREVAWVIFDE  298 (1108)
T ss_dssp             EEESSHHHHHHHHHHHHHHTS-----SEEEECSSCBC-------CCSCSEEEEEHHHHHHHHHH-CSSHHHHEEEEEEET
T ss_pred             EEcCcHHHHHHHHHHHHHHhC-----CccEEeCcccc-------CCCCCEEEeChHHHHHHHHc-CccccccCCEEEEhh
Confidence            999999999999999988764     34455665542       34589999999999999987 344567899999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchh--HHHHHHHhcCCCEEEEcCCCC
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEK--VNHLTKISLETPVLIGLDEKK  266 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~--v~~~~~~~l~~p~~i~~~~~~  266 (316)
                      ||++.+++|+..+..++..++.               ..|++++|||+|..  +..+......+|+.+......
T Consensus       299 aH~l~d~~rg~~~e~ii~~l~~---------------~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~r  357 (1108)
T 3l9o_A          299 VHYMRDKERGVVWEETIILLPD---------------KVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNFR  357 (1108)
T ss_dssp             GGGTTSHHHHHHHHHHHHHSCT---------------TSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECCC
T ss_pred             hhhccccchHHHHHHHHHhcCC---------------CceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCCC
Confidence            9999999999999999999887               89999999999875  345666677778777655443

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.95  E-value=2.6e-27  Score=235.54  Aligned_cols=188  Identities=21%  Similarity=0.256  Sum_probs=153.9

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPV-ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~-il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ..+|++++|++.+.+.+ +++||..|+++|.++++. +.++++++++||||||||++|.+|+++.+...        +.+
T Consensus         7 ~~~~~~l~l~~~~~~~l-~~~g~~~l~~~Q~~~i~~~~~~~~~~lv~apTGsGKT~~~~l~il~~~~~~--------~~~   77 (715)
T 2va8_A            7 WMPIEDLKLPSNVIEII-KKRGIKKLNPPQTEAVKKGLLEGNRLLLTSPTGSGKTLIAEMGIISFLLKN--------GGK   77 (715)
T ss_dssp             CCBGGGSSSCHHHHHHH-HTTSCCBCCHHHHHHHHTTTTTTCCEEEECCTTSCHHHHHHHHHHHHHHHS--------CSE
T ss_pred             cCcHHHcCCCHHHHHHH-HhCCCCCCCHHHHHHHHHHhcCCCcEEEEcCCCCcHHHHHHHHHHHHHHHC--------CCe
Confidence            35799999999999999 678999999999999999 78899999999999999999999999887641        457


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      ++|++|+++|+.|+++.++.+.. .+ ..+....|+......  . ...++|+|+||+++..++.+ ....+++++++|+
T Consensus        78 il~i~P~r~La~q~~~~~~~~~~-~g-~~v~~~~G~~~~~~~--~-~~~~~Iiv~Tpe~l~~~~~~-~~~~l~~~~~vIi  151 (715)
T 2va8_A           78 AIYVTPLRALTNEKYLTFKDWEL-IG-FKVAMTSGDYDTDDA--W-LKNYDIIITTYEKLDSLWRH-RPEWLNEVNYFVL  151 (715)
T ss_dssp             EEEECSCHHHHHHHHHHHGGGGG-GT-CCEEECCSCSSSCCG--G-GGGCSEEEECHHHHHHHHHH-CCGGGGGEEEEEE
T ss_pred             EEEEeCcHHHHHHHHHHHHHhhc-CC-CEEEEEeCCCCCchh--h-cCCCCEEEEcHHHHHHHHhC-ChhHhhccCEEEE
Confidence            99999999999999998864432 22 455555565443222  1 23689999999999998887 3344679999999


Q ss_pred             ecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHh
Q 043110          193 DEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKIS  253 (316)
Q Consensus       193 DEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~  253 (316)
                      ||||.+.+.+++..++.++..++                ..|++++|||+++ ...+...+
T Consensus       152 DE~H~l~~~~~~~~l~~i~~~~~----------------~~~ii~lSATl~n-~~~~~~~l  195 (715)
T 2va8_A          152 DELHYLNDPERGPVVESVTIRAK----------------RRNLLALSATISN-YKQIAKWL  195 (715)
T ss_dssp             CSGGGGGCTTTHHHHHHHHHHHH----------------TSEEEEEESCCTT-HHHHHHHH
T ss_pred             echhhcCCcccchHHHHHHHhcc----------------cCcEEEEcCCCCC-HHHHHHHh
Confidence            99999998889999999998886                6799999999985 45555543

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=99.95  E-value=1.4e-27  Score=228.97  Aligned_cols=196  Identities=23%  Similarity=0.270  Sum_probs=147.8

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      .+|++++|++.+.+.|.+.+||..|+|+|.++|+.+++|+|+++.+|||+|||++|++|++..            ...+|
T Consensus         2 ~~fe~l~L~~~~~~~l~~~~g~~~~r~~Q~~~i~~il~g~d~lv~apTGsGKTl~~~lp~l~~------------~g~~l   69 (523)
T 1oyw_A            2 AQAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLL------------NGLTV   69 (523)
T ss_dssp             CCCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHS------------SSEEE
T ss_pred             CChhhCCCCHHHHHHHHHHhCCCCCCHHHHHHHHHHHcCCCEEEECCCCcHHHHHHHHHHHHh------------CCCEE
Confidence            479999999999999966699999999999999999999999999999999999999998742            23499


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHH---HH-HhcCCcEEEeCcHHHHHHHhcCCccccCceeEE
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK---AR-LRKGISILVATPGHLLDHLKHTSSFLHTNLRWI  190 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~-l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~l  190 (316)
                      |++|+++|+.|+.+.++.++     .....+.++.......   .. ....++|+|+||++|...... ..+...+++++
T Consensus        70 vi~P~~aL~~q~~~~l~~~g-----i~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~-~~l~~~~~~~v  143 (523)
T 1oyw_A           70 VVSPLISLMKDQVDQLQANG-----VAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFL-EHLAHWNPVLL  143 (523)
T ss_dssp             EECSCHHHHHHHHHHHHHTT-----CCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHH-HHHTTSCEEEE
T ss_pred             EECChHHHHHHHHHHHHHcC-----CcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHH-HHHhhCCCCEE
Confidence            99999999999999888742     3445555665544332   22 234589999999998532111 11223689999


Q ss_pred             EEecchhhhcCC--cHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHH-H-HhcCCCEEEE
Q 043110          191 IFDEADRILELG--FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLT-K-ISLETPVLIG  261 (316)
Q Consensus       191 ViDEad~l~~~~--~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~-~-~~l~~p~~i~  261 (316)
                      ||||||++.++|  |.+.+..+......             .+..+++++|||+++.+...+ + ..+.+|..+.
T Consensus       144 ViDEaH~i~~~g~~fr~~~~~l~~l~~~-------------~~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~  205 (523)
T 1oyw_A          144 AVDEAHCISQWGHDFRPEYAALGQLRQR-------------FPTLPFMALTATADDTTRQDIVRLLGLNDPLIQI  205 (523)
T ss_dssp             EESSGGGGCTTSSCCCHHHHGGGGHHHH-------------CTTSCEEEEESCCCHHHHHHHHHHHTCCSCEEEE
T ss_pred             EEeCccccCcCCCccHHHHHHHHHHHHh-------------CCCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEe
Confidence            999999999886  77766654332221             116799999999998876533 3 3456776554

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.95  E-value=5.4e-27  Score=241.14  Aligned_cols=185  Identities=18%  Similarity=0.177  Sum_probs=145.7

Q ss_pred             HHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           44 STLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        44 ~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      +.+.+.+...+||. |+|+|.+++|.++.|+|++++||||||||++|++|++..+.         .+.++||++||++||
T Consensus        65 ~~~~~~~~~~~gf~-pt~iQ~~ai~~il~g~dvlv~ApTGSGKTl~~l~~il~~~~---------~~~~~Lil~PtreLa  134 (1104)
T 4ddu_A           65 EDFRSFFKKKFGKD-LTGYQRLWAKRIVQGKSFTMVAPTGVGKTTFGMMTALWLAR---------KGKKSALVFPTVTLV  134 (1104)
T ss_dssp             HHHHHHHHHHSSSC-CCHHHHHHHHHHTTTCCEEECCSTTCCHHHHHHHHHHHHHT---------TTCCEEEEESSHHHH
T ss_pred             HHHHHHHHHhcCCC-CCHHHHHHHHHHHcCCCEEEEeCCCCcHHHHHHHHHHHHHh---------cCCeEEEEechHHHH
Confidence            34455665678995 99999999999999999999999999999999888887763         256799999999999


Q ss_pred             HHHHHHHHHHHhhcCCceeEEeeCCCCh---HHHHHHHhcC-CcEEEeCcHHHHHHHhcCCccccCceeEEEEecchh--
Q 043110          124 LLVYEILQKLLHRFRWIVPGYVMGGGNR---SKEKARLRKG-ISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADR--  197 (316)
Q Consensus       124 ~Q~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~l~~~-~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~--  197 (316)
                      .|+++.++.++  ...+.+..++||.+.   ..+...+..+ ++|+|+||++|.+++..   +.+.++++||+||||+  
T Consensus       135 ~Q~~~~l~~l~--~~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~---l~~~~l~~lViDEaH~l~  209 (1104)
T 4ddu_A          135 KQTLERLQKLA--DEKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK---LSQKRFDFVFVDDVDAVL  209 (1104)
T ss_dssp             HHHHHHHHTTS--CTTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH---HHTSCCSEEEESCHHHHT
T ss_pred             HHHHHHHHHhh--CCCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh---hcccCcCEEEEeCCCccc
Confidence            99999999966  234677788888877   6667777776 99999999999888763   4557899999999965  


Q ss_pred             --------hhc-CCcHHH-HHHHHHHhccCcccccCCCCccccccceEEEEeee-cchhHH
Q 043110          198 --------ILE-LGFGKE-IEEILDILGSRNIASIGEGNEVSNVKRQNLLLSAT-LNEKVN  247 (316)
Q Consensus       198 --------l~~-~~~~~~-i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT-~~~~v~  247 (316)
                              +++ +||... +..+++.++..    ...........+|+++|||| .|..+.
T Consensus       210 ~~~r~~Dr~L~~~gf~~~~i~~il~~l~~~----~~~~~~~~~~~~q~ll~SAT~~p~~~~  266 (1104)
T 4ddu_A          210 KASRNIDTLLMMVGIPEEIIRKAFSTIKQG----KIYERPKNLKPGILVVSSATAKPRGIR  266 (1104)
T ss_dssp             TSSHHHHHHHHTSSCCHHHHHHHHHHHHHT----SCCCCCSSCCCCEEEEECBSSCCCSST
T ss_pred             cccccchhhhHhcCCCHHHHHHHHHhcccc----hhhhhhccCCCceEEEEcCCCCcHHHH
Confidence                    455 888888 89999988710    00000011137899999999 666655

>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=99.94  E-value=1.1e-27  Score=237.84  Aligned_cols=188  Identities=21%  Similarity=0.227  Sum_probs=149.6

Q ss_pred             CcccCC--CCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           36 CFSSLG--LDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        36 ~f~~~~--l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      +|++++  |++.+.+.+ +++||.+|+|+|.++++.+.+|+++++++|||||||++|.+|+++.+..         +.++
T Consensus         2 ~f~~l~~~l~~~~~~~l-~~~g~~~l~~~Q~~~i~~i~~~~~~lv~apTGsGKT~~~~l~il~~~~~---------~~~~   71 (702)
T 2p6r_A            2 KVEELAESISSYAVGIL-KEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK---------GGKS   71 (702)
T ss_dssp             CSHHHHHHHHHHHHHHH-HCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT---------TCCE
T ss_pred             chhhhhhccCHHHHHHH-HhCCCCCCCHHHHHHHHHHhCCCcEEEEcCCccHHHHHHHHHHHHHHHh---------CCcE
Confidence            588888  999999999 6789999999999999999999999999999999999999999988764         3469


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      +|++|+++|+.|+++.++.+.. . ...+....|+......   ....++|+|+||+++..++.+. ...+++++++|+|
T Consensus        72 l~i~P~r~La~q~~~~~~~~~~-~-g~~v~~~~G~~~~~~~---~~~~~~Iiv~Tpe~l~~~l~~~-~~~l~~~~~vIiD  145 (702)
T 2p6r_A           72 LYVVPLRALAGEKYESFKKWEK-I-GLRIGISTGDYESRDE---HLGDCDIIVTTSEKADSLIRNR-ASWIKAVSCLVVD  145 (702)
T ss_dssp             EEEESSHHHHHHHHHHHTTTTT-T-TCCEEEECSSCBCCSS---CSTTCSEEEEEHHHHHHHHHTT-CSGGGGCCEEEET
T ss_pred             EEEeCcHHHHHHHHHHHHHHHh-c-CCEEEEEeCCCCcchh---hccCCCEEEECHHHHHHHHHcC-hhHHhhcCEEEEe
Confidence            9999999999999998864432 2 2455555555433221   1236899999999999988873 3446789999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHH
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKI  252 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~  252 (316)
                      |||.+.+++++..++.++..+...            .+..|++++|||+++ ...++..
T Consensus       146 E~H~l~~~~r~~~~~~ll~~l~~~------------~~~~~ii~lSATl~n-~~~~~~~  191 (702)
T 2p6r_A          146 EIHLLDSEKRGATLEILVTKMRRM------------NKALRVIGLSATAPN-VTEIAEW  191 (702)
T ss_dssp             TGGGGGCTTTHHHHHHHHHHHHHH------------CTTCEEEEEECCCTT-HHHHHHH
T ss_pred             eeeecCCCCcccHHHHHHHHHHhc------------CcCceEEEECCCcCC-HHHHHHH
Confidence            999999988999999998887521            127899999999985 5556553

>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=99.94  E-value=3.3e-27  Score=242.46  Aligned_cols=196  Identities=21%  Similarity=0.274  Sum_probs=151.5

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH
Q 043110           46 LCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL  125 (316)
Q Consensus        46 l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q  125 (316)
                      +.+.+.+.+||. | ++|.++||.++.|+|++++||||||||+ |.+|++..+..        .++++||++||++||.|
T Consensus        46 ~~~~~~~~~g~~-p-~iQ~~ai~~il~g~dvlv~apTGSGKTl-~~lp~l~~~~~--------~~~~~lil~PtreLa~Q  114 (1054)
T 1gku_B           46 FVEFFRKCVGEP-R-AIQKMWAKRILRKESFAATAPTGVGKTS-FGLAMSLFLAL--------KGKRCYVIFPTSLLVIQ  114 (1054)
T ss_dssp             HHHHHHTTTCSC-C-HHHHHHHHHHHTTCCEECCCCBTSCSHH-HHHHHHHHHHT--------TSCCEEEEESCHHHHHH
T ss_pred             HHHHHHHhcCCC-H-HHHHHHHHHHHhCCCEEEEcCCCCCHHH-HHHHHHHHHhh--------cCCeEEEEeccHHHHHH
Confidence            446676779999 9 9999999999999999999999999998 88999888764        25679999999999999


Q ss_pred             HHHHHHHHHhhcCC---ceeEEeeCCCChHHH---HHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhh
Q 043110          126 VYEILQKLLHRFRW---IVPGYVMGGGNRSKE---KARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       126 ~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~---~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~  199 (316)
                      +++.++.++...+.   ..+..++|+.....+   ...+.. ++|+|+||++|.+++.+     +.+++++|+||||+++
T Consensus       115 ~~~~l~~l~~~~~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~-----L~~l~~lViDEah~~l  188 (1054)
T 1gku_B          115 AAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE-----LGHFDFIFVDDVDAIL  188 (1054)
T ss_dssp             HHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT-----SCCCSEEEESCHHHHH
T ss_pred             HHHHHHHHHhhcCCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH-----hccCCEEEEeChhhhh
Confidence            99999999876542   156777788776553   344445 89999999999997764     5689999999999999


Q ss_pred             cCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          200 ELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       200 ~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                      +  ++..++.++..++....    .........+|++++|||++.. ..+...++.+|..+.+...
T Consensus       189 ~--~~~~~~~i~~~lgf~~~----~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~~~  247 (1054)
T 1gku_B          189 K--ASKNVDKLLHLLGFHYD----LKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIGSS  247 (1054)
T ss_dssp             T--STHHHHHHHHHTTEEEE----TTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCSCC
T ss_pred             h--ccccHHHHHHHhCcchh----hhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEccCc
Confidence            8  67889999988753100    0012223478999999999987 6455555555554444433

>4a2p_A RIG-I, retinoic acid inducible protein I; hydrolase, superfamily 2 RNA helicase, ATP and dsRNA binding antiviral signalling pathway; 3.00A {Anas platyrhynchos} PDB: 4a36_A*

Probab=99.94  E-value=8.9e-26  Score=217.64  Aligned_cols=173  Identities=16%  Similarity=0.165  Sum_probs=129.3

Q ss_pred             CCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           55 GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      +.-+|+|+|.++++.++.|+|+++.+|||+|||++|++|+++.+.....    ..+.++||++||++|+.|+++.++.++
T Consensus         4 ~~~~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~----~~~~~~lil~P~~~L~~q~~~~~~~~~   79 (556)
T 4a2p_A            4 ETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA----GRKAKVVFLATKVPVYEQQKNVFKHHF   79 (556)
T ss_dssp             ----CCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS----SCCCCEEEECSSHHHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHcCCCEEEEcCCCChHHHHHHHHHHHHHHhCcc----cCCCeEEEEeCCHHHHHHHHHHHHHHh
Confidence            4457999999999999999999999999999999999999998876321    225679999999999999999999998


Q ss_pred             hhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHH-HHHHHH
Q 043110          135 HRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEI-EEILDI  213 (316)
Q Consensus       135 ~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i-~~i~~~  213 (316)
                      ...+ ..+..+.|+.........+..+++|+|+||++|.+++.......+.+++++|+||||++.++++...+ ...+..
T Consensus        80 ~~~~-~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~  158 (556)
T 4a2p_A           80 ERQG-YSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYLEQ  158 (556)
T ss_dssp             GGGT-CCEEECCCC-----CHHHHHHHCSEEEECHHHHHHHHHSSSCCCSTTCSEEEEETGGGCSTTSHHHHHHHHHHHH
T ss_pred             cccC-ceEEEEeCCCCcchhHHHhhCCCCEEEECHHHHHHHHHhCcccccccCCEEEEECCcccCCcchHHHHHHHHHHh
Confidence            7653 55666777776666666666778999999999999998744336788999999999999987643333 122221


Q ss_pred             hccCcccccCCCCccccccceEEEEeeecc
Q 043110          214 LGSRNIASIGEGNEVSNVKRQNLLLSATLN  243 (316)
Q Consensus       214 l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~  243 (316)
                      ...           ...+..|++++|||++
T Consensus       159 ~~~-----------~~~~~~~~l~lSAT~~  177 (556)
T 4a2p_A          159 KFN-----------SASQLPQILGLTASVG  177 (556)
T ss_dssp             HHC-----------C---CCEEEEEESCCC
T ss_pred             hhc-----------ccCCCCeEEEEeCCcc
Confidence            110           0123689999999995

>1tf5_A Preprotein translocase SECA subunit; ATPase, helicase, translocation, secretion, protein transport; 2.18A {Bacillus subtilis} SCOP: a.162.1.1 a.172.1.1 c.37.1.19 c.37.1.19 PDB: 1tf2_A 3iqy_A 1m6n_A 1m74_A* 3iqm_A 3jv2_A* 2ibm_A* 3dl8_A 1sx0_A 1sx1_A 1tm6_A

Probab=99.94  E-value=5.8e-26  Score=222.65  Aligned_cols=172  Identities=19%  Similarity=0.235  Sum_probs=135.8

Q ss_pred             HcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           53 RLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        53 ~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      .+|| +|+|+|..++|.++.|+  +++++||+|||++|.+|++.....         |..++||+||++||.|+++++..
T Consensus        79 ~lG~-~pt~VQ~~~ip~ll~G~--Iaea~TGeGKTlaf~LP~~l~aL~---------g~~vlVltptreLA~qd~e~~~~  146 (844)
T 1tf5_A           79 VTGM-FPFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT---------GKGVHVVTVNEYLASRDAEQMGK  146 (844)
T ss_dssp             HHSC-CCCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT---------SSCEEEEESSHHHHHHHHHHHHH
T ss_pred             HcCC-CCcHHHHHhhHHHhCCC--EEEccCCcHHHHHHHHHHHHHHHc---------CCCEEEEeCCHHHHHHHHHHHHH
Confidence            5799 89999999999999999  999999999999999999854432         34599999999999999999999


Q ss_pred             HHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcC-----CccccCceeEEEEecchhhh-cCC---
Q 043110          133 LLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHT-----SSFLHTNLRWIIFDEADRIL-ELG---  202 (316)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~-----~~~~~~~l~~lViDEad~l~-~~~---  202 (316)
                      +...++ +.+.+++||.+....  ....+++|+||||++| ++++...     ....++.+.++|+||||+|+ |.+   
T Consensus       147 l~~~lg-l~v~~i~gg~~~~~r--~~~~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~lr~~~~lVlDEaD~mLiDea~tp  223 (844)
T 1tf5_A          147 IFEFLG-LTVGLNLNSMSKDEK--REAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTP  223 (844)
T ss_dssp             HHHHTT-CCEEECCTTSCHHHH--HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHHTTTTTCE
T ss_pred             HHhhcC-CeEEEEeCCCCHHHH--HHhcCCCEEEECchhhhHHHHHHhhhcchhhhcccCCCEEEECchhhhhhhccccc
Confidence            998765 677788888775433  3334689999999999 6766542     23456789999999999998 764   


Q ss_pred             ------------cHHHHHHHHHHhccCcccccCCCCccccccceEE-----------------EEeeecchh
Q 043110          203 ------------FGKEIEEILDILGSRNIASIGEGNEVSNVKRQNL-----------------LLSATLNEK  245 (316)
Q Consensus       203 ------------~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i-----------------~~SAT~~~~  245 (316)
                                  |...+..|+..++..      ..-......+|++                 +||||++.-
T Consensus       224 lIisg~~~~~~~~~~~i~~iv~~l~~~------~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~Lfsat~~~~  289 (844)
T 1tf5_A          224 LIISGQAAKSTKLYVQANAFVRTLKAE------KDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVAL  289 (844)
T ss_dssp             EEEEEEEECCCHHHHHHHHHHTTCCSS------SSBCCCSSSCCCCBCHHHHHHHHHHTTCSCTTSGGGHHH
T ss_pred             hhhcCCcccchhHHHHHHHHHHhCccc------ccceeccccceEEecHHHHHHHHHHhCccccCCCccchh
Confidence                        667888888887631      0011122367777                 899998753

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.93  E-value=2.1e-25  Score=221.06  Aligned_cols=180  Identities=17%  Similarity=0.184  Sum_probs=134.2

Q ss_pred             HHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHH
Q 043110           48 DQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY  127 (316)
Q Consensus        48 ~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~  127 (316)
                      ..+ +.+||..|+++|.++++.++.|+|+++++|||+|||++|++|+++.+.....    ..+.++||++||++|+.|+.
T Consensus         4 ~~l-~~~g~~~lr~~Q~~~i~~~l~g~~~iv~~~TGsGKTl~~~~~i~~~l~~~~~----~~~~~~lvl~Pt~~L~~Q~~   78 (696)
T 2ykg_A            4 SDT-NLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQ----GQKGKVVFFANQIPVYEQNK   78 (696)
T ss_dssp             ----CTTC--CCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHHSCT----TCCCCEEEECSSHHHHHHHH
T ss_pred             Ccc-cccCCCCccHHHHHHHHHHHcCCCEEEEcCCCchHHHHHHHHHHHHHHhCcc----CCCCeEEEEECCHHHHHHHH
Confidence            455 6789999999999999999999999999999999999999999998866321    12357999999999999999


Q ss_pred             HHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCC-cHHH
Q 043110          128 EILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELG-FGKE  206 (316)
Q Consensus       128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~-~~~~  206 (316)
                      +.+++++...+ ..+..+.|+.....+...+..+++|+|+||++|.+.+.......+.+++++|+||||++.+.. +...
T Consensus        79 ~~~~~~~~~~~-~~v~~~~g~~~~~~~~~~~~~~~~Iiv~Tp~~L~~~l~~~~~~~l~~~~~vViDEaH~~~~~~~~~~i  157 (696)
T 2ykg_A           79 SVFSKYFERHG-YRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMI  157 (696)
T ss_dssp             HHHHHHTTTTT-CCEEEECSSSCSSSCHHHHHHTCSEEEECHHHHHHHHHTTSSCCGGGCSEEEEETGGGCSTTCHHHHH
T ss_pred             HHHHHHhccCC-ceEEEEeCCccccccHHHhccCCCEEEECHHHHHHHHhcCcccccccccEEEEeCCCcccCcccHHHH
Confidence            99999875433 556667777655555555566799999999999999986433357789999999999988654 2222


Q ss_pred             HHHHHHHhccCcccccCCCCccccccceEEEEeeecc
Q 043110          207 IEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLN  243 (316)
Q Consensus       207 i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~  243 (316)
                      +...+...-.          ....+..+++++|||+.
T Consensus       158 ~~~~l~~~~~----------~~~~~~~~il~LTATp~  184 (696)
T 2ykg_A          158 MFNYLDQKLG----------GSSGPLPQVIGLTASVG  184 (696)
T ss_dssp             HHHHHHHHHT----------TCCSCCCEEEEEESCCC
T ss_pred             HHHHHHHhhc----------ccCCCCCeEEEEeCccc
Confidence            2222222100          11123689999999986

>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=99.93  E-value=5e-26  Score=193.12  Aligned_cols=180  Identities=19%  Similarity=0.161  Sum_probs=118.2

Q ss_pred             cCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH-HHHHHHH
Q 043110           54 LGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL-VYEILQK  132 (316)
Q Consensus        54 ~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q-~~~~~~~  132 (316)
                      .+...|+++|.++++.++.++++++.+|||+|||++|+++++..+.....   ...+.++||++|+++|+.| +.+.+..
T Consensus        29 ~~~~~l~~~Q~~~i~~~~~~~~~li~~~tGsGKT~~~~~~~~~~~~~~~~---~~~~~~~lil~p~~~L~~q~~~~~~~~  105 (216)
T 3b6e_A           29 EPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKK---ASEPGKVIVLVNKVLLVEQLFRKEFQP  105 (216)
T ss_dssp             SCCCCCCHHHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHHHHHHHH---TTCCCCEEEEESSHHHHHHHHHHTHHH
T ss_pred             cCCCCchHHHHHHHHHHhcCCCEEEEcCCCCCHHHHHHHHHHHHHhhccc---ccCCCcEEEEECHHHHHHHHHHHHHHH
Confidence            34457999999999999999999999999999999999999887755321   1235569999999999999 7778888


Q ss_pred             HHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCc-----cccCceeEEEEecchhhhcCCcHHHH
Q 043110          133 LLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSS-----FLHTNLRWIIFDEADRILELGFGKEI  207 (316)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~-----~~~~~l~~lViDEad~l~~~~~~~~i  207 (316)
                      +...  ...+....|+.........+..+++|+|+||+++...+.....     ..+.+++++|+||||++.+.++...+
T Consensus       106 ~~~~--~~~v~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~~~~~~iIiDEah~~~~~~~~~~~  183 (216)
T 3b6e_A          106 FLKK--WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNI  183 (216)
T ss_dssp             HHTT--TSCEEECCC---CCCCHHHHHHHCSEEEEEHHHHHHHHHC-------CCCGGGCSEEEETTC-------CHHHH
T ss_pred             Hhcc--CceEEEEeCCcccchhHHhhccCCCEEEECHHHHHHHHhccCcccccccchhcccEEEEECchhhccCCcHHHH
Confidence            7654  2444555555544333334445689999999999998876432     45678999999999999877655544


Q ss_pred             -HHHHHHh-ccCcccccCCCCccccccceEEEEeee
Q 043110          208 -EEILDIL-GSRNIASIGEGNEVSNVKRQNLLLSAT  241 (316)
Q Consensus       208 -~~i~~~l-~~~~~~~~~~~~~~~~~~~q~i~~SAT  241 (316)
                       ..++... +....   ........+..+++++|||
T Consensus       184 ~~~~~~~~~~~~~~---~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          184 MRHYLMQKLKNNRL---KKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             HHHHHHHHHHHHHH---HHTTCCCCCCCEEEEEECC
T ss_pred             HHHHHHHhcccccc---cccccCCCCcceEEEeecC
Confidence             2322221 10000   0000111237899999998

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.93  E-value=2.9e-25  Score=226.51  Aligned_cols=176  Identities=26%  Similarity=0.255  Sum_probs=144.6

Q ss_pred             HHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH
Q 043110           52 ERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ  131 (316)
Q Consensus        52 ~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~  131 (316)
                      ..++|. |+++|.++++.+..|+++++++|||+|||++|.+|++..+..         +.++||++|+++|+.|+++.+.
T Consensus        81 ~~~~f~-L~~~Q~eai~~l~~g~~vLV~apTGSGKTlva~lai~~~l~~---------g~rvL~l~PtkaLa~Q~~~~l~  150 (1010)
T 2xgj_A           81 RTYPFT-LDPFQDTAISCIDRGESVLVSAHTSAGKTVVAEYAIAQSLKN---------KQRVIYTSPIKALSNQKYRELL  150 (1010)
T ss_dssp             CCCSSC-CCHHHHHHHHHHHHTCEEEEECCTTSCHHHHHHHHHHHHHHT---------TCEEEEEESSHHHHHHHHHHHH
T ss_pred             HhCCCC-CCHHHHHHHHHHHcCCCEEEECCCCCChHHHHHHHHHHHhcc---------CCeEEEECChHHHHHHHHHHHH
Confidence            567887 999999999999999999999999999999999999888753         5679999999999999999998


Q ss_pred             HHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHH
Q 043110          132 KLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEIL  211 (316)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~  211 (316)
                      .++.     .++.+.|+....       ..++|+|+||++|.+++.+ ....+.+++++||||||++.+++++..++.++
T Consensus       151 ~~~~-----~vglltGd~~~~-------~~~~IvV~Tpe~L~~~L~~-~~~~l~~l~lVViDEaH~l~d~~rg~~~e~il  217 (1010)
T 2xgj_A          151 AEFG-----DVGLMTGDITIN-------PDAGCLVMTTEILRSMLYR-GSEVMREVAWVIFDEVHYMRDKERGVVWEETI  217 (1010)
T ss_dssp             HHHS-----CEEEECSSCEEC-------TTCSEEEEEHHHHHHHHHH-TCTTGGGEEEEEEETGGGGGCTTTHHHHHHHH
T ss_pred             HHhC-----CEEEEeCCCccC-------CCCCEEEEcHHHHHHHHHc-CcchhhcCCEEEEechhhhcccchhHHHHHHH
Confidence            8764     344555655432       3578999999999998876 44556799999999999999999999999999


Q ss_pred             HHhccCcccccCCCCccccccceEEEEeeecchhHH--HHHHHhcCCCEEEEcCCC
Q 043110          212 DILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVN--HLTKISLETPVLIGLDEK  265 (316)
Q Consensus       212 ~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~--~~~~~~l~~p~~i~~~~~  265 (316)
                      ..++.               ..|++++|||+++...  .........|+.+...+.
T Consensus       218 ~~l~~---------------~~~il~LSATi~n~~e~a~~l~~~~~~~~~vi~~~~  258 (1010)
T 2xgj_A          218 ILLPD---------------KVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNF  258 (1010)
T ss_dssp             HHSCT---------------TCEEEEEECCCTTHHHHHHHHHHHHTSCEEEEEECC
T ss_pred             HhcCC---------------CCeEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCC
Confidence            98876               8999999999986533  233334466776665543

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.93  E-value=1.5e-25  Score=215.72  Aligned_cols=172  Identities=17%  Similarity=0.187  Sum_probs=134.5

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      +|+|+|.++++.++.|+|+++.+|||+|||++|++|+++.+.....    ..+.++||++||++|+.|+++.++.++...
T Consensus         4 ~~~~~Q~~~i~~~~~~~~~l~~~~tGsGKT~~~~~~~~~~~~~~~~----~~~~~~lil~P~~~L~~q~~~~~~~~~~~~   79 (555)
T 3tbk_A            4 KPRNYQLELALPAKKGKNTIICAPTGCGKTFVSLLICEHHLKKFPC----GQKGKVVFFANQIPVYEQQATVFSRYFERL   79 (555)
T ss_dssp             CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS----SCCCCEEEECSSHHHHHHHHHHHHHHHHTT
T ss_pred             CCcHHHHHHHHHHhCCCCEEEEeCCCChHHHHHHHHHHHHHHhccc----CCCCEEEEEeCCHHHHHHHHHHHHHHhccC
Confidence            5999999999999999999999999999999999999998876321    235679999999999999999999998765


Q ss_pred             CCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCc-HHHHHHHHHHhcc
Q 043110          138 RWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGF-GKEIEEILDILGS  216 (316)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~-~~~i~~i~~~l~~  216 (316)
                      + ..+..+.|+.....+...+..+++|+|+||++|..++.......+.+++++|+||||++.+.+. ...+...+.....
T Consensus        80 ~-~~~~~~~g~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~vViDEah~~~~~~~~~~~~~~~~~~~~~  158 (555)
T 3tbk_A           80 G-YNIASISGATSDSVSVQHIIEDNDIIILTPQILVNNLNNGAIPSLSVFTLMIFDECHNTSKNHPYNQIMFRYLDHKLG  158 (555)
T ss_dssp             T-CCEEEECTTTGGGSCHHHHHHHCSEEEECHHHHHHHHHTSSSCCGGGCSEEEETTGGGCSTTCHHHHHHHHHHHHHTS
T ss_pred             C-cEEEEEcCCCcchhhHHHHhcCCCEEEECHHHHHHHHhcCcccccccCCEEEEECccccCCcchHHHHHHHHHHhhhc
Confidence            3 5666777777665555566667899999999999999874443677899999999999988653 2222233322211


Q ss_pred             CcccccCCCCccccccceEEEEeeecch
Q 043110          217 RNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       217 ~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                                ....+..|++++|||++.
T Consensus       159 ----------~~~~~~~~~l~lSAT~~~  176 (555)
T 3tbk_A          159 ----------ESRDPLPQVVGLTASVGV  176 (555)
T ss_dssp             ----------SCCSCCCEEEEEESCCCC
T ss_pred             ----------cccCCCCeEEEEecCccc
Confidence                      112236899999999954

>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=99.93  E-value=7.9e-25  Score=220.03  Aligned_cols=175  Identities=16%  Similarity=0.159  Sum_probs=131.1

Q ss_pred             HcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           53 RLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        53 ~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      .+|+..|+|+|.++++.++.|+|+++.+|||+|||++|++|+++.+.....    ..+.++|||+||++|+.|+++.++.
T Consensus       243 ~~g~~~l~~~Q~~~i~~~l~~~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~----~~~~~~Lvl~Pt~~L~~Q~~~~~~~  318 (797)
T 4a2q_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMPA----GRKAKVVFLATKVPVYEQQKNVFKH  318 (797)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHHHTCCS----SCCCCEEEECSSHHHHHHHHHHHHH
T ss_pred             hcCCCCCCHHHHHHHHHHHhCCCEEEEeCCCChHHHHHHHHHHHHHHhccc----cCCCeEEEEeCCHHHHHHHHHHHHH
Confidence            467889999999999999999999999999999999999999999876321    2356799999999999999999999


Q ss_pred             HHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHH-HHHHH
Q 043110          133 LLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKE-IEEIL  211 (316)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~-i~~i~  211 (316)
                      ++...+ ..+..++|+.........+..+++|+|+||++|.+++.......+.+++++|+||||++.+.+.... +..++
T Consensus       319 ~~~~~~-~~v~~~~g~~~~~~~~~~~~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~iViDEaH~~~~~~~~~~i~~~~~  397 (797)
T 4a2q_A          319 HFERQG-YSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYL  397 (797)
T ss_dssp             HHGGGT-CCEEEECCC-----CHHHHHHTCSEEEECHHHHHHHHHSSSCCCGGGCSEEEETTGGGCSTTSHHHHHHHHHH
T ss_pred             hcccCC-ceEEEEeCCcchhhhHHHhhCCCCEEEEchHHHHHHHHhccccccccCCEEEEECccccCCCccHHHHHHHHH
Confidence            987553 5667777887766666677778999999999999999864333678899999999999987653222 22222


Q ss_pred             HHhccCcccccCCCCccccccceEEEEeeecc
Q 043110          212 DILGSRNIASIGEGNEVSNVKRQNLLLSATLN  243 (316)
Q Consensus       212 ~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~  243 (316)
                      .....           ...+..|++++|||++
T Consensus       398 ~~~~~-----------~~~~~~~~l~lSATp~  418 (797)
T 4a2q_A          398 EQKFN-----------SASQLPQILGLTASVG  418 (797)
T ss_dssp             HHHHT-----------TCCCCCEEEEEESCCC
T ss_pred             HHhhc-----------cCCCCCeEEEEcCCcc
Confidence            22110           0123689999999985

>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=99.93  E-value=2.5e-25  Score=236.39  Aligned_cols=192  Identities=18%  Similarity=0.149  Sum_probs=142.6

Q ss_pred             CCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhC-CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCC
Q 043110           41 GLDSTLCDQLRERLGFEAPTKVQAQAIPVILS-GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPT  119 (316)
Q Consensus        41 ~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~-g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt  119 (316)
                      .|.....+.+ ...+|..++|+|.++++.++. ++|++++||||||||++|.+|+++.+.+.       .+.++||++|+
T Consensus       910 ~L~~~~~e~l-~~~~f~~fnpiQ~q~~~~l~~~~~nvlv~APTGSGKTliaelail~~l~~~-------~~~kavyi~P~  981 (1724)
T 4f92_B          910 ALRNSAFESL-YQDKFPFFNPIQTQVFNTVYNSDDNVFVGAPTGSGKTICAEFAILRMLLQS-------SEGRCVYITPM  981 (1724)
T ss_dssp             GSCCHHHHTT-TTTTCSBCCHHHHHHHHHHHSCCSCEEEECCTTSCCHHHHHHHHHHHHHHC-------TTCCEEEECSC
T ss_pred             cccCHHHHHH-HHhcCCCCCHHHHHHHHHHhcCCCcEEEEeCCCCCchHHHHHHHHHHHHhC-------CCCEEEEEcCh
Confidence            3555566666 345899999999999999975 56799999999999999999999998762       34569999999


Q ss_pred             hHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCc-cccCceeEEEEecchhh
Q 043110          120 SELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSS-FLHTNLRWIIFDEADRI  198 (316)
Q Consensus       120 ~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~-~~~~~l~~lViDEad~l  198 (316)
                      ++||.|+++.+++.........+....|+....  . ....+++|+|+|||++..++++... ..+.+++++|+||+|.+
T Consensus       982 raLa~q~~~~~~~~f~~~~g~~V~~ltGd~~~~--~-~~~~~~~IiV~TPEkld~llr~~~~~~~l~~v~lvViDE~H~l 1058 (1724)
T 4f92_B          982 EALAEQVYMDWYEKFQDRLNKKVVLLTGETSTD--L-KLLGKGNIIISTPEKWDILSRRWKQRKNVQNINLFVVDEVHLI 1058 (1724)
T ss_dssp             HHHHHHHHHHHHHHHTTTSCCCEEECCSCHHHH--H-HHHHHCSEEEECHHHHHHHHTTTTTCHHHHSCSEEEECCGGGG
T ss_pred             HHHHHHHHHHHHHHhchhcCCEEEEEECCCCcc--h-hhcCCCCEEEECHHHHHHHHhCcccccccceeeEEEeechhhc
Confidence            999999999987755432234555555543322  2 2234579999999999887765433 24678999999999988


Q ss_pred             hcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHh
Q 043110          199 LELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKIS  253 (316)
Q Consensus       199 ~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~  253 (316)
                      .+ .++..++.++.++...        ......+.|+|++|||+++ ..+++++.
T Consensus      1059 ~d-~rg~~le~il~rl~~i--------~~~~~~~~riI~lSATl~N-~~dla~WL 1103 (1724)
T 4f92_B         1059 GG-ENGPVLEVICSRMRYI--------SSQIERPIRIVALSSSLSN-AKDVAHWL 1103 (1724)
T ss_dssp             GS-TTHHHHHHHHHHHHHH--------HHTTSSCCEEEEEESCBTT-HHHHHHHH
T ss_pred             CC-CCCccHHHHHHHHHHH--------HhhcCCCceEEEEeCCCCC-HHHHHHHh
Confidence            76 4778888777766421        0112337899999999984 56666644

>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=99.93  E-value=4e-25  Score=190.79  Aligned_cols=185  Identities=21%  Similarity=0.222  Sum_probs=131.8

Q ss_pred             CCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           42 LDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        42 l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      .++.+.+.+..+ +.-.++++|.++++.+..|+++++.||||||||.++.+++++.......    ..+.++++++|+++
T Consensus        46 ~~~~~~~~~~~~-~~~p~~~~q~~~i~~i~~g~~~~i~g~TGsGKTt~~~~~~~~~~~~~~~----~~~~~~l~~~p~~~  120 (235)
T 3llm_A           46 QDHDLQAILQER-ELLPVKKFESEILEAISQNSVVIIRGATGCGKTTQVPQFILDDFIQNDR----AAECNIVVTQPRRI  120 (235)
T ss_dssp             HCHHHHHHHHHH-HTSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHHHHHHHHHHHHHHTTC----GGGCEEEEEESSHH
T ss_pred             cCHHHHHHHHHH-hcCChHHHHHHHHHHHhcCCEEEEEeCCCCCcHHhHHHHHhcchhhcCC----CCceEEEEeccchH
Confidence            344444444333 3334789999999999999999999999999999999998887665322    23567999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhh-hc
Q 043110          122 LCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRI-LE  200 (316)
Q Consensus       122 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l-~~  200 (316)
                      |+.|+.+.+............+.......     .....+++|+|+|||++.+++..    .+.+++++|+||||.+ ++
T Consensus       121 la~q~~~~~~~~~~~~~~~~~g~~~~~~~-----~~~~~~~~Ivv~Tpg~l~~~l~~----~l~~~~~lVlDEah~~~~~  191 (235)
T 3llm_A          121 SAVSVAERVAFERGEEPGKSCGYSVRFES-----ILPRPHASIMFCTVGVLLRKLEA----GIRGISHVIVDEIHERDIN  191 (235)
T ss_dssp             HHHHHHHHHHHTTTCCTTSSEEEEETTEE-----ECCCSSSEEEEEEHHHHHHHHHH----CCTTCCEEEECCTTSCCHH
T ss_pred             HHHHHHHHHHHHhccccCceEEEeechhh-----ccCCCCCeEEEECHHHHHHHHHh----hhcCCcEEEEECCccCCcc
Confidence            99999887765443211112222111110     00013478999999999999875    3678999999999986 66


Q ss_pred             CCcH-HHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCE
Q 043110          201 LGFG-KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPV  258 (316)
Q Consensus       201 ~~~~-~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~  258 (316)
                      .+|. ..++.++...+                +.|+++||||++.+.  +.+.+...|+
T Consensus       192 ~~~~~~~l~~i~~~~~----------------~~~~il~SAT~~~~~--~~~~~~~~pv  232 (235)
T 3llm_A          192 TDFLLVVLRDVVQAYP----------------EVRIVLMSATIDTSM--FCEYFFNCPI  232 (235)
T ss_dssp             HHHHHHHHHHHHHHCT----------------TSEEEEEECSSCCHH--HHHHTTSCCC
T ss_pred             hHHHHHHHHHHHhhCC----------------CCeEEEEecCCCHHH--HHHHcCCCCE
Confidence            6666 45666665543                689999999999876  6666666665

>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=99.92  E-value=9.7e-25  Score=213.96  Aligned_cols=176  Identities=19%  Similarity=0.223  Sum_probs=138.9

Q ss_pred             HHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           49 QLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        49 ~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      +..+.+|+ +|+++|..++|.++.|+  +++++||+|||++|.+|++.....         |..++||+||++||.|.++
T Consensus       103 a~~R~lG~-rP~~VQ~~~ip~Ll~G~--Iaem~TGeGKTLa~~LP~~l~aL~---------g~~v~VvTpTreLA~Qdae  170 (922)
T 1nkt_A          103 AAWRVLDQ-RPFDVQVMGAAALHLGN--VAEMKTGEGKTLTCVLPAYLNALA---------GNGVHIVTVNDYLAKRDSE  170 (922)
T ss_dssp             HHHHHHSC-CCCHHHHHHHHHHHTTE--EEECCTTSCHHHHTHHHHHHHHTT---------TSCEEEEESSHHHHHHHHH
T ss_pred             HHHHHcCC-CCCHHHHHHHHhHhcCC--EEEecCCCccHHHHHHHHHHHHHh---------CCCeEEEeCCHHHHHHHHH
Confidence            44346899 79999999999999998  999999999999999999755443         3359999999999999999


Q ss_pred             HHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcCC-----ccccCceeEEEEecchhhh-cC
Q 043110          129 ILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHTS-----SFLHTNLRWIIFDEADRIL-EL  201 (316)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~~-----~~~~~~l~~lViDEad~l~-~~  201 (316)
                      ++..+...++ +.+++++||.+....  ....+++|+||||++| ++++...-     ...+..+.++||||||+|+ |.
T Consensus       171 ~m~~l~~~lG-Lsv~~i~gg~~~~~r--~~~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~lr~l~~lIVDEaDsmLiDe  247 (922)
T 1nkt_A          171 WMGRVHRFLG-LQVGVILATMTPDER--RVAYNADITYGTNNEFGFDYLRDNMAHSLDDLVQRGHHYAIVDEVDSILIDE  247 (922)
T ss_dssp             HHHHHHHHTT-CCEEECCTTCCHHHH--HHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEETTHHHHHTTG
T ss_pred             HHHHHHhhcC-CeEEEEeCCCCHHHH--HHhcCCCEEEECchHhhHHHHHhhhhccHhhhccCCCCEEEEeChHHHHHhc
Confidence            9999998865 677888888775433  3334689999999999 78876531     3456789999999999999 43


Q ss_pred             ---------------CcHHHHHHHHHHhccCcccccCCCCccccccceEE-----------------EEeeecchh
Q 043110          202 ---------------GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNL-----------------LLSATLNEK  245 (316)
Q Consensus       202 ---------------~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i-----------------~~SAT~~~~  245 (316)
                                     +|...+..|+..++...      .-....+.+|++                 ++|||++.-
T Consensus       248 artPLiiSg~~~~~~~~y~~i~~iv~~L~~~~------dy~vDek~rqv~Lte~G~~~~e~~l~i~~Lfsat~~~l  317 (922)
T 1nkt_A          248 ARTPLIISGPADGASNWYTEFARLAPLMEKDV------HYEVDLRKRTVGVHEKGVEFVEDQLGIDNLYEAANSPL  317 (922)
T ss_dssp             GGSCEEEEEECCCCHHHHHHHHHHHHHSCBTT------TEEEETTTTEEEECHHHHHHHHHHHTCSSTTCSTTCCH
T ss_pred             CccceeecCCCCcchhHHHHHHHHHHhCcccc------cceeccCcceEEecHhHHHHHHHHhCCccccCCcchhH
Confidence                           47789999999997210      001112378888                 999998753

>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=99.92  E-value=9.7e-25  Score=213.58  Aligned_cols=150  Identities=21%  Similarity=0.203  Sum_probs=113.0

Q ss_pred             HHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH
Q 043110           52 ERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ  131 (316)
Q Consensus        52 ~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~  131 (316)
                      +.+|. +|+++|..++|.++.|+  +++++||+|||++|++|++.....         +.+++|++||++||.|+++++.
T Consensus        69 R~lg~-~p~~VQ~~~i~~ll~G~--Iaem~TGsGKTlaf~LP~l~~~l~---------g~~vlVltPTreLA~Q~~e~~~  136 (853)
T 2fsf_A           69 RVFGM-RHFDVQLLGGMVLNERC--IAEMRTGEGKTLTATLPAYLNALT---------GKGVHVVTVNDYLAQRDAENNR  136 (853)
T ss_dssp             HHHSC-CCCHHHHHHHHHHHSSE--EEECCTTSCHHHHHHHHHHHHHTT---------SSCCEEEESSHHHHHHHHHHHH
T ss_pred             HHcCC-CCChHHHhhcccccCCe--eeeecCCchHHHHHHHHHHHHHHc---------CCcEEEEcCCHHHHHHHHHHHH
Confidence            44686 69999999999999998  999999999999999999865433         4469999999999999999999


Q ss_pred             HHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcCC-----ccccCceeEEEEecchhhh-cCC--
Q 043110          132 KLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHTS-----SFLHTNLRWIIFDEADRIL-ELG--  202 (316)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~~-----~~~~~~l~~lViDEad~l~-~~~--  202 (316)
                      .++..++ +.+.+++||.+..  .+.+..+++|+||||++| ++++...-     ...++.+.++|+||||+|+ |.+  
T Consensus       137 ~l~~~lg-l~v~~i~GG~~~~--~r~~~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~~~l~~lVlDEaD~mLiD~a~t  213 (853)
T 2fsf_A          137 PLFEFLG-LTVGINLPGMPAP--AKREAYAADITYGTNNEYGFDYLRDNMAFSPEERVQRKLHYALVDEVDSILIDEART  213 (853)
T ss_dssp             HHHHHTT-CCEEECCTTCCHH--HHHHHHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCSCCEEEESCHHHHTTTTTTC
T ss_pred             HHHHhcC-CeEEEEeCCCCHH--HHHHhcCCCEEEECCchhhHHHHHhhhhccHhHhcccCCcEEEECchHHHHHhcCcc
Confidence            9998865 6777888887754  333444689999999999 78887532     2456789999999999999 543  


Q ss_pred             -------------cHHHHHHHHHHhcc
Q 043110          203 -------------FGKEIEEILDILGS  216 (316)
Q Consensus       203 -------------~~~~i~~i~~~l~~  216 (316)
                                   |...+..|+..++.
T Consensus       214 pLIiSg~~~~~~~~y~~i~~iv~~L~~  240 (853)
T 2fsf_A          214 PLIISGPAEDSSEMYKRVNKIIPHLIR  240 (853)
T ss_dssp             EEEEEEC--------------------
T ss_pred             cccccCCCccchhHHHHHHHHHHhchh
Confidence                         56788888888864

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.92  E-value=1.8e-24  Score=220.65  Aligned_cols=163  Identities=23%  Similarity=0.252  Sum_probs=136.1

Q ss_pred             HHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH
Q 043110           52 ERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ  131 (316)
Q Consensus        52 ~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~  131 (316)
                      ..++|. |+++|.++|+.+++|+|+++.+|||+|||++|++|+...+..         +.++||++|+++|+.|+++.++
T Consensus        34 ~~~~f~-l~~~Q~~aI~~il~g~~vlv~apTGsGKTlv~~~~i~~~~~~---------g~~vlvl~PtraLa~Q~~~~l~  103 (997)
T 4a4z_A           34 RSWPFE-LDTFQKEAVYHLEQGDSVFVAAHTSAGKTVVAEYAIAMAHRN---------MTKTIYTSPIKALSNQKFRDFK  103 (997)
T ss_dssp             CCCSSC-CCHHHHHHHHHHHTTCEEEEECCTTSCSHHHHHHHHHHHHHT---------TCEEEEEESCGGGHHHHHHHHH
T ss_pred             HhCCCC-CCHHHHHHHHHHHcCCCEEEEECCCCcHHHHHHHHHHHHHhc---------CCeEEEEeCCHHHHHHHHHHHH
Confidence            456786 899999999999999999999999999999999998877643         5679999999999999999888


Q ss_pred             HHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHH
Q 043110          132 KLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEIL  211 (316)
Q Consensus       132 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~  211 (316)
                      .++.   ...+..+.|+...       ...++|+|+||++|.+++.. ....+.+++++||||||++.+++++..++.++
T Consensus       104 ~~~~---~~~v~~l~G~~~~-------~~~~~IlV~Tpe~L~~~l~~-~~~~l~~l~lvViDEaH~l~d~~~g~~~e~ii  172 (997)
T 4a4z_A          104 ETFD---DVNIGLITGDVQI-------NPDANCLIMTTEILRSMLYR-GADLIRDVEFVIFDEVHYVNDQDRGVVWEEVI  172 (997)
T ss_dssp             TTC-----CCEEEECSSCEE-------CTTSSEEEEEHHHHHHHHHH-TCSGGGGEEEEEECCTTCCCTTCTTCCHHHHH
T ss_pred             HHcC---CCeEEEEeCCCcc-------CCCCCEEEECHHHHHHHHHh-CchhhcCCCEEEEECcccccccchHHHHHHHH
Confidence            7542   3455666666543       23479999999999998876 34456789999999999999999999999999


Q ss_pred             HHhccCcccccCCCCccccccceEEEEeeecchhHHHHHH
Q 043110          212 DILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK  251 (316)
Q Consensus       212 ~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~  251 (316)
                      ..++.               ..|++++|||+++.. .+..
T Consensus       173 ~~l~~---------------~v~iIlLSAT~~n~~-ef~~  196 (997)
T 4a4z_A          173 IMLPQ---------------HVKFILLSATVPNTY-EFAN  196 (997)
T ss_dssp             HHSCT---------------TCEEEEEECCCTTHH-HHHH
T ss_pred             Hhccc---------------CCCEEEEcCCCCChH-HHHH
Confidence            99887               899999999998654 4444

>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=99.91  E-value=3.7e-24  Score=227.49  Aligned_cols=194  Identities=20%  Similarity=0.206  Sum_probs=144.5

Q ss_pred             CCHHHHHHHHHHcCCCCCcHHHHHHHHHHh-CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCC--CCCCCCeeEEEEeC
Q 043110           42 LDSTLCDQLRERLGFEAPTKVQAQAIPVIL-SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPR--IDRSSGTFALVLVP  118 (316)
Q Consensus        42 l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il-~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~--~~~~~~~~~lil~P  118 (316)
                      |++.....+   -||++++++|++++|.++ .++|++++||||||||++|.+|+++.+.+....  .....+.++||++|
T Consensus        66 Lp~~~~~~f---~g~~~ln~iQs~~~~~al~~~~N~lv~APTGsGKTlva~l~il~~l~~~~~~~~~~~~~~~k~lyiaP  142 (1724)
T 4f92_B           66 LPKYAQAGF---EGFKTLNRIQSKLYRAALETDENLLLCAPTGAGKTNVALMCMLREIGKHINMDGTINVDDFKIIYIAP  142 (1724)
T ss_dssp             SCGGGSTTC---TTCSBCCHHHHHTHHHHHTCCCCEEEECCTTSCCHHHHHHHHHHHHGGGCCTTSSCCTTSCEEEEECS
T ss_pred             cCHHHHHhc---CCCCCCCHHHHHHHHHHHcCCCcEEEEeCCcchHHHHHHHHHHHHHHhhccccccccCCCCEEEEECC
Confidence            455544444   289999999999999877 578999999999999999999999999764332  12345788999999


Q ss_pred             ChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCc-cccCceeEEEEecchh
Q 043110          119 TSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSS-FLHTNLRWIIFDEADR  197 (316)
Q Consensus       119 t~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~-~~~~~l~~lViDEad~  197 (316)
                      +++||.|+++.+.+.+...+ +.+....|+......   ....++|+|+||+++..++++... ..+++++++|+||+|.
T Consensus       143 ~kALa~e~~~~l~~~~~~~g-i~V~~~tGd~~~~~~---~~~~~~IlVtTpEkld~llr~~~~~~~l~~v~~vIiDEvH~  218 (1724)
T 4f92_B          143 MRSLVQEMVGSFGKRLATYG-ITVAELTGDHQLCKE---EISATQIIVCTPEKWDIITRKGGERTYTQLVRLIILDEIHL  218 (1724)
T ss_dssp             SHHHHHHHHHHHHHHHTTTT-CCEEECCSSCSSCCT---TGGGCSEEEECHHHHHHHTTSSTTHHHHTTEEEEEETTGGG
T ss_pred             HHHHHHHHHHHHHHHHhhCC-CEEEEEECCCCCCcc---ccCCCCEEEECHHHHHHHHcCCccchhhcCcCEEEEecchh
Confidence            99999999999998887655 455666676544321   134589999999998666654322 2467899999999998


Q ss_pred             hhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHH
Q 043110          198 ILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKI  252 (316)
Q Consensus       198 l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~  252 (316)
                      +-+ .++..++.++.++...        .....+..|+|++|||+| +..++++.
T Consensus       219 l~d-~RG~~lE~~l~rl~~~--------~~~~~~~~riI~LSATl~-N~~dvA~w  263 (1724)
T 4f92_B          219 LHD-DRGPVLEALVARAIRN--------IEMTQEDVRLIGLSATLP-NYEDVATF  263 (1724)
T ss_dssp             GGS-TTHHHHHHHHHHHHHH--------HHHHTCCCEEEEEECSCT-THHHHHHH
T ss_pred             cCC-ccHHHHHHHHHHHHHH--------HHhCCCCCcEEEEecccC-CHHHHHHH
Confidence            766 6888888777654310        011223789999999998 45666654

>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=99.91  E-value=6.9e-24  Score=215.94  Aligned_cols=175  Identities=16%  Similarity=0.153  Sum_probs=129.1

Q ss_pred             HcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           53 RLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        53 ~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      -.|+..|+++|.++++.++.|+|+++.+|||+|||++|++|+++.+....    ...+.++|||+||++|+.|+++.++.
T Consensus       243 l~~~~~~r~~Q~~ai~~il~g~~~ll~a~TGsGKTl~~~~~i~~~l~~~~----~~~~~~vLvl~Pt~~L~~Q~~~~~~~  318 (936)
T 4a2w_A          243 VYETKKARSYQIELAQPAINGKNALICAPTGSGKTFVSILICEHHFQNMP----AGRKAKVVFLATKVPVYEQQKNVFKH  318 (936)
T ss_dssp             -----CCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHTTTTTCC----SSCCCCEEEECSSHHHHHHHHHHHHH
T ss_pred             ccCCCCCCHHHHHHHHHHHcCCCEEEEeCCCchHHHHHHHHHHHHHHhcc----ccCCCeEEEEeCCHHHHHHHHHHHHH
Confidence            34688899999999999999999999999999999999999988876532    12256799999999999999999999


Q ss_pred             HHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCc-HHHHHHHH
Q 043110          133 LLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGF-GKEIEEIL  211 (316)
Q Consensus       133 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~-~~~i~~i~  211 (316)
                      ++... ...+..++|+.....+...+..+++|+|+||++|.+++.......+.+++++|+||||++...+. ...+..++
T Consensus       319 ~~~~~-~~~v~~~~G~~~~~~~~~~~~~~~~IvI~Tp~~L~~~l~~~~~~~l~~~~liViDEaH~~~~~~~~~~i~~~~~  397 (936)
T 4a2w_A          319 HFERQ-GYSVQGISGENFSNVSVEKVIEDSDIIVVTPQILVNSFEDGTLTSLSIFTLMIFDECHNTTGNHPYNVLMTRYL  397 (936)
T ss_dssp             HHHTT-TCCEEEECCC-----CCHHHHHHCSEEEECHHHHHHHHHSSSCCCGGGCSEEEEETGGGCSTTCHHHHHHHHHH
T ss_pred             Hhccc-CceEEEEECCcchhhHHHHhccCCCEEEecHHHHHHHHHcCccccccCCCEEEEECccccCCCccHHHHHHHHH
Confidence            98754 35666777777666555566667899999999999999864443677899999999999887643 22222222


Q ss_pred             HHhccCcccccCCCCccccccceEEEEeeecc
Q 043110          212 DILGSRNIASIGEGNEVSNVKRQNLLLSATLN  243 (316)
Q Consensus       212 ~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~  243 (316)
                      .....           ...+..|++++|||+.
T Consensus       398 ~~~~~-----------~~~~~~~~l~LSATp~  418 (936)
T 4a2w_A          398 EQKFN-----------SASQLPQILGLTASVG  418 (936)
T ss_dssp             HHHHT-----------TCSCCCEEEEEESCCC
T ss_pred             HHhhc-----------cCCCcCeEEEecCCcc
Confidence            22110           0123689999999985

>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=99.90  E-value=6.1e-23  Score=203.79  Aligned_cols=170  Identities=25%  Similarity=0.340  Sum_probs=127.9

Q ss_pred             HHHHHHHHHHcCCCCCcHHHHHHHHHHhCC------CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEe
Q 043110           44 STLCDQLRERLGFEAPTKVQAQAIPVILSG------RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLV  117 (316)
Q Consensus        44 ~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g------~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~  117 (316)
                      ..+.+.+.+.++| .||++|+++++.++.+      ++++++++||||||++|++|++..+..         +.+++|++
T Consensus       355 ~~~~~~~~~~lpf-~lt~~Q~~ai~~I~~~l~~~~~~~~Ll~a~TGSGKTlvall~il~~l~~---------g~qvlvla  424 (780)
T 1gm5_A          355 GKLAEEFIKSLPF-KLTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---------GFQTAFMV  424 (780)
T ss_dssp             THHHHHHHHHSSS-CCCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---------TSCEEEEC
T ss_pred             hHHHHHHHHhCCC-CCCHHHHHHHHHHHhhccccCCCcEEEEcCCCCCHHHHHHHHHHHHHHc---------CCeEEEEe
Confidence            3455555588999 7999999999999865      589999999999999999999998865         45699999


Q ss_pred             CChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH---HHHHhc-CCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          118 PTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE---KARLRK-GISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       118 Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      ||++|+.|+++.+.+++...+ ..+..++|+......   ...+.. .++|+|+||+.+.+      ...+.+++++|+|
T Consensus       425 Ptr~La~Q~~~~l~~~~~~~g-i~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~------~~~~~~l~lVVID  497 (780)
T 1gm5_A          425 PTSILAIQHYRRTVESFSKFN-IHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE------DVHFKNLGLVIID  497 (780)
T ss_dssp             SCHHHHHHHHHHHHHHHTCSS-CCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH------CCCCSCCCEEEEE
T ss_pred             CcHHHHHHHHHHHHHHhhhcC-ceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh------hhhccCCceEEec
Confidence            999999999999999886543 566677777766543   333444 48999999998754      2345789999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHH
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLT  250 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~  250 (316)
                      |+|++...   .  ...   +.            .....+++++||||+.+....+.
T Consensus       498 EaHr~g~~---q--r~~---l~------------~~~~~~~vL~mSATp~p~tl~~~  534 (780)
T 1gm5_A          498 EQHRFGVK---Q--REA---LM------------NKGKMVDTLVMSATPIPRSMALA  534 (780)
T ss_dssp             SCCCC----------CC---CC------------SSSSCCCEEEEESSCCCHHHHHH
T ss_pred             ccchhhHH---H--HHH---HH------------HhCCCCCEEEEeCCCCHHHHHHH
Confidence            99995221   1  000   00            01136899999999877655544

>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=99.89  E-value=3.8e-22  Score=206.27  Aligned_cols=188  Identities=23%  Similarity=0.262  Sum_probs=146.2

Q ss_pred             cCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhC----CC--cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           39 SLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILS----GR--DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        39 ~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~----g~--d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      .++.+....+.+.+.++|. |||+|.++++.++.    |+  |++++++||+|||++|+++++..+..         +.+
T Consensus       585 ~~~~~~~~~~~~~~~f~~~-~t~~Q~~ai~~il~~~~~g~p~d~ll~~~TGsGKT~val~aa~~~~~~---------g~~  654 (1151)
T 2eyq_A          585 AFKHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN---------HKQ  654 (1151)
T ss_dssp             CCCCCHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT---------TCE
T ss_pred             CCCCCHHHHHHHHHhCCCC-CCHHHHHHHHHHHHHHhcCCcCcEEEECCCCCCHHHHHHHHHHHHHHh---------CCe
Confidence            4567888888888889997 79999999999886    66  99999999999999999998876643         557


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH---HHHHhc-CCcEEEeCcHHHHHHHhcCCccccCcee
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE---KARLRK-GISILVATPGHLLDHLKHTSSFLHTNLR  188 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~~l~  188 (316)
                      ++|++||++|+.|+++.+.+++...+ ..+..+.+.......   ...+.. .++|+|+||+.+.      ....+.+++
T Consensus       655 vlvlvPt~~La~Q~~~~~~~~~~~~~-i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~------~~~~~~~l~  727 (1151)
T 2eyq_A          655 VAVLVPTTLLAQQHYDNFRDRFANWP-VRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ------SDVKFKDLG  727 (1151)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHSTTTT-CCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH------SCCCCSSEE
T ss_pred             EEEEechHHHHHHHHHHHHHHhhcCC-CeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh------CCccccccc
Confidence            99999999999999999998775543 444555555444332   333444 4899999997663      234567999


Q ss_pred             EEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcC
Q 043110          189 WIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD  263 (316)
Q Consensus       189 ~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~  263 (316)
                      ++|+||||++     +.....++..++.               ..+++++|||+++....+....+.++..+...
T Consensus       728 lvIiDEaH~~-----g~~~~~~l~~l~~---------------~~~vl~lSATp~p~~l~~~~~~~~~~~~i~~~  782 (1151)
T 2eyq_A          728 LLIVDEEHRF-----GVRHKERIKAMRA---------------NVDILTLTATPIPRTLNMAMSGMRDLSIIATP  782 (1151)
T ss_dssp             EEEEESGGGS-----CHHHHHHHHHHHT---------------TSEEEEEESSCCCHHHHHHHTTTSEEEECCCC
T ss_pred             eEEEechHhc-----ChHHHHHHHHhcC---------------CCCEEEEcCCCChhhHHHHHhcCCCceEEecC
Confidence            9999999993     3455666666665               78999999999888888877777776665443

>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=99.89  E-value=1.9e-23  Score=207.15  Aligned_cols=179  Identities=19%  Similarity=0.186  Sum_probs=125.5

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH-HHHHHHHHhh
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV-YEILQKLLHR  136 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~-~~~~~~~~~~  136 (316)
                      .|+++|.++++.++.|+|+++.+|||+|||++|++|+++.+.....   .+.+.++|||+|+++|+.|+ ++.++.++..
T Consensus         7 ~l~~~Q~~~i~~il~g~~~ll~~~TGsGKTl~~~~~i~~~l~~~~~---~~~~~~vlvl~P~~~L~~Q~~~~~l~~~~~~   83 (699)
T 4gl2_A            7 QLRPYQMEVAQPALEGKNIIICLPTGCGKTRVAVYIAKDHLDKKKK---ASEPGKVIVLVNKVLLVEQLFRKEFQPFLKK   83 (699)
T ss_dssp             CCCHHHHHHHHHHHSSCCEEECCCTTSCHHHHHHHHHHHHHHHHHH---HTCCCCBCCEESCSHHHHHHHHHTHHHHHTT
T ss_pred             CccHHHHHHHHHHHhCCCEEEEcCCCCcHHHHHHHHHHHHHHhccc---cCCCCeEEEEECCHHHHHHHHHHHHHHHcCc
Confidence            5999999999999999999999999999999999999998766321   11235699999999999999 9999998754


Q ss_pred             cCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhc-----CCccccCceeEEEEecchhhhcCC-cHHHHHHH
Q 043110          137 FRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKH-----TSSFLHTNLRWIIFDEADRILELG-FGKEIEEI  210 (316)
Q Consensus       137 ~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~-----~~~~~~~~l~~lViDEad~l~~~~-~~~~i~~i  210 (316)
                        ...+..+.|+.........+...++|+|+||++|...+.+     ...+.+.++++|||||||++...+ +...+..+
T Consensus        84 --~~~v~~~~g~~~~~~~~~~~~~~~~Ilv~Tp~~L~~~l~~~~~~~~~~~~~~~~~lvViDEaH~~~~~~~~~~i~~~~  161 (699)
T 4gl2_A           84 --WYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHY  161 (699)
T ss_dssp             --TSCEEEEC----CCCCHHHHHHSCSEEEEEHHHHHHHTC--------CCCGGGCSEEEEESGGGCBTTBSSCSHHHHH
T ss_pred             --CceEEEEeCCcchhhHHHhhhcCCCEEEECHHHHHHHHhccccccccceecccCcEEEEECccccCccchHHHHHHHH
Confidence              2556666776655544455567789999999999988842     234566789999999999986543 33333333


Q ss_pred             HHHh-ccCcccccCCCCccccccceEEEEeeecch
Q 043110          211 LDIL-GSRNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       211 ~~~l-~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                      +... .....   ........+..|++++|||++.
T Consensus       162 l~~~~~~~~~---~~~~~~~~~~~~il~lTATp~~  193 (699)
T 4gl2_A          162 LMQKLKNNRL---KKENKPVIPLPQILGLTASPGV  193 (699)
T ss_dssp             HHHHHHHHHH---HC----CCCCCEEEEECSCCCC
T ss_pred             HHhhhccccc---ccccccCCCCCEEEEecccccc
Confidence            3221 10000   0000011126799999999986

>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=99.89  E-value=2.8e-23  Score=184.02  Aligned_cols=160  Identities=18%  Similarity=0.206  Sum_probs=121.0

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      .|+++|.++++.++.+++.++++|||+|||+++++++...+...        +.++||++|+++|+.|+.+.+++++.. 
T Consensus       113 ~l~~~Q~~ai~~~l~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~--------~~~~lil~Pt~~L~~q~~~~l~~~~~~-  183 (282)
T 1rif_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--------EGKILIIVPTTALTTQMADDFVDYRLF-  183 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHHC--------SSEEEEECSSHHHHHHHHHHHHHHTSC-
T ss_pred             CccHHHHHHHHHHHhcCCeEEEcCCCCCcHHHHHHHHHHHHHcC--------CCeEEEEECCHHHHHHHHHHHHHhccc-
Confidence            79999999999999888899999999999999988887766541        236999999999999999999987643 


Q ss_pred             CCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccC
Q 043110          138 RWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSR  217 (316)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~  217 (316)
                      .......+.+|.....   ....+.+|+|+||+.+...    ....+.+++++|+||||++.+    ..+..++..+.. 
T Consensus       184 ~~~~~~~~~~~~~~~~---~~~~~~~I~v~T~~~l~~~----~~~~~~~~~~vIiDEaH~~~~----~~~~~il~~~~~-  251 (282)
T 1rif_A          184 SHAMIKKIGGGASKDD---KYKNDAPVVVGTWQTVVKQ----PKEWFSQFGMMMNDECHLATG----KSISSIISGLNN-  251 (282)
T ss_dssp             CGGGEEECSTTCSSTT---CCCTTCSEEEECHHHHTTS----CGGGGGGEEEEEEETGGGCCH----HHHHHHTTTCTT-
T ss_pred             ccceEEEEeCCCcchh---hhccCCcEEEEchHHHHhh----HHHHHhhCCEEEEECCccCCc----ccHHHHHHHhhc-
Confidence            2234455555544321   1124579999999977542    223456899999999999864    466666666644 


Q ss_pred             cccccCCCCccccccceEEEEeeecchhHHHHHHH
Q 043110          218 NIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKI  252 (316)
Q Consensus       218 ~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~  252 (316)
                                    ..+++++|||++.....+...
T Consensus       252 --------------~~~~l~lSATp~~~~~~~~~l  272 (282)
T 1rif_A          252 --------------CMFKFGLSGSLRDGKANIMQY  272 (282)
T ss_dssp             --------------CCEEEEECSSCCTTSTTHHHH
T ss_pred             --------------CCeEEEEeCCCCCcchHHHHH
Confidence                          789999999998765544443

>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=99.89  E-value=3.3e-22  Score=188.47  Aligned_cols=164  Identities=20%  Similarity=0.174  Sum_probs=127.8

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      .|+|+|.++++.++.+ ++++.+|||+|||++++++++..+..        .+.++||++|+++|+.|+.+.+.+++.. 
T Consensus         9 ~l~~~Q~~~i~~~~~~-~~ll~~~tG~GKT~~~~~~~~~~~~~--------~~~~~liv~P~~~L~~q~~~~~~~~~~~-   78 (494)
T 1wp9_A            9 QPRIYQEVIYAKCKET-NCLIVLPTGLGKTLIAMMIAEYRLTK--------YGGKVLMLAPTKPLVLQHAESFRRLFNL-   78 (494)
T ss_dssp             CCCHHHHHHHHHGGGS-CEEEECCTTSCHHHHHHHHHHHHHHH--------SCSCEEEECSSHHHHHHHHHHHHHHBCS-
T ss_pred             CccHHHHHHHHHHhhC-CEEEEcCCCCCHHHHHHHHHHHHHhc--------CCCeEEEEECCHHHHHHHHHHHHHHhCc-
Confidence            5999999999999999 99999999999999999999888762        2445999999999999999999987632 


Q ss_pred             CCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccC
Q 043110          138 RWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSR  217 (316)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~  217 (316)
                      ....+....|+..... ......+++|+|+||+.+...+.. ....+.+++++|+||||++.+......+...+..... 
T Consensus        79 ~~~~v~~~~g~~~~~~-~~~~~~~~~ivv~T~~~l~~~~~~-~~~~~~~~~~vIiDEaH~~~~~~~~~~~~~~~~~~~~-  155 (494)
T 1wp9_A           79 PPEKIVALTGEKSPEE-RSKAWARAKVIVATPQTIENDLLA-GRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAK-  155 (494)
T ss_dssp             CGGGEEEECSCSCHHH-HHHHHHHCSEEEECHHHHHHHHHT-TSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCS-
T ss_pred             chhheEEeeCCcchhh-hhhhccCCCEEEecHHHHHHHHhc-CCcchhhceEEEEECCcccCCCCcHHHHHHHHHhcCC-
Confidence            2234555666665543 334444689999999999998876 4455678999999999999876544555555554444 


Q ss_pred             cccccCCCCccccccceEEEEeeecchhHHH
Q 043110          218 NIASIGEGNEVSNVKRQNLLLSATLNEKVNH  248 (316)
Q Consensus       218 ~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~  248 (316)
                                    ..+++++|||+..+...
T Consensus       156 --------------~~~~l~lTaTp~~~~~~  172 (494)
T 1wp9_A          156 --------------NPLVIGLTASPGSTPEK  172 (494)
T ss_dssp             --------------SCCEEEEESCSCSSHHH
T ss_pred             --------------CCeEEEEecCCCCCcHH
Confidence                          78999999999754433

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.87  E-value=3.6e-22  Score=191.02  Aligned_cols=172  Identities=16%  Similarity=0.198  Sum_probs=128.4

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      .|+++|.++++.++.+++++++++||+|||++|+.++...+...        +.++|||+|+++|+.|+++.+++++.. 
T Consensus       113 ~l~~~Q~~ai~~~~~~~~~ll~~~tGsGKT~~~~~~~~~~~~~~--------~~~vlvl~P~~~L~~Q~~~~~~~~~~~-  183 (510)
T 2oca_A          113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLENY--------EGKILIIVPTTALTTQMADDFVDYRLF-  183 (510)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEEECCSTTTHHHHHHHHHHHHHHHC--------SSEEEEEESSHHHHHHHHHHHHHTTSS-
T ss_pred             CCCHHHHHHHHHHHhcCCcEEEeCCCCCHHHHHHHHHHHHHhCC--------CCeEEEEECcHHHHHHHHHHHHHhhcC-
Confidence            69999999999999999999999999999999999988877541        236999999999999999999877433 


Q ss_pred             CCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccC
Q 043110          138 RWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSR  217 (316)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~  217 (316)
                      ....+..+.++.....+   +..+++|+|+||+.+...    ....+.+++++|+||||++..    ..+..++..+.. 
T Consensus       184 ~~~~v~~~~~~~~~~~~---~~~~~~I~i~T~~~l~~~----~~~~~~~~~liIiDE~H~~~~----~~~~~il~~~~~-  251 (510)
T 2oca_A          184 SHAMIKKIGGGASKDDK---YKNDAPVVVGTWQTVVKQ----PKEWFSQFGMMMNDECHLATG----KSISSIISGLNN-  251 (510)
T ss_dssp             CGGGEEECGGGCCTTGG---GCTTCSEEEEEHHHHTTS----CGGGGGGEEEEEEETGGGCCH----HHHHHHGGGCTT-
T ss_pred             CccceEEEecCCccccc---cccCCcEEEEeHHHHhhc----hhhhhhcCCEEEEECCcCCCc----ccHHHHHHhccc-
Confidence            23455566666554332   345689999999976432    334567899999999999865    456666666544 


Q ss_pred             cccccCCCCccccccceEEEEeeecchhHHHHHH-HhcCCCEEEEcCC
Q 043110          218 NIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK-ISLETPVLIGLDE  264 (316)
Q Consensus       218 ~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~-~~l~~p~~i~~~~  264 (316)
                                    ..+++++|||++.....+.. ..+.+|..+.+..
T Consensus       252 --------------~~~~l~lSATp~~~~~~~~~~~~~~~~~~~~~~~  285 (510)
T 2oca_A          252 --------------CMFKFGLSGSLRDGKANIMQYVGMFGEIFKPVTT  285 (510)
T ss_dssp             --------------CCEEEEEESCGGGCSSCHHHHHHHHCSEECCCCC
T ss_pred             --------------CcEEEEEEeCCCCCcccHHHhHHhhCCeEEeeCH
Confidence                          67999999999876543222 2344565544443

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.86  E-value=3.1e-21  Score=188.88  Aligned_cols=139  Identities=20%  Similarity=0.239  Sum_probs=113.8

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           47 CDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        47 ~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .++-.+.+|+ +|+++|..++|.++.|+  +++++||+|||++|.+|++.....         |..++|++||++||.|.
T Consensus        69 REAs~R~lG~-~Pt~VQ~~~ip~LlqG~--IaeakTGeGKTLvf~Lp~~L~aL~---------G~qv~VvTPTreLA~Qd  136 (997)
T 2ipc_A           69 RESAKRYLGM-RHFDVQLIGGAVLHEGK--IAEMKTGEGKTLVATLAVALNALT---------GKGVHVVTVNDYLARRD  136 (997)
T ss_dssp             HHHHHHHTCC-CCCHHHHHHHHHHHTTS--EEECCSTHHHHHHHHHHHHHHHTT---------CSCCEEEESSHHHHHHH
T ss_pred             HHHHHHHhCC-CCcHHHHhhcccccCCc--eeeccCCCchHHHHHHHHHHHHHh---------CCCEEEEeCCHHHHHHH
Confidence            3444446899 79999999999999998  999999999999999999654433         34599999999999999


Q ss_pred             HHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcCC-----ccccC---ceeEEEEecchh
Q 043110          127 YEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHTS-----SFLHT---NLRWIIFDEADR  197 (316)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~~-----~~~~~---~l~~lViDEad~  197 (316)
                      ++.+..+...++ +.+.+++||.+...  +....+++|+||||++| ++++...-     ...++   .+.++|+||+|.
T Consensus       137 ae~m~~l~~~lG-Lsv~~i~Gg~~~~~--r~~ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~r~d~~l~~lIIDEaDs  213 (997)
T 2ipc_A          137 AEWMGPVYRGLG-LSVGVIQHASTPAE--RRKAYLADVTYVTNSELGFDYLRDNMAISPDQLVLRHDHPLHYAIIDEVDS  213 (997)
T ss_dssp             HHHHHHHHHTTT-CCEEECCTTCCHHH--HHHHHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCSCSSSSSCEEEETTHHH
T ss_pred             HHHHHHHHHhcC-CeEEEEeCCCCHHH--HHHHcCCCEEEECchhhhhHHHHHhhhcchhhcccccCCCcceEEEechHH
Confidence            999999998765 67778888877433  33344689999999999 88887642     24566   899999999999


Q ss_pred             hhc
Q 043110          198 ILE  200 (316)
Q Consensus       198 l~~  200 (316)
                      |+.
T Consensus       214 mLi  216 (997)
T 2ipc_A          214 ILI  216 (997)
T ss_dssp             HTT
T ss_pred             HHH
Confidence            873

>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=99.85  E-value=4.4e-22  Score=187.63  Aligned_cols=167  Identities=15%  Similarity=0.099  Sum_probs=117.6

Q ss_pred             CCCCCcHHHHHHHHHHhCCCcE-EEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           55 GFEAPTKVQAQAIPVILSGRDV-LVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~il~g~d~-li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      |+..|+|+|+ +||.+++|+++ ++++|||||||++|++|++..+..        .+.++||++||++|+.|+++.+..+
T Consensus         1 G~~q~~~iq~-~i~~~l~~~~~~lv~a~TGsGKT~~~~~~~l~~~~~--------~~~~~lvl~Ptr~La~Q~~~~l~g~   71 (451)
T 2jlq_A            1 GSAMGEPDYE-VDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALL--------RRLRTLILAPTRVVAAEMEEALRGL   71 (451)
T ss_dssp             CCCCCSCCCC-CCGGGGSTTCEEEECCCTTSSCCTTHHHHHHHHHHH--------TTCCEEEEESSHHHHHHHHHHTTTS
T ss_pred             CCCCCCCcHH-HHHHHHhcCCeEEEECCCCCCHhhHHHHHHHHHHHh--------cCCcEEEECCCHHHHHHHHHHhcCc
Confidence            6788999986 79999999986 999999999999999999987765        2456999999999999999877421


Q ss_pred             HhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHH
Q 043110          134 LHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDI  213 (316)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~  213 (316)
                             ...........     ....+..|.++|++.+...+.+.  ..+.+++++|+||||++ +.++...+..+...
T Consensus        72 -------~v~~~~~~~~~-----~~~~~~~i~~~t~~~l~~~l~~~--~~l~~~~~iViDEah~~-~~~~~~~~~~~~~~  136 (451)
T 2jlq_A           72 -------PIRYQTPAVKS-----DHTGREIVDLMCHATFTTRLLSS--TRVPNYNLIVMDEAHFT-DPCSVAARGYISTR  136 (451)
T ss_dssp             -------CEEECCTTCSC-----CCCSSCCEEEEEHHHHHHHHHHC--SCCCCCSEEEEETTTCC-SHHHHHHHHHHHHH
T ss_pred             -------eeeeeeccccc-----cCCCCceEEEEChHHHHHHhhCc--ccccCCCEEEEeCCccC-CcchHHHHHHHHHh
Confidence                   11111111110     11234579999999998888653  44678999999999986 43333333333332


Q ss_pred             hccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEc
Q 043110          214 LGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGL  262 (316)
Q Consensus       214 l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~  262 (316)
                      ..              .+.+|+++||||++..+..+   +..++..+.+
T Consensus       137 ~~--------------~~~~~~i~~SAT~~~~~~~~---~~~~~~~~~~  168 (451)
T 2jlq_A          137 VE--------------MGEAAAIFMTATPPGSTDPF---PQSNSPIEDI  168 (451)
T ss_dssp             HH--------------TTSCEEEEECSSCTTCCCSS---CCCSSCEEEE
T ss_pred             hc--------------CCCceEEEEccCCCccchhh---hcCCCceEec
Confidence            21              12789999999998755432   3345555544

>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=99.84  E-value=9e-23  Score=198.66  Aligned_cols=182  Identities=13%  Similarity=0.094  Sum_probs=128.2

Q ss_pred             CCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCC
Q 043110           40 LGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPT  119 (316)
Q Consensus        40 ~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt  119 (316)
                      +++++.+.+++ .. ....|+|+|+.++|.+++|+|+++.||||||||++|++|+++.+..        .+.++||++||
T Consensus       155 l~~~~~~~~~l-~~-~~~~~lpiq~~~i~~l~~g~dvlv~a~TGSGKT~~~~lpil~~l~~--------~~~~vLvl~Pt  224 (618)
T 2whx_A          155 VTKSGDYVSAI-TQ-AERIGEPDYEVDEDIFRKKRLTIMDLHPGAGKTKRILPSIVREALK--------RRLRTLILAPT  224 (618)
T ss_dssp             -------CEEC-BC-CCCCCCCCCCCCGGGGSTTCEEEECCCTTSSTTTTHHHHHHHHHHH--------TTCCEEEEESS
T ss_pred             ccchHHHHHHH-hh-ccccCCCccccCHHHHhcCCeEEEEcCCCCCHHHHHHHHHHHHHHh--------CCCeEEEEcCh
Confidence            56777766666 32 2578999998899999999999999999999999999999998865        24569999999


Q ss_pred             hHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhh
Q 043110          120 SELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       120 ~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~  199 (316)
                      |+||.|+++.++.       ....+.......     ....+..+.++|.+.+...+...  ..+.+++++||||||++ 
T Consensus       225 reLa~Qi~~~l~~-------~~v~~~~~~l~~-----~~tp~~~i~~~t~~~l~~~l~~~--~~l~~~~~iViDEah~~-  289 (618)
T 2whx_A          225 RVVAAEMEEALRG-------LPIRYQTPAVKS-----DHTGREIVDLMCHATFTTRLLSS--TRVPNYNLIVMDEAHFT-  289 (618)
T ss_dssp             HHHHHHHHHHTTT-------SCEEECCTTSSC-----CCCSSSCEEEEEHHHHHHHHHHC--SSCCCCSEEEEESTTCC-
T ss_pred             HHHHHHHHHHhcC-------CceeEeccccee-----ccCCCceEEEEChHHHHHHHhcc--ccccCCeEEEEECCCCC-
Confidence            9999999987752       111111111000     00112356778888877666542  34678999999999998 


Q ss_pred             cCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcC
Q 043110          200 ELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD  263 (316)
Q Consensus       200 ~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~  263 (316)
                      +.+|...+..++..++..              .+|+++||||++..+..+..   .+|..+.+.
T Consensus       290 ~~~~~~~~~~i~~~l~~~--------------~~q~il~SAT~~~~~~~~~~---~~~~~~~v~  336 (618)
T 2whx_A          290 DPCSVAARGYISTRVEMG--------------EAAAIFMTATPPGSTDPFPQ---SNSPIEDIE  336 (618)
T ss_dssp             SHHHHHHHHHHHHHHHHT--------------SCEEEEECSSCTTCCCSSCC---CSSCEEEEE
T ss_pred             CccHHHHHHHHHHHhccc--------------CccEEEEECCCchhhhhhhc---cCCceeeec
Confidence            667888888888887521              78999999999987654433   355555443

>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=99.83  E-value=1.5e-20  Score=178.09  Aligned_cols=136  Identities=23%  Similarity=0.184  Sum_probs=108.6

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      .|+|+|.++++.++.++++++.+|||+|||++|+.++...            +.++||++|+++|+.|+++.+.++    
T Consensus        93 ~l~~~Q~~ai~~i~~~~~~ll~~~TGsGKT~~~l~~i~~~------------~~~~Lvl~P~~~L~~Q~~~~~~~~----  156 (472)
T 2fwr_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------------STPTLIVVPTLALAEQWKERLGIF----  156 (472)
T ss_dssp             CBCHHHHHHHHHHTTTTEEEEECCTTSCHHHHHHHHHHHH------------CSCEEEEESSHHHHHHHHHHGGGG----
T ss_pred             CcCHHHHHHHHHHHhcCCEEEEeCCCCCHHHHHHHHHHHc------------CCCEEEEECCHHHHHHHHHHHHhC----
Confidence            5999999999999999999999999999999999888754            234999999999999999988873    


Q ss_pred             CCce-eEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          138 RWIV-PGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       138 ~~~~-~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      + .. +..+.|+..         ...+|+|+||+.+...+...    ..+++++|+||||++.+.+|..    +++.++ 
T Consensus       157 ~-~~~v~~~~g~~~---------~~~~Ivv~T~~~l~~~~~~~----~~~~~liIvDEaH~~~~~~~~~----~~~~~~-  217 (472)
T 2fwr_A          157 G-EEYVGEFSGRIK---------ELKPLTVSTYDSAYVNAEKL----GNRFMLLIFDEVHHLPAESYVQ----IAQMSI-  217 (472)
T ss_dssp             C-GGGEEEBSSSCB---------CCCSEEEEEHHHHHHTHHHH----TTTCSEEEEETGGGTTSTTTHH----HHHTCC-
T ss_pred             C-CcceEEECCCcC---------CcCCEEEEEcHHHHHHHHHh----cCCCCEEEEECCcCCCChHHHH----HHHhcC-
Confidence            2 33 455555543         24689999999998766421    1358999999999998877654    444443 


Q ss_pred             CcccccCCCCccccccceEEEEeeecc
Q 043110          217 RNIASIGEGNEVSNVKRQNLLLSATLN  243 (316)
Q Consensus       217 ~~~~~~~~~~~~~~~~~q~i~~SAT~~  243 (316)
                                     ..+++++|||+.
T Consensus       218 ---------------~~~~l~lSATp~  229 (472)
T 2fwr_A          218 ---------------APFRLGLTATFE  229 (472)
T ss_dssp             ---------------CSEEEEEESCCC
T ss_pred             ---------------CCeEEEEecCcc
Confidence                           568999999987

>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=99.81  E-value=9.4e-20  Score=157.25  Aligned_cols=138  Identities=23%  Similarity=0.198  Sum_probs=105.3

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      .|+++|.++++.++.++++++++|||+|||.+++.++...            +.++||++|+++|+.|+.+.+.++    
T Consensus        93 ~l~~~Q~~ai~~~~~~~~~ll~~~tG~GKT~~a~~~~~~~------------~~~~liv~P~~~L~~q~~~~~~~~----  156 (237)
T 2fz4_A           93 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------------STPTLIVVPTLALAEQWKERLGIF----  156 (237)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHHHHS------------CSCEEEEESSHHHHHHHHHHHGGG----
T ss_pred             CcCHHHHHHHHHHHhCCCEEEEeCCCCCHHHHHHHHHHHc------------CCCEEEEeCCHHHHHHHHHHHHhC----
Confidence            6999999999999999999999999999999988776542            234999999999999999888773    


Q ss_pred             CCce-eEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          138 RWIV-PGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       138 ~~~~-~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      + .. +..+.|+..         ...+|+|+||+.+......    ....++++|+||||++.+..+.    .+++.++ 
T Consensus       157 ~-~~~v~~~~g~~~---------~~~~i~v~T~~~l~~~~~~----~~~~~~llIiDEaH~l~~~~~~----~i~~~~~-  217 (237)
T 2fz4_A          157 G-EEYVGEFSGRIK---------ELKPLTVSTYDSAYVNAEK----LGNRFMLLIFDEVHHLPAESYV----QIAQMSI-  217 (237)
T ss_dssp             C-GGGEEEESSSCB---------CCCSEEEEEHHHHHHTHHH----HTTTCSEEEEECSSCCCTTTHH----HHHHTCC-
T ss_pred             C-CCeEEEEeCCCC---------CcCCEEEEeHHHHHhhHHH----hcccCCEEEEECCccCCChHHH----HHHHhcc-
Confidence            2 23 444444433         2468999999998765542    1245889999999999876543    3444443 


Q ss_pred             CcccccCCCCccccccceEEEEeeecchh
Q 043110          217 RNIASIGEGNEVSNVKRQNLLLSATLNEK  245 (316)
Q Consensus       217 ~~~~~~~~~~~~~~~~~q~i~~SAT~~~~  245 (316)
                                     ..+++++|||++..
T Consensus       218 ---------------~~~~l~LSATp~r~  231 (237)
T 2fz4_A          218 ---------------APFRLGLTATFERE  231 (237)
T ss_dssp             ---------------CSEEEEEEESCC--
T ss_pred             ---------------CCEEEEEecCCCCC
Confidence                           56889999998754

>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=99.80  E-value=1.7e-20  Score=181.99  Aligned_cols=144  Identities=22%  Similarity=0.167  Sum_probs=110.4

Q ss_pred             CcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcC
Q 043110           59 PTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFR  138 (316)
Q Consensus        59 p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~  138 (316)
                      +.+.|+.+++.+..+++++++||||||||++|.+|+++.            +.++||++|||+||.|+++.+.+...   
T Consensus       218 ~~~~q~~i~~~L~~~~~vlv~ApTGSGKT~a~~l~ll~~------------g~~vLVl~PTReLA~Qia~~l~~~~g---  282 (666)
T 3o8b_A          218 VFTDNSSPPAVPQSFQVAHLHAPTGSGKSTKVPAAYAAQ------------GYKVLVLNPSVAATLGFGAYMSKAHG---  282 (666)
T ss_dssp             SCCCCCSCCCCCSSCEEEEEECCTTSCTTTHHHHHHHHT------------TCCEEEEESCHHHHHHHHHHHHHHHS---
T ss_pred             cHHHHHHHHHHHHcCCeEEEEeCCchhHHHHHHHHHHHC------------CCeEEEEcchHHHHHHHHHHHHHHhC---
Confidence            345555555666688899999999999999999988751            34599999999999999987765542   


Q ss_pred             CceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCc
Q 043110          139 WIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRN  218 (316)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~  218 (316)
                       .......|+..       ...+++|+|+||++|+   .. ..+.+++++++||||||+ ++.+|...+..+++.++.  
T Consensus       283 -~~vg~~vG~~~-------~~~~~~IlV~TPGrLl---~~-~~l~l~~l~~lVlDEAH~-l~~~~~~~l~~Il~~l~~--  347 (666)
T 3o8b_A          283 -IDPNIRTGVRT-------ITTGAPVTYSTYGKFL---AD-GGCSGGAYDIIICDECHS-TDSTTILGIGTVLDQAET--  347 (666)
T ss_dssp             -CCCEEECSSCE-------ECCCCSEEEEEHHHHH---HT-TSCCTTSCSEEEETTTTC-CSHHHHHHHHHHHHHTTT--
T ss_pred             -CCeeEEECcEe-------ccCCCCEEEECcHHHH---hC-CCcccCcccEEEEccchh-cCccHHHHHHHHHHhhhh--
Confidence             23344455533       2456899999999983   32 456677899999999965 667788889999999876  


Q ss_pred             ccccCCCCccccccce--EEEEeeecchh
Q 043110          219 IASIGEGNEVSNVKRQ--NLLLSATLNEK  245 (316)
Q Consensus       219 ~~~~~~~~~~~~~~~q--~i~~SAT~~~~  245 (316)
                                   .+|  ++++|||++..
T Consensus       348 -------------~~~~llil~SAT~~~~  363 (666)
T 3o8b_A          348 -------------AGARLVVLATATPPGS  363 (666)
T ss_dssp             -------------TTCSEEEEEESSCTTC
T ss_pred             -------------cCCceEEEECCCCCcc
Confidence                         444  77889999974

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.80  E-value=6.5e-22  Score=193.96  Aligned_cols=161  Identities=17%  Similarity=0.151  Sum_probs=105.1

Q ss_pred             HcCCC-----CCcHHHH-----HHHHHHh------CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEE
Q 043110           53 RLGFE-----APTKVQA-----QAIPVIL------SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVL  116 (316)
Q Consensus        53 ~~g~~-----~p~~~Q~-----~~i~~il------~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil  116 (316)
                      .+||.     .|+++|+     ++||.++      .|+|+++++|||||||++|++|+++.+..        .+.++||+
T Consensus       205 ~~Gf~~~~~~~pt~IQ~~~r~~~aIp~~l~~~~l~~g~dvlv~apTGSGKTl~~ll~il~~l~~--------~~~~~lil  276 (673)
T 2wv9_A          205 GNGVILGNGAYVSAIVQGERVEEPVPEAYNPEMLKKRQLTVLDLHPGAGKTRRILPQIIKDAIQ--------KRLRTAVL  276 (673)
T ss_dssp             EEEEECSSSCEEEEEECC-------CCCCCGGGGSTTCEEEECCCTTTTTTTTHHHHHHHHHHH--------TTCCEEEE
T ss_pred             eccccccCCCccCceeeccccccchHHHhhHHHHhcCCeEEEEeCCCCCHHHHHHHHHHHHHHh--------CCCcEEEE
Confidence            34666     8999999     9999988      89999999999999999999999988765        24669999


Q ss_pred             eCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecch
Q 043110          117 VPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEAD  196 (316)
Q Consensus       117 ~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad  196 (316)
                      +||++||.|+++.++.+.       .....+....     ....+.-+-+.+.+.+...+..  ...+.+++++||||||
T Consensus       277 aPTr~La~Q~~~~l~~~~-------i~~~~~~l~~-----v~tp~~ll~~l~~~~l~~~l~~--~~~l~~l~lvViDEaH  342 (673)
T 2wv9_A          277 APTRVVAAEMAEALRGLP-------VRYLTPAVQR-----EHSGNEIVDVMCHATLTHRLMS--PLRVPNYNLFVMDEAH  342 (673)
T ss_dssp             ESSHHHHHHHHHHTTTSC-------CEECCC---C-----CCCSCCCEEEEEHHHHHHHHHS--SSCCCCCSEEEEESTT
T ss_pred             ccHHHHHHHHHHHHhcCC-------eeeecccccc-----cCCHHHHHHHHHhhhhHHHHhc--ccccccceEEEEeCCc
Confidence            999999999998876431       1111110000     0000011223333444333332  1346789999999999


Q ss_pred             hhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHH
Q 043110          197 RILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLT  250 (316)
Q Consensus       197 ~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~  250 (316)
                      ++ +..+...+..+...++.              ..+|+++||||++..+..+.
T Consensus       343 ~~-~~~~~~~~~~l~~~~~~--------------~~~~vl~~SAT~~~~i~~~~  381 (673)
T 2wv9_A          343 FT-DPASIAARGYIATRVEA--------------GEAAAIFMTATPPGTSDPFP  381 (673)
T ss_dssp             CC-CHHHHHHHHHHHHHHHT--------------TSCEEEEECSSCTTCCCSSC
T ss_pred             cc-CccHHHHHHHHHHhccc--------------cCCcEEEEcCCCChhhhhhc
Confidence            97 32233344444444431              17899999999998765443

>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=99.80  E-value=9.2e-19  Score=174.50  Aligned_cols=197  Identities=17%  Similarity=0.191  Sum_probs=130.4

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhC-CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILS-GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~-g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ...|+++++++.+.+.+..+ + ..|++.|+++|+.++. |+++++.||||||||+  ++|++......    ..+.+.+
T Consensus        71 ~~~f~~~~l~~~~~~~l~~r-~-~lP~~~q~~~i~~~l~~~~~vii~gpTGSGKTt--llp~ll~~~~~----~~~~g~~  142 (773)
T 2xau_A           71 INPFTGREFTPKYVDILKIR-R-ELPVHAQRDEFLKLYQNNQIMVFVGETGSGKTT--QIPQFVLFDEM----PHLENTQ  142 (773)
T ss_dssp             BCTTTCSBCCHHHHHHHHHH-T-TSGGGGGHHHHHHHHHHCSEEEEECCTTSSHHH--HHHHHHHHHHC----GGGGTCE
T ss_pred             CCCccccCCCHHHHHHHHHh-h-cCChHHHHHHHHHHHhCCCeEEEECCCCCCHHH--HHHHHHHHhcc----ccCCCce
Confidence            45799999999999999554 6 6799999999988775 5679999999999999  46665222110    0112567


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      ++|++|+++|+.|+++.+...........++.......      ......+|+++|||++...+...  ..+.++++||+
T Consensus       143 ilvl~P~r~La~q~~~~l~~~~~~~v~~~vG~~i~~~~------~~~~~~~I~v~T~G~l~r~l~~~--~~l~~~~~lIl  214 (773)
T 2xau_A          143 VACTQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFEN------KTSNKTILKYMTDGMLLREAMED--HDLSRYSCIIL  214 (773)
T ss_dssp             EEEEESCHHHHHHHHHHHHHHTTCCBTTTEEEEETTEE------ECCTTCSEEEEEHHHHHHHHHHS--TTCTTEEEEEE
T ss_pred             EEecCchHHHHHHHHHHHHHHhCCchhheecceecccc------ccCCCCCEEEECHHHHHHHHhhC--ccccCCCEEEe
Confidence            99999999999999876655432111111111111100      01235789999999999877653  34679999999


Q ss_pred             ecchh-hhcCCc-HHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcCCC
Q 043110          193 DEADR-ILELGF-GKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDEK  265 (316)
Q Consensus       193 DEad~-l~~~~~-~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  265 (316)
                      ||+|. .++..+ ...+..+....+                ..|++++|||++.  ..+.. ++.++..+.+...
T Consensus       215 DEah~R~ld~d~~~~~l~~l~~~~~----------------~~~iIl~SAT~~~--~~l~~-~~~~~~vi~v~gr  270 (773)
T 2xau_A          215 DEAHERTLATDILMGLLKQVVKRRP----------------DLKIIIMSATLDA--EKFQR-YFNDAPLLAVPGR  270 (773)
T ss_dssp             CSGGGCCHHHHHHHHHHHHHHHHCT----------------TCEEEEEESCSCC--HHHHH-HTTSCCEEECCCC
T ss_pred             cCccccccchHHHHHHHHHHHHhCC----------------CceEEEEeccccH--HHHHH-HhcCCCcccccCc
Confidence            99995 555322 233334433322                6899999999964  44544 4444444554443

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.78  E-value=9.6e-20  Score=177.28  Aligned_cols=157  Identities=24%  Similarity=0.219  Sum_probs=90.6

Q ss_pred             CCcHHHHHHHHHHhC----C-CcEEEEcCCCCchHHHHHHHHHHHhhhcC-CCCCCCCCeeEEEEeCChHHHHHHH-HHH
Q 043110           58 APTKVQAQAIPVILS----G-RDVLVNAATGTGKTVAYLAPIINHLQSYS-PRIDRSSGTFALVLVPTSELCLLVY-EIL  130 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~----g-~d~li~a~TGsGKT~~~~lp~l~~l~~~~-~~~~~~~~~~~lil~Pt~~L~~Q~~-~~~  130 (316)
                      .|+++|.++++.++.    | ++++++++||+|||++++. ++..+.... .......+.++|||+|+++|+.|+. +.+
T Consensus       178 ~lr~~Q~~ai~~~~~~~~~~~~~~ll~~~TGsGKT~~~~~-~~~~l~~~~~~~~~~~~~~~vlil~P~~~L~~Q~~~~~~  256 (590)
T 3h1t_A          178 SPRYYQQIAINRAVQSVLQGKKRSLITMATGTGKTVVAFQ-ISWKLWSARWNRTGDYRKPRILFLADRNVLVDDPKDKTF  256 (590)
T ss_dssp             -CCHHHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHHHHTTCCSSCSSSCCCEEEEEC-----------CC
T ss_pred             CchHHHHHHHHHHHHHHhcCCCceEEEecCCCChHHHHHH-HHHHHHhcccccccccCCCeEEEEeCCHHHHHHHHHHHH
Confidence            599999999998875    4 5699999999999999655 444443321 1111124667999999999999998 666


Q ss_pred             HHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCC---ccccCceeEEEEecchhhhcCCcHHHH
Q 043110          131 QKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTS---SFLHTNLRWIIFDEADRILELGFGKEI  207 (316)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~---~~~~~~l~~lViDEad~l~~~~~~~~i  207 (316)
                      +.++.     ....+.++        ....+.+|+|+||++|........   .+....+++||+||||++...+ ...+
T Consensus       257 ~~~~~-----~~~~~~~~--------~~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~~lvIiDEaH~~~~~~-~~~~  322 (590)
T 3h1t_A          257 TPFGD-----ARHKIEGG--------KVVKSREIYFAIYQSIASDERRPGLYKEFPQDFFDLIIIDECHRGSARD-NSNW  322 (590)
T ss_dssp             TTTCS-----SEEECCC----------CCSSCSEEEEEGGGC------CCGGGGSCTTSCSEEEESCCC----------C
T ss_pred             Hhcch-----hhhhhhcc--------CCCCCCcEEEEEhhhhccccccccccccCCCCccCEEEEECCccccccc-hHHH
Confidence            65432     11222221        123467999999999988764221   2334578999999999987642 2456


Q ss_pred             HHHHHHhccCcccccCCCCccccccceEEEEeeecchh
Q 043110          208 EEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEK  245 (316)
Q Consensus       208 ~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~  245 (316)
                      ..+++.++                ..+++++|||....
T Consensus       323 ~~il~~~~----------------~~~~l~lTATP~~~  344 (590)
T 3h1t_A          323 REILEYFE----------------PAFQIGMTATPLRE  344 (590)
T ss_dssp             HHHHHHST----------------TSEEEEEESSCSCT
T ss_pred             HHHHHhCC----------------cceEEEeccccccc
Confidence            77777775                46899999997744

>1yks_A Genome polyprotein [contains: flavivirin protease NS3 catalytic subunit]; helicase, flavivirus, DEAD-BOX, ATPase, rtpase, hydrolase; 1.80A {Yellow fever virus} SCOP: c.37.1.14 c.37.1.14 PDB: 1ymf_A*

Probab=99.77  E-value=5.7e-20  Score=172.62  Aligned_cols=139  Identities=18%  Similarity=0.172  Sum_probs=96.7

Q ss_pred             HHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCC
Q 043110           69 VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGG  148 (316)
Q Consensus        69 ~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~  148 (316)
                      .+++|+|+++++|||||||++|++|+++.+..        .+.+++|++||++||.|+++.++.+.       .....+.
T Consensus         4 ~l~~g~~vlv~a~TGSGKT~~~l~~~l~~~~~--------~~~~~lil~Ptr~La~Q~~~~l~~~~-------v~~~~~~   68 (440)
T 1yks_A            4 MLKKGMTTVLDFHPGAGKTRRFLPQILAECAR--------RRLRTLVLAPTRVVLSEMKEAFHGLD-------VKFHTQA   68 (440)
T ss_dssp             TTSTTCEEEECCCTTSSTTTTHHHHHHHHHHH--------TTCCEEEEESSHHHHHHHHHHTTTSC-------EEEESSC
T ss_pred             HhhCCCCEEEEcCCCCCHHHHHHHHHHHHHHh--------cCCeEEEEcchHHHHHHHHHHHhcCC-------eEEeccc
Confidence            35689999999999999999999999998765        24569999999999999998876321       1111111


Q ss_pred             CChHHHHHHHhcCCcEEEeCcHHHHHHHhcC-------CccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccc
Q 043110          149 GNRSKEKARLRKGISILVATPGHLLDHLKHT-------SSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIAS  221 (316)
Q Consensus       149 ~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~-------~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~  221 (316)
                      .              -.|+||+++.+++...       ....+.+++++|+||||++ +.++...+..+...+..     
T Consensus        69 ~--------------~~v~Tp~~l~~~l~~~~l~~~~~~~~~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~-----  128 (440)
T 1yks_A           69 F--------------SAHGSGREVIDAMCHATLTYRMLEPTRVVNWEVIIMDEAHFL-DPASIAARGWAAHRARA-----  128 (440)
T ss_dssp             C--------------CCCCCSSCCEEEEEHHHHHHHHTSSSCCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHT-----
T ss_pred             c--------------eeccCCccceeeecccchhHhhhCcccccCccEEEEECcccc-CcchHHHHHHHHHHhcc-----
Confidence            0              0377776654433221       1223678999999999998 44444444444444431     


Q ss_pred             cCCCCccccccceEEEEeeecchhHHHHHH
Q 043110          222 IGEGNEVSNVKRQNLLLSATLNEKVNHLTK  251 (316)
Q Consensus       222 ~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~  251 (316)
                               .++|+++||||+++.+..+..
T Consensus       129 ---------~~~~~l~~SAT~~~~~~~~~~  149 (440)
T 1yks_A          129 ---------NESATILMTATPPGTSDEFPH  149 (440)
T ss_dssp             ---------TSCEEEEECSSCTTCCCSSCC
T ss_pred             ---------CCceEEEEeCCCCchhhhhhh
Confidence                     178999999999887654443

>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=99.77  E-value=2.5e-18  Score=174.99  Aligned_cols=154  Identities=19%  Similarity=0.124  Sum_probs=115.6

Q ss_pred             CCcHHHHHHHHHHhC--------------CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           58 APTKVQAQAIPVILS--------------GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~--------------g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      .|+|+|..|++.++.              +++.+++++||||||+++ ++++..+...      ....++|||+|+++|+
T Consensus       271 ~~R~~Q~~AI~~il~~i~~~~~~~~~~~~~~~gli~~~TGSGKT~t~-~~l~~ll~~~------~~~~rvLvlvpr~eL~  343 (1038)
T 2w00_A          271 VMRPYQIAATERILWKIKSSFTAKNWSKPESGGYIWHTTGSGKTLTS-FKAARLATEL------DFIDKVFFVVDRKDLD  343 (1038)
T ss_dssp             ECCHHHHHHHHHHHHHHHHHHHHTCCSSGGGSEEEEECTTSSHHHHH-HHHHHHHTTC------TTCCEEEEEECGGGCC
T ss_pred             cCCHHHHHHHHHHHHHHHhcccccccccCCCCEEEEecCCCCHHHHH-HHHHHHHHhc------CCCceEEEEeCcHHHH
Confidence            599999999999875              368999999999999997 6666555321      1235799999999999


Q ss_pred             HHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHh-cCCcEEEeCcHHHHHHHhcCCc-cccCceeEEEEecchhhhcC
Q 043110          124 LLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLR-KGISILVATPGHLLDHLKHTSS-FLHTNLRWIIFDEADRILEL  201 (316)
Q Consensus       124 ~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~-~~~~IlV~Tp~~l~~~l~~~~~-~~~~~l~~lViDEad~l~~~  201 (316)
                      .|+.+.+..++..       .+.++.+.......+. .+++|+|+||++|..++..... ..+....++|+||||++.. 
T Consensus       344 ~Q~~~~f~~f~~~-------~v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lvIiDEAHrs~~-  415 (1038)
T 2w00_A          344 YQTMKEYQRFSPD-------SVNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVFIFDECHRSQF-  415 (1038)
T ss_dssp             HHHHHHHHTTSTT-------CSSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEEEEESCCTTHH-
T ss_pred             HHHHHHHHHhccc-------ccccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEEEEEccchhcc-
Confidence            9999988876532       1234455555555554 4689999999999998765321 2345778999999999753 


Q ss_pred             CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecch
Q 043110          202 GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       202 ~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                        +.....|...++                +.++++||||+..
T Consensus       416 --~~~~~~I~~~~p----------------~a~~lgfTATP~~  440 (1038)
T 2w00_A          416 --GEAQKNLKKKFK----------------RYYQFGFTGTPIF  440 (1038)
T ss_dssp             --HHHHHHHHHHCS----------------SEEEEEEESSCCC
T ss_pred             --hHHHHHHHHhCC----------------cccEEEEeCCccc
Confidence              344566777665                6799999999874

>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=99.75  E-value=6.3e-19  Score=166.39  Aligned_cols=149  Identities=19%  Similarity=0.180  Sum_probs=99.6

Q ss_pred             HHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeC
Q 043110           68 PVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMG  147 (316)
Q Consensus        68 ~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~  147 (316)
                      ..+.+|+++++++|||||||++|++|+++.+..        .+.++||++||++|+.|+++.+..+       ......+
T Consensus        16 ~~l~~~~~vlv~a~TGsGKT~~~~l~il~~~~~--------~~~~~lvl~Ptr~La~Q~~~~l~g~-------~v~~~~~   80 (459)
T 2z83_A           16 NMLRKRQMTVLDLHPGSGKTRKILPQIIKDAIQ--------QRLRTAVLAPTRVVAAEMAEALRGL-------PVRYQTS   80 (459)
T ss_dssp             GGGSTTCEEEECCCTTSCTTTTHHHHHHHHHHH--------TTCCEEEEECSHHHHHHHHHHTTTS-------CEEECC-
T ss_pred             HHHhcCCcEEEECCCCCCHHHHHHHHHHHHHHh--------CCCcEEEECchHHHHHHHHHHhcCc-------eEeEEec
Confidence            345678899999999999999999999988765        2456999999999999999887621       1111111


Q ss_pred             CCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchh-----hhcCCcHHHHHHHHHHhccCccccc
Q 043110          148 GGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADR-----ILELGFGKEIEEILDILGSRNIASI  222 (316)
Q Consensus       148 ~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~-----l~~~~~~~~i~~i~~~l~~~~~~~~  222 (316)
                      ....     .-..+..+.++|.+.+...+...  ..+.+++++||||||+     ++..+|...+.     ...      
T Consensus        81 ~~~~-----~~t~~~~i~~~~~~~l~~~l~~~--~~l~~~~~iViDEaH~~~~~~~~~~~~~~~~~-----~~~------  142 (459)
T 2z83_A           81 AVQR-----EHQGNEIVDVMCHATLTHRLMSP--NRVPNYNLFVMDEAHFTDPASIAARGYIATKV-----ELG------  142 (459)
T ss_dssp             ------------CCCSEEEEEHHHHHHHHHSC--C-CCCCSEEEESSTTCCSHHHHHHHHHHHHHH-----HTT------
T ss_pred             cccc-----CCCCCcEEEEEchHHHHHHhhcc--ccccCCcEEEEECCccCCchhhHHHHHHHHHh-----ccC------
Confidence            1110     01223457788888887766542  4467899999999998     44433322211     112      


Q ss_pred             CCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEE
Q 043110          223 GEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI  260 (316)
Q Consensus       223 ~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i  260 (316)
                               ..|+++||||++..+..+...  ..|+..
T Consensus       143 ---------~~~~il~SAT~~~~~~~~~~~--~~pi~~  169 (459)
T 2z83_A          143 ---------EAAAIFMTATPPGTTDPFPDS--NAPIHD  169 (459)
T ss_dssp             ---------SCEEEEECSSCTTCCCSSCCC--SSCEEE
T ss_pred             ---------CccEEEEEcCCCcchhhhccC--CCCeEE
Confidence                     789999999999876544332  455543

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.74  E-value=5.2e-18  Score=158.86  Aligned_cols=140  Identities=15%  Similarity=0.113  Sum_probs=95.3

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCCh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR  151 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (316)
                      +|+++++++|||||||++|++|+++.+..        .+.+++|++||++|+.|+++.+..       ..+.+..++...
T Consensus         1 kg~~~lv~a~TGsGKT~~~l~~~l~~~~~--------~g~~~lvl~Pt~~La~Q~~~~~~~-------~~v~~~~~~~~~   65 (431)
T 2v6i_A            1 KRELTVLDLHPGAGKTRRVLPQLVREAVK--------KRLRTVILAPTRVVASEMYEALRG-------EPIRYMTPAVQS   65 (431)
T ss_dssp             -CCEEEEECCTTSCTTTTHHHHHHHHHHH--------TTCCEEEEESSHHHHHHHHHHTTT-------SCEEEC------
T ss_pred             CCCEEEEEcCCCCCHHHHHHHHHHHHHHh--------CCCCEEEECcHHHHHHHHHHHhCC-------CeEEEEecCccc
Confidence            47899999999999999999999976654        245699999999999999877651       222333332111


Q ss_pred             HHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccc
Q 043110          152 SKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNV  231 (316)
Q Consensus       152 ~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~  231 (316)
                           .-..+..+.+.|.+.+...+..  ...+.+++++|+||||++ +.++......+......              +
T Consensus        66 -----~~~~~~~~~~~~~~~l~~~l~~--~~~~~~l~~vViDEaH~~-~~~~~~~~~~l~~~~~~--------------~  123 (431)
T 2v6i_A           66 -----ERTGNEIVDFMCHSTFTMKLLQ--GVRVPNYNLYIMDEAHFL-DPASVAARGYIETRVSM--------------G  123 (431)
T ss_dssp             --------CCCSEEEEEHHHHHHHHHH--TCCCCCCSEEEEESTTCC-SHHHHHHHHHHHHHHHT--------------T
T ss_pred             -----cCCCCceEEEEchHHHHHHHhc--CccccCCCEEEEeCCccC-CccHHHHHHHHHHHhhC--------------C
Confidence                 1112345777888888766654  334678999999999996 43344444444444311              1


Q ss_pred             cceEEEEeeecchhHHH
Q 043110          232 KRQNLLLSATLNEKVNH  248 (316)
Q Consensus       232 ~~q~i~~SAT~~~~v~~  248 (316)
                      .+|+++||||+++.+..
T Consensus       124 ~~~~l~~SAT~~~~~~~  140 (431)
T 2v6i_A          124 DAGAIFMTATPPGTTEA  140 (431)
T ss_dssp             SCEEEEEESSCTTCCCS
T ss_pred             CCcEEEEeCCCCcchhh
Confidence            78999999999975443

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=99.72  E-value=3.4e-17  Score=157.92  Aligned_cols=132  Identities=17%  Similarity=0.091  Sum_probs=96.1

Q ss_pred             CCCCCcHHHHHHHHH----HhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHH
Q 043110           55 GFEAPTKVQAQAIPV----ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEIL  130 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~----il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~  130 (316)
                      || +|+|.|.+++..    +..|++++++||||+|||++|++|++..            +.+++|++||++|+.|+.+.+
T Consensus         1 ~~-~~r~~Q~~~~~~v~~~l~~~~~~~~~a~TGtGKT~~~l~p~l~~------------~~~v~i~~pt~~l~~q~~~~~   67 (551)
T 3crv_A            1 MV-KLRDWQEKLKDKVIEGLRNNFLVALNAPTGSGKTLFSLLVSLEV------------KPKVLFVVRTHNEFYPIYRDL   67 (551)
T ss_dssp             CC-SCCHHHHHHHHHHHHHHHTTCEEEEECCTTSSHHHHHHHHHHHH------------CSEEEEEESSGGGHHHHHHHH
T ss_pred             CC-CCCHHHHHHHHHHHHHHHcCCcEEEECCCCccHHHHHHHHHHhC------------CCeEEEEcCCHHHHHHHHHHH
Confidence            45 489999987654    4589999999999999999999999871            456999999999999999888


Q ss_pred             HHHHhhcCCceeEEeeCCCC---------------------------------hHHH------------------HHHHh
Q 043110          131 QKLLHRFRWIVPGYVMGGGN---------------------------------RSKE------------------KARLR  159 (316)
Q Consensus       131 ~~~~~~~~~~~~~~~~~~~~---------------------------------~~~~------------------~~~l~  159 (316)
                      ..+....+ .....+.|+.+                                 ....                  .+...
T Consensus        68 ~~l~~~~~-~~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~~~G~~~~~Cpy~~ar~~~  146 (551)
T 3crv_A           68 TKIREKRN-ITFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLKKDGLQDKFCPYYSLLNSL  146 (551)
T ss_dssp             TTCCCSSC-CCEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHHHHHHHHTCCHHHHHHHHG
T ss_pred             HHHhhhcC-ccEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHHHcCCcCCcCccHHHHhhh
Confidence            87754332 33333333110                                 0111                  12334


Q ss_pred             cCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          160 KGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       160 ~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                      ..++|||+|++.|++...........+..++||||||.|.+
T Consensus       147 ~~adIVV~~~~~l~~~~~~~~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          147 YKADVIALTYPYFFIDRYREFIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             GGCSEEEEETHHHHCHHHHTTSCCCSTTEEEEETTGGGGGG
T ss_pred             hcCCEEEeCchHhcCHHHHHhcCCCcCCeEEEEecccchHH
Confidence            56899999999999886443322224678999999999988

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.65  E-value=1.1e-16  Score=156.77  Aligned_cols=141  Identities=17%  Similarity=0.065  Sum_probs=99.1

Q ss_pred             HHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCC
Q 043110           69 VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGG  148 (316)
Q Consensus        69 ~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~  148 (316)
                      ..+.|++++++||||||||+    ++++.+...         ..++|++|||+||.|+++.++..+     ..+....|+
T Consensus       151 r~l~rk~vlv~apTGSGKT~----~al~~l~~~---------~~gl~l~PtR~LA~Qi~~~l~~~g-----~~v~lltG~  212 (677)
T 3rc3_A          151 RAMQRKIIFHSGPTNSGKTY----HAIQKYFSA---------KSGVYCGPLKLLAHEIFEKSNAAG-----VPCDLVTGE  212 (677)
T ss_dssp             HTSCCEEEEEECCTTSSHHH----HHHHHHHHS---------SSEEEEESSHHHHHHHHHHHHHTT-----CCEEEECSS
T ss_pred             HhcCCCEEEEEcCCCCCHHH----HHHHHHHhc---------CCeEEEeCHHHHHHHHHHHHHhcC-----CcEEEEECC
Confidence            34688999999999999998    344444442         126999999999999999987752     345556565


Q ss_pred             CChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCcc
Q 043110          149 GNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEV  228 (316)
Q Consensus       149 ~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~  228 (316)
                      ......  .-....+++++|++.+.         ....++++||||||++++.+|+..+..++..++..           
T Consensus       213 ~~~iv~--TpGr~~~il~~T~e~~~---------l~~~v~lvVIDEaH~l~d~~~g~~~~~~l~~l~~~-----------  270 (677)
T 3rc3_A          213 ERVTVQ--PNGKQASHVSCTVEMCS---------VTTPYEVAVIDEIQMIRDPARGWAWTRALLGLCAE-----------  270 (677)
T ss_dssp             CEECCS--TTCCCCSEEEEEGGGCC---------SSSCEEEEEECSGGGGGCTTTHHHHHHHHHHCCEE-----------
T ss_pred             eeEEec--CCCcccceeEecHhHhh---------hcccCCEEEEecceecCCccchHHHHHHHHccCcc-----------
Confidence            433000  00011456677764331         23578999999999999999999999999888731           


Q ss_pred             ccccceEEEEeeecchhHHHHHHHh
Q 043110          229 SNVKRQNLLLSATLNEKVNHLTKIS  253 (316)
Q Consensus       229 ~~~~~q~i~~SAT~~~~v~~~~~~~  253 (316)
                         ..|++++|||.+ .+..+....
T Consensus       271 ---~i~il~~SAT~~-~i~~l~~~~  291 (677)
T 3rc3_A          271 ---EVHLCGEPAAID-LVMELMYTT  291 (677)
T ss_dssp             ---EEEEEECGGGHH-HHHHHHHHH
T ss_pred             ---ceEEEeccchHH-HHHHHHHhc
Confidence               789999999953 455555443

>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=99.62  E-value=1.7e-15  Score=144.28  Aligned_cols=149  Identities=19%  Similarity=0.182  Sum_probs=102.4

Q ss_pred             CCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        58 ~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .|+|+|.++++.+.    .++++++..+||+|||+.++..+ ..+...      +...++||||| .+|+.|+.+.++++
T Consensus        37 ~L~~~Q~~~v~~l~~~~~~~~~~ilad~~GlGKT~~ai~~i-~~~~~~------~~~~~~LIv~P-~~l~~qw~~e~~~~  108 (500)
T 1z63_A           37 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIAVF-SDAKKE------NELTPSLVICP-LSVLKNWEEELSKF  108 (500)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHHHH-HHHHHT------TCCSSEEEEEC-STTHHHHHHHHHHH
T ss_pred             cchHHHHHHHHHHHHHhhCCCCEEEEeCCCCcHHHHHHHHH-HHHHhc------CCCCCEEEEcc-HHHHHHHHHHHHHH
Confidence            59999999998763    67899999999999999975544 444331      12345999999 56999999999887


Q ss_pred             HhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHH
Q 043110          134 LHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDI  213 (316)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~  213 (316)
                      +..   ..+....|+...     .....++|+|+|++.+.....    +....++++|+||||++...+.  .....+..
T Consensus       109 ~~~---~~v~~~~g~~~~-----~~~~~~~ivi~t~~~l~~~~~----l~~~~~~~vIvDEaH~~kn~~~--~~~~~l~~  174 (500)
T 1z63_A          109 APH---LRFAVFHEDRSK-----IKLEDYDIILTTYAVLLRDTR----LKEVEWKYIVIDEAQNIKNPQT--KIFKAVKE  174 (500)
T ss_dssp             CTT---SCEEECSSSTTS-----CCGGGSSEEEEEHHHHTTCHH----HHTCCEEEEEEETGGGGSCTTS--HHHHHHHT
T ss_pred             CCC---ceEEEEecCchh-----ccccCCcEEEeeHHHHhccch----hcCCCcCEEEEeCccccCCHhH--HHHHHHHh
Confidence            632   333344444321     112357899999998865332    2224689999999999876432  23334443


Q ss_pred             hccCcccccCCCCccccccceEEEEeeecch
Q 043110          214 LGSRNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       214 l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                      ++                ..+.+++|||...
T Consensus       175 l~----------------~~~~l~LTaTP~~  189 (500)
T 1z63_A          175 LK----------------SKYRIALTGTPIE  189 (500)
T ss_dssp             SC----------------EEEEEEECSSCST
T ss_pred             hc----------------cCcEEEEecCCCC
Confidence            43                4577999999843

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=99.61  E-value=7.3e-16  Score=148.22  Aligned_cols=129  Identities=24%  Similarity=0.270  Sum_probs=85.2

Q ss_pred             cCCCCCcHHHHHHHH----HHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHH
Q 043110           54 LGFEAPTKVQAQAIP----VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI  129 (316)
Q Consensus        54 ~g~~~p~~~Q~~~i~----~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~  129 (316)
                      .|| +|+|+|.+++.    .+..|++++++||||+|||++|++|++..            +.+++|++||++|+.|+.+.
T Consensus         4 ~~~-~~r~~Q~~~~~~v~~~~~~~~~~~~~a~TGtGKT~~~l~~~~~~------------~~~~~~~~~t~~l~~q~~~~   70 (540)
T 2vl7_A            4 LKL-QLRQWQAEKLGEAINALKHGKTLLLNAKPGLGKTVFVEVLGMQL------------KKKVLIFTRTHSQLDSIYKN   70 (540)
T ss_dssp             ------CCHHHHHHHHHHHHHHTTCEEEEECCTTSCHHHHHHHHHHHH------------TCEEEEEESCHHHHHHHHHH
T ss_pred             CCC-CCCHHHHHHHHHHHHHHHcCCCEEEEcCCCCcHHHHHHHHHHhC------------CCcEEEEcCCHHHHHHHHHH
Confidence            477 69999999864    45689999999999999999999998753            34599999999999999988


Q ss_pred             HHHHHhhcCCceeEEeeCCCC--------hH------------------------HHH---------------HHHhcCC
Q 043110          130 LQKLLHRFRWIVPGYVMGGGN--------RS------------------------KEK---------------ARLRKGI  162 (316)
Q Consensus       130 ~~~~~~~~~~~~~~~~~~~~~--------~~------------------------~~~---------------~~l~~~~  162 (316)
                      +..+.     .....+.|...        ..                        ..+               +.....+
T Consensus        71 ~~~l~-----~~~~~l~gr~~lC~~~~~~~~~~~~~c~~c~~~~~~~~~gd~~~~~~~~~~~~~~~~Cpy~~~r~~~~~a  145 (540)
T 2vl7_A           71 AKLLG-----LKTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKDAVDYCPYYSLRANLKDK  145 (540)
T ss_dssp             HGGGT-----CCEEEC---------------------------------------------------------CTTGGGC
T ss_pred             HHhcC-----CcEEEecCCccccCCchhcccccccCCCCCCchhcccccccCCcHHHHHHHhhhcCCChHHHHHHHhhcC
Confidence            77632     11111111100        00                        000               1112347


Q ss_pred             cEEEeCcHHHHHHHhcCCcc------ccCceeEEEEecchhhhc
Q 043110          163 SILVATPGHLLDHLKHTSSF------LHTNLRWIIFDEADRILE  200 (316)
Q Consensus       163 ~IlV~Tp~~l~~~l~~~~~~------~~~~l~~lViDEad~l~~  200 (316)
                      +|||+|++.|++........      .+.+..++|+||||.|.+
T Consensus       146 diVV~n~~~l~~~~~~~~~~~~~~~~~~~~~~~vIiDEAHnl~~  189 (540)
T 2vl7_A          146 DVIAMTYPYLFQKPIRNSVFCNKDDCLKLEDYLIVIDEAHNLLE  189 (540)
T ss_dssp             SEEEEETHHHHSHHHHHHHSCSSTTSCCGGGEEEEETTGGGGGG
T ss_pred             CEEEEChHHhcCHHHHHhhCcccccccCcCCCEEEEEccccHHH
Confidence            99999999998855431111      235678999999999943

>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=99.53  E-value=9.9e-15  Score=149.02  Aligned_cols=159  Identities=14%  Similarity=0.100  Sum_probs=103.0

Q ss_pred             CCcHHHHHHHHHHhC--CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           58 APTKVQAQAIPVILS--GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~--g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      .|+|+|.+++..++.  +.++++.++||+|||+.++..+...+...       ...++|||||+ +|+.|+.+.+.+.+ 
T Consensus       153 ~LrpyQ~eav~~~l~~~~~~~LLad~tGlGKTi~Ai~~i~~l~~~g-------~~~rvLIVvP~-sLl~Qw~~E~~~~f-  223 (968)
T 3dmq_A          153 SLIPHQLNIAHDVGRRHAPRVLLADEVGLGKTIEAGMILHQQLLSG-------AAERVLIIVPE-TLQHQWLVEMLRRF-  223 (968)
T ss_dssp             CCCHHHHHHHHHHHHSSSCEEEECCCTTSCHHHHHHHHHHHHHHTS-------SCCCEEEECCT-TTHHHHHHHHHHHS-
T ss_pred             CCcHHHHHHHHHHHHhcCCCEEEECCCCCcHHHHHHHHHHHHHHhC-------CCCeEEEEeCH-HHHHHHHHHHHHHh-
Confidence            689999999988875  44799999999999999977776665441       22359999999 99999998886654 


Q ss_pred             hcCCceeEEeeCCCChHHHHH---HHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcH-HHHHHHH
Q 043110          136 RFRWIVPGYVMGGGNRSKEKA---RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFG-KEIEEIL  211 (316)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~---~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~-~~i~~i~  211 (316)
                        + .....+ ++........   ......+|+|+|++.+.........+...+++++|+||||++...+.. ......+
T Consensus       224 --~-l~v~v~-~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlVIvDEAH~~kn~~~~~s~~~~~l  299 (968)
T 3dmq_A          224 --N-LRFALF-DDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLLVVDEAHHLVWSEDAPSREYQAI  299 (968)
T ss_dssp             --C-CCCEEC-CHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEEEECCSSCCCCBTTBCCHHHHHH
T ss_pred             --C-CCEEEE-ccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEEEehhhHhhcCCCCcchHHHHHH
Confidence              2 222222 2222111111   111246899999998854322111233357899999999998654321 1112233


Q ss_pred             HHhccCcccccCCCCccccccceEEEEeeecc
Q 043110          212 DILGSRNIASIGEGNEVSNVKRQNLLLSATLN  243 (316)
Q Consensus       212 ~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~  243 (316)
                      ..+...              ..+++++|||.-
T Consensus       300 ~~L~~~--------------~~~~L~LTATPi  317 (968)
T 3dmq_A          300 EQLAEH--------------VPGVLLLTATPE  317 (968)
T ss_dssp             HHHHTT--------------CSSEEESCSSCS
T ss_pred             HHHhhc--------------CCcEEEEEcCCc
Confidence            333211              457899999974

>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=99.46  E-value=2.1e-12  Score=126.71  Aligned_cols=160  Identities=18%  Similarity=0.239  Sum_probs=105.5

Q ss_pred             CCcHHHHHHHHHHh---------CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           58 APTKVQAQAIPVIL---------SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        58 ~p~~~Q~~~i~~il---------~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      .++|+|.+++..+.         .+...++..+||.|||+.++..+...+.. .+. ......++|||+|+ +|+.|+.+
T Consensus        55 ~LrpyQ~~gv~~l~~~~~~~~~~~~~g~ILad~mGlGKT~~~i~~i~~l~~~-~~~-~~p~~~~~LiV~P~-sll~qW~~  131 (644)
T 1z3i_X           55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCITLIWTLLKQ-SPD-CKPEIDKVIVVSPS-SLVRNWYN  131 (644)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHHHHHHHHHC-CTT-SSCSCSCEEEEECH-HHHHHHHH
T ss_pred             cccHHHHHHHHHHHHhhhcccccCCCCeEeeeCCCchHHHHHHHHHHHHHHh-Ccc-ccCCCCcEEEEecH-HHHHHHHH
Confidence            58999999998874         45679999999999999986666555433 211 11123459999996 89999999


Q ss_pred             HHHHHHhhcCCceeEEeeCCCChHH--HHHHHhc------CCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          129 ILQKLLHRFRWIVPGYVMGGGNRSK--EKARLRK------GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~l~~------~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                      .+.++...  ........+|.....  .......      ..+|+|+|++.+.....   .+....++++|+||||++-.
T Consensus       132 E~~~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~~---~l~~~~~~~vI~DEaH~ikn  206 (644)
T 1z3i_X          132 EVGKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE---VLHKGKVGLVICDEGHRLKN  206 (644)
T ss_dssp             HHHHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT---TTTTSCCCEEEETTGGGCCT
T ss_pred             HHHHHcCC--CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhHH---HhhcCCccEEEEECceecCC
Confidence            99998754  133334444433221  1112211      36899999998876442   22234678999999999865


Q ss_pred             CCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecc
Q 043110          201 LGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLN  243 (316)
Q Consensus       201 ~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~  243 (316)
                      ..  ......+..+.                ....+++|||.-
T Consensus       207 ~~--~~~~~al~~l~----------------~~~rl~LTgTPi  231 (644)
T 1z3i_X          207 SD--NQTYLALNSMN----------------AQRRVLISGTPI  231 (644)
T ss_dssp             TC--HHHHHHHHHHC----------------CSEEEEECSSCS
T ss_pred             hh--hHHHHHHHhcc----------------cCcEEEEecCcc
Confidence            32  23334444454                456799999974

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=99.44  E-value=4.9e-13  Score=130.29  Aligned_cols=71  Identities=24%  Similarity=0.216  Sum_probs=60.5

Q ss_pred             CCcHHHHHHHH----HHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIP----VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        58 ~p~~~Q~~~i~----~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      +|+|.|.+.+.    .+.+|++++++||||+|||++|++|++..+...        +.+++|++||++|+.|+.+.+..+
T Consensus         3 ~~R~~Q~~~~~~v~~~l~~~~~~~~~apTGtGKT~a~l~p~l~~~~~~--------~~kvli~t~T~~l~~Qi~~el~~l   74 (620)
T 4a15_A            3 ENRQYQVEAIDFLRSSLQKSYGVALESPTGSGKTIMALKSALQYSSER--------KLKVLYLVRTNSQEEQVIKELRSL   74 (620)
T ss_dssp             --CHHHHHHHHHHHHHHHHSSEEEEECCTTSCHHHHHHHHHHHHHHHH--------TCEEEEEESSHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHHHcCCCEEEECCCCCCHHHHHHHHHHHhhhhc--------CCeEEEECCCHHHHHHHHHHHHHH
Confidence            58999988875    456899999999999999999999999987652        456999999999999999999888


Q ss_pred             Hhh
Q 043110          134 LHR  136 (316)
Q Consensus       134 ~~~  136 (316)
                      ...
T Consensus        75 ~~~   77 (620)
T 4a15_A           75 SST   77 (620)
T ss_dssp             HHH
T ss_pred             hhc
Confidence            754

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=99.43  E-value=6.6e-13  Score=133.34  Aligned_cols=154  Identities=17%  Similarity=0.171  Sum_probs=104.1

Q ss_pred             CCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        58 ~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .++|+|.+++..+.    .+++.++..+||.|||+..+..+...+....      ....+||||| .+|+.|+.+.+.++
T Consensus       236 ~Lr~yQ~egv~~l~~~~~~~~~~ILademGlGKT~~ai~~i~~l~~~~~------~~~~~LIV~P-~sll~qW~~E~~~~  308 (800)
T 3mwy_W          236 ELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIFARR------QNGPHIIVVP-LSTMPAWLDTFEKW  308 (800)
T ss_dssp             CCCTHHHHHHHHHHHHHTTTCCEEECCCTTSSTTHHHHHHHHHHHHHHS------CCSCEEEECC-TTTHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHHHHHHhhcCCCEEEEeCCCcchHHHHHHHHHHHHHhcC------CCCCEEEEEC-chHHHHHHHHHHHH
Confidence            57899999998765    7889999999999999987665544443321      1223899999 78899999988887


Q ss_pred             HhhcCCceeEEeeCCCChHHHHHHH------------hcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcC
Q 043110          134 LHRFRWIVPGYVMGGGNRSKEKARL------------RKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL  201 (316)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~l------------~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~  201 (316)
                      +.   ...+.+..|+..........            ...++|+|+|++.+......   +....+++||+||||++-..
T Consensus       309 ~p---~~~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~---l~~~~w~~vIvDEaH~lkn~  382 (800)
T 3mwy_W          309 AP---DLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE---LGSIKWQFMAVDEAHRLKNA  382 (800)
T ss_dssp             ST---TCCEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH---HHTSEEEEEEETTGGGGCCS
T ss_pred             CC---CceEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH---HhcCCcceeehhhhhhhcCc
Confidence            63   34444444444433332221            12468999999998764322   11236789999999998543


Q ss_pred             CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeec
Q 043110          202 GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATL  242 (316)
Q Consensus       202 ~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~  242 (316)
                      +  ......+..+.                ....+++|||.
T Consensus       383 ~--s~~~~~l~~l~----------------~~~rl~LTgTP  405 (800)
T 3mwy_W          383 E--SSLYESLNSFK----------------VANRMLITGTP  405 (800)
T ss_dssp             S--SHHHHHHTTSE----------------EEEEEEECSCC
T ss_pred             h--hHHHHHHHHhh----------------hccEEEeeCCc
Confidence            2  23333444443                45668899997

>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=99.33  E-value=2.2e-11  Score=117.82  Aligned_cols=138  Identities=20%  Similarity=0.201  Sum_probs=102.2

Q ss_pred             HHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHH
Q 043110           47 CDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLV  126 (316)
Q Consensus        47 ~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~  126 (316)
                      .++-.+.+|+. |+++|....-.+..|+  ++.+.||+|||+++.+|++-....         |..+.|++|++.||.|-
T Consensus        65 REAa~R~lg~r-~~dvQligg~~L~~G~--iaEM~TGEGKTLva~lp~~lnAL~---------G~~vhVvT~ndyLA~rd  132 (822)
T 3jux_A           65 REAARRTLGMR-PFDVQVMGGIALHEGK--VAEMKTGEGKTLAATMPIYLNALI---------GKGVHLVTVNDYLARRD  132 (822)
T ss_dssp             HHHHHHHTSCC-CCHHHHHHHHHHHTTC--EEECCTTSCHHHHTHHHHHHHHTT---------SSCEEEEESSHHHHHHH
T ss_pred             HHHHHHHhCCC-CcHHHHHHHHHHhCCC--hhhccCCCCccHHHHHHHHHHHhc---------CCceEEEeccHHHHHhH
Confidence            33444567886 9999999988888887  999999999999999999755544         44499999999999999


Q ss_pred             HHHHHHHHhhcCCceeEEeeCC--------------------------------------------------CChHHHHH
Q 043110          127 YEILQKLLHRFRWIVPGYVMGG--------------------------------------------------GNRSKEKA  156 (316)
Q Consensus       127 ~~~~~~~~~~~~~~~~~~~~~~--------------------------------------------------~~~~~~~~  156 (316)
                      ++++..+...++ +.++++...                                                  .+. .+.+
T Consensus       133 ae~m~~l~~~Lg-lsvg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~-~err  210 (822)
T 3jux_A          133 ALWMGPVYLFLG-LRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEAVEAFQVELKE-ITRK  210 (822)
T ss_dssp             HHHHHHHHHHTT-CCEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHHHTTTCEECCB-CCHH
T ss_pred             HHHHHHHHHHhC-CEEEEEcCCCcccccccccchhhhhhhcccccccccccccccccccccccccchhccccCCH-HHHH
Confidence            999999998877 455555541                                                  111 1222


Q ss_pred             HHhcCCcEEEeCcHHH-HHHHhcC-----CccccCceeEEEEecchhhh
Q 043110          157 RLRKGISILVATPGHL-LDHLKHT-----SSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       157 ~l~~~~~IlV~Tp~~l-~~~l~~~-----~~~~~~~l~~lViDEad~l~  199 (316)
                      ..+ .+||..||..-| +++++..     .......+.+.|+||+|.++
T Consensus       211 ~aY-~~DItYgTn~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiL  258 (822)
T 3jux_A          211 EAY-LCDVTYGTNNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVL  258 (822)
T ss_dssp             HHH-HSSEEEEEHHHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHH
T ss_pred             HHh-cCCCEEccCcchhhHhHHhhccCCHHHhccCCCCeEEEeccccee
Confidence            333 379999999876 4555432     12234568899999999876

>1w36_D RECD, exodeoxyribonuclease V alpha chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 PDB: 3k70_D*

Probab=99.12  E-value=3.2e-10  Score=110.29  Aligned_cols=160  Identities=23%  Similarity=0.305  Sum_probs=94.9

Q ss_pred             CCHH-HHHHHHHHc-CCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchH--HHHHHHHHHHhhhcCCCCCCCCCeeEEEEe
Q 043110           42 LDST-LCDQLRERL-GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKT--VAYLAPIINHLQSYSPRIDRSSGTFALVLV  117 (316)
Q Consensus        42 l~~~-l~~~l~~~~-g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT--~~~~lp~l~~l~~~~~~~~~~~~~~~lil~  117 (316)
                      +++. +...| ..+ +-..-++.|+.+++.++.++++++.|++|+|||  ++++++.+..+..       ..+.++++++
T Consensus       132 ~~~~~~~~~l-~~~~~~~~~~~~Q~~Ai~~~l~~~~~vi~G~pGTGKTt~l~~ll~~l~~~~~-------~~~~~vll~A  203 (608)
T 1w36_D          132 VDEALLAQTL-DKLFPVSDEINWQKVAAAVALTRRISVISGGPGTGKTTTVAKLLAALIQMAD-------GERCRIRLAA  203 (608)
T ss_dssp             CCHHHHHHHH-HTTCCCTTSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHHHHHHHHHHTCS-------SCCCCEEEEB
T ss_pred             CCHHHHHHHH-HHHhccCCCCHHHHHHHHHHhcCCCEEEEeCCCCCHHHHHHHHHHHHHHhhh-------cCCCeEEEEe
Confidence            4443 44455 432 222237899999999999999999999999999  5677777665421       1345699999


Q ss_pred             CChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCc-EEEeCcHHHHHHHhcCCccccCceeEEEEecch
Q 043110          118 PTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGIS-ILVATPGHLLDHLKHTSSFLHTNLRWIIFDEAD  196 (316)
Q Consensus       118 Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~-IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad  196 (316)
                      ||..++.++.+.+...+...+. ..... .+...  +    ....+ ++-.+|+.. . +....... ..++++|||||+
T Consensus       204 PTg~AA~~L~e~~~~~~~~l~l-~~~~~-~~~~~--~----~~Tih~ll~~~~~~~-~-~~~~~~~~-l~~d~lIIDEAs  272 (608)
T 1w36_D          204 PTGKAAARLTESLGKALRQLPL-TDEQK-KRIPE--D----ASTLHRLLGAQPGSQ-R-LRHHAGNP-LHLDVLVVDEAS  272 (608)
T ss_dssp             SSHHHHHHHHHHHTHHHHHSSC-CSCCC-CSCSC--C----CBTTTSCC-------------CTTSC-CSCSEEEECSGG
T ss_pred             CChhHHHHHHHHHHHHHhcCCC-CHHHH-hccch--h----hhhhHhhhccCCCch-H-HHhccCCC-CCCCEEEEechh
Confidence            9999999999888776654421 10000 00000  0    00111 222223221 1 11111112 268899999999


Q ss_pred             hhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEe
Q 043110          197 RILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLS  239 (316)
Q Consensus       197 ~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~S  239 (316)
                       |++   ...+..++..++.               ..|++++.
T Consensus       273 -ml~---~~~~~~Ll~~l~~---------------~~~liLvG  296 (608)
T 1w36_D          273 -MID---LPMMSRLIDALPD---------------HARVIFLG  296 (608)
T ss_dssp             -GCB---HHHHHHHHHTCCT---------------TCEEEEEE
T ss_pred             -hCC---HHHHHHHHHhCCC---------------CCEEEEEc
Confidence             555   4677888887765               67777764

>3upu_A ATP-dependent DNA helicase DDA; RECA-like domain, SH3 domain, PIN-tower interface, coupling hydrolysis to DNA unwinding, ssDNA; 3.30A {Enterobacteria phage T4}

Probab=98.28  E-value=6.1e-06  Score=77.42  Aligned_cols=70  Identities=24%  Similarity=0.324  Sum_probs=50.8

Q ss_pred             HcCCCCCcHHHHHHHHHHhCC----C-cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHH
Q 043110           53 RLGFEAPTKVQAQAIPVILSG----R-DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVY  127 (316)
Q Consensus        53 ~~g~~~p~~~Q~~~i~~il~g----~-d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~  127 (316)
                      -+.|..+++-|++++..++..    + .+++.|+.|+|||... ..++..+.....       ..+++++||...+..+.
T Consensus        20 p~~~~~Ln~~Q~~av~~~~~~i~~~~~~~li~G~aGTGKT~ll-~~~~~~l~~~~~-------~~il~~a~T~~Aa~~l~   91 (459)
T 3upu_A           20 HMTFDDLTEGQKNAFNIVMKAIKEKKHHVTINGPAGTGATTLT-KFIIEALISTGE-------TGIILAAPTHAAKKILS   91 (459)
T ss_dssp             -CCSSCCCHHHHHHHHHHHHHHHSSSCEEEEECCTTSCHHHHH-HHHHHHHHHTTC-------CCEEEEESSHHHHHHHH
T ss_pred             CCccccCCHHHHHHHHHHHHHHhcCCCEEEEEeCCCCCHHHHH-HHHHHHHHhcCC-------ceEEEecCcHHHHHHHH
Confidence            467889999999999876532    3 8999999999999754 445555554211       24899999988876655


Q ss_pred             HHH
Q 043110          128 EIL  130 (316)
Q Consensus       128 ~~~  130 (316)
                      +.+
T Consensus        92 ~~~   94 (459)
T 3upu_A           92 KLS   94 (459)
T ss_dssp             HHH
T ss_pred             hhh
Confidence            443

>4b3f_X DNA-binding protein smubp-2; hydrolase, helicase; 2.50A {Homo sapiens} PDB: 4b3g_A

Probab=98.25  E-value=3.7e-06  Score=82.37  Aligned_cols=67  Identities=22%  Similarity=0.294  Sum_probs=52.4

Q ss_pred             CCcHHHHHHHHHHhCCCc-EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSGRD-VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d-~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .+++-|.+|+..++..++ .+|+||.|+|||.+..-.+.+.+..         +.++|+++||..-+.++.+.+...
T Consensus       189 ~LN~~Q~~AV~~al~~~~~~lI~GPPGTGKT~ti~~~I~~l~~~---------~~~ILv~a~TN~AvD~i~erL~~~  256 (646)
T 4b3f_X          189 CLDTSQKEAVLFALSQKELAIIHGPPGTGKTTTVVEIILQAVKQ---------GLKVLCCAPSNIAVDNLVERLALC  256 (646)
T ss_dssp             TCCHHHHHHHHHHHHCSSEEEEECCTTSCHHHHHHHHHHHHHHT---------TCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCHHHHHHHHHHhcCCCceEEECCCCCCHHHHHHHHHHHHHhC---------CCeEEEEcCchHHHHHHHHHHHhc
Confidence            468999999999887776 7999999999998855444444332         445999999999998888777543

>3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, HYD; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A*

Probab=98.24  E-value=5e-06  Score=80.11  Aligned_cols=62  Identities=21%  Similarity=0.231  Sum_probs=48.7

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      .+++.|++++..++.++.+++.|+.|+|||... ..++..+..        .+.++++++||...+..+.+
T Consensus       189 ~L~~~Q~~Av~~~~~~~~~~I~G~pGTGKTt~i-~~l~~~l~~--------~g~~Vl~~ApT~~Aa~~L~e  250 (574)
T 3e1s_A          189 GLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTT-KAVADLAES--------LGLEVGLCAPTGKAARRLGE  250 (574)
T ss_dssp             TCCHHHHHHHHHHTTCSEEEEECCTTSCHHHHH-HHHHHHHHH--------TTCCEEEEESSHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhCCEEEEEcCCCCCHHHHH-HHHHHHHHh--------cCCeEEEecCcHHHHHHhHh
Confidence            478999999999999999999999999999763 334444443        24459999999988876654

>2gk6_A Regulator of nonsense transcripts 1; UPF1, helicase, NMD, hydrolase; HET: ADP; 2.40A {Homo sapiens} PDB: 2gjk_A* 2gk7_A 2xzo_A* 2xzp_A

Probab=98.18  E-value=2.7e-05  Score=75.93  Aligned_cols=69  Identities=25%  Similarity=0.273  Sum_probs=53.6

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           57 EAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      ..+++.|.+|+..++.+.-.++.||+|+|||.+.. .++..+...       .+.++++++||...+.++.+.+...
T Consensus       179 ~~ln~~Q~~av~~~l~~~~~li~GppGTGKT~~~~-~~i~~l~~~-------~~~~ilv~a~tn~A~~~l~~~l~~~  247 (624)
T 2gk6_A          179 PDLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ-------GNGPVLVCAPSNIAVDQLTEKIHQT  247 (624)
T ss_dssp             CCCCHHHHHHHHHHHTCSEEEEECCTTSCHHHHHH-HHHHHHHTS-------SSCCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCCCHHHHHHHHHHhcCCCeEEECCCCCCHHHHHH-HHHHHHHHc-------CCCeEEEEeCcHHHHHHHHHHHHhc
Confidence            35789999999998887789999999999998753 344444331       2345999999999999988877653

>2xzl_A ATP-dependent helicase NAM7; hydrolase-RNA complex, NMD, RNA degradation, allosteric REGU; HET: ADP 1PE; 2.40A {Saccharomyces cerevisiae}

Probab=98.14  E-value=4.4e-05  Score=76.30  Aligned_cols=69  Identities=26%  Similarity=0.301  Sum_probs=53.6

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           57 EAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      ..+++.|.+|+..++.+.-+++.||.|+|||.+..- ++..+...       .+.++|+++||...+.++.+.+...
T Consensus       359 ~~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~~i~~-~i~~l~~~-------~~~~ILv~a~tn~A~d~l~~rL~~~  427 (802)
T 2xzl_A          359 AQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSAT-IVYHLSKI-------HKDRILVCAPSNVAVDHLAAKLRDL  427 (802)
T ss_dssp             CCCCHHHHHHHHHHTTCSEEEEECSTTSSHHHHHHH-HHHHHHHH-------HCCCEEEEESSHHHHHHHHHHHHHT
T ss_pred             ccCCHHHHHHHHHHhcCCCEEEECCCCCCHHHHHHH-HHHHHHhC-------CCCeEEEEcCcHHHHHHHHHHHHhh
Confidence            457899999999998877799999999999987543 33333321       1344999999999999998887764

>2wjy_A Regulator of nonsense transcripts 1; nonsense mediated decay, zinc-finger, ATP-binding, metal-BIN UPF2, UPF1, helicase, hydrolase; 2.50A {Homo sapiens} PDB: 2wjv_A 2iyk_A

Probab=98.03  E-value=6.4e-05  Score=75.11  Aligned_cols=68  Identities=25%  Similarity=0.279  Sum_probs=53.1

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .+++.|.+|+..++.+.-.++.||+|+|||.+.. .++..+...       .+.++++++||..-+.++.+.+...
T Consensus       356 ~Ln~~Q~~Av~~~l~~~~~lI~GppGTGKT~ti~-~~i~~l~~~-------~~~~ilv~a~tn~A~~~l~~~l~~~  423 (800)
T 2wjy_A          356 DLNHSQVYAVKTVLQRPLSLIQGPPGTGKTVTSA-TIVYHLARQ-------GNGPVLVCAPSNIAVDQLTEKIHQT  423 (800)
T ss_dssp             CCCHHHHHHHHHHHTSSEEEEECCTTSCHHHHHH-HHHHHHHTT-------CSSCEEEEESSHHHHHHHHHHHHTT
T ss_pred             CCCHHHHHHHHHhccCCeEEEEcCCCCCHHHHHH-HHHHHHHHc-------CCCcEEEEcCcHHHHHHHHHHHHHh
Confidence            4689999999998888789999999999998743 344444431       2345999999999998888777553

>2o0j_A Terminase, DNA packaging protein GP17; nucleotide-binding fold, hydrolase; HET: DNA ADP; 1.80A {Enterobacteria phage T4} PDB: 2o0h_A* 2o0k_A*

Probab=97.58  E-value=0.0006  Score=62.12  Aligned_cols=74  Identities=12%  Similarity=0.103  Sum_probs=57.6

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      .++|+|...+..+...+-+++..+-+.|||.+....++..+..       ..+..+++++|+++.|..+.+.++.+....
T Consensus       163 ~L~p~Qk~il~~l~~~R~~vi~~sRq~GKT~l~a~~~l~~a~~-------~~g~~v~~vA~t~~qA~~vf~~i~~mi~~~  235 (385)
T 2o0j_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCF-------NKDKAVGILAHKGSMSAEVLDRTKQAIELL  235 (385)
T ss_dssp             CCCHHHHHHHHHHHHSSEEEEEECSSSCHHHHHHHHHHHHHHS-------SSSCEEEEEESSHHHHHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHHhhccCcEEEEEEcCcCChhHHHHHHHHHHHHh-------CCCCeEEEEeCCHHHHHHHHHHHHHHHHhC
Confidence            5899999999876555668999999999999865555544333       135569999999999998988888887654


Q ss_pred             C
Q 043110          138 R  138 (316)
Q Consensus       138 ~  138 (316)
                      +
T Consensus       236 P  236 (385)
T 2o0j_A          236 P  236 (385)
T ss_dssp             C
T ss_pred             h
Confidence            3

>3cpe_A Terminase, DNA packaging protein GP17; large terminase, alternative initiation, ATP-binding, DNA- binding, hydrolase, nuclease; HET: DNA; 2.80A {Bacteriophage T4} PDB: 3ezk_A*

Probab=97.37  E-value=0.0065  Score=58.67  Aligned_cols=74  Identities=12%  Similarity=0.103  Sum_probs=57.8

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      .|+|+|+..+..+...+-.++..+-|+|||.+...-++..+..       ..+..+++++|+++.|..+.+.++.+....
T Consensus       163 ~l~p~Q~~i~~~l~~~r~~~i~~~Rq~GKS~~~a~~~l~~~~~-------~~~~~i~~va~t~~qA~~~~~~i~~~i~~~  235 (592)
T 3cpe_A          163 QLRDYQRDMLKIMSSKRMTVCNLSRQLGKTTVVAIFLAHFVCF-------NKDKAVGILAHKGSMSAEVLDRTKQAIELL  235 (592)
T ss_dssp             CCCHHHHHHHHHHHHCSEEEEEECSSSCHHHHHHHHHHHHHHT-------SSSCEEEEEESSHHHHHHHHHHHHHHHTTS
T ss_pred             cCCHHHHHHHHhhccccEEEEEEcCccChHHHHHHHHHHHHHh-------CCCCeEEEEECCHHHHHHHHHHHHHHHHhC
Confidence            4799999999877556779999999999999865544444433       124569999999999999998888887654


Q ss_pred             C
Q 043110          138 R  138 (316)
Q Consensus       138 ~  138 (316)
                      +
T Consensus       236 p  236 (592)
T 3cpe_A          236 P  236 (592)
T ss_dssp             C
T ss_pred             h
Confidence            3

>3ec2_A DNA replication protein DNAC; helicase loader, replication initiation factor, ATP-binding, nucleotide-binding; HET: DNA ADP; 2.70A {Aquifex aeolicus} PDB: 3ecc_A*

Probab=97.11  E-value=0.0035  Score=50.42  Aligned_cols=19  Identities=26%  Similarity=0.408  Sum_probs=16.7

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .|+.+++.||+|+|||...
T Consensus        37 ~g~~~~l~G~~G~GKTtL~   55 (180)
T 3ec2_A           37 EGKGLTFVGSPGVGKTHLA   55 (180)
T ss_dssp             GCCEEEECCSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4788999999999999764

>3lfu_A DNA helicase II; SF1 helicase, ATP-binding, DNA damage, DNA REP replication, DNA-binding, hydrolase, nucleotide-B SOS response; HET: DNA; 1.80A {Escherichia coli} PDB: 2is6_A* 2is2_A* 2is1_A* 2is4_A*

Probab=97.07  E-value=0.0016  Score=63.38  Aligned_cols=71  Identities=18%  Similarity=0.184  Sum_probs=53.7

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           57 EAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      ..+++-|.+++..  .+..++|.|+.|||||.+.+--+...+.....     ..-++|++++|+..+.++.+.+..+.
T Consensus         8 ~~Ln~~Q~~av~~--~~~~~lV~a~aGsGKT~~l~~ri~~l~~~~~~-----~~~~iL~ltft~~aa~e~~~rl~~~~   78 (647)
T 3lfu_A            8 DSLNDKQREAVAA--PRSNLLVLAGAGSGKTRVLVHRIAWLMSVENC-----SPYSIMAVTFTNKAAAEMRHRIGQLM   78 (647)
T ss_dssp             TTCCHHHHHHHTC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTSCC-----CGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hcCCHHHHHHHhC--CCCCEEEEECCCCCHHHHHHHHHHHHHHhCCC-----ChhhEEEEeccHHHHHHHHHHHHHHh
Confidence            3689999999963  35679999999999998865545444433111     12359999999999999999888764

>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=97.00  E-value=0.0011  Score=64.90  Aligned_cols=67  Identities=36%  Similarity=0.438  Sum_probs=51.5

Q ss_pred             CCCCCcHHHHHHHHHHh----CCC-cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHH
Q 043110           55 GFEAPTKVQAQAIPVIL----SGR-DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEI  129 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~il----~g~-d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~  129 (316)
                      +| .|++.|..++..+.    .|. ..++.+.||||||+++.- ++.....           .+|||+|+..+|.|+++.
T Consensus         6 ~~-~~~~~q~~ai~~l~~~~~~~~~~~~l~g~tgs~kt~~~a~-~~~~~~~-----------~~lvv~~~~~~A~ql~~e   72 (664)
T 1c4o_A            6 GP-SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTMAK-VIEALGR-----------PALVLAPNKILAAQLAAE   72 (664)
T ss_dssp             SC-CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHHTC-----------CEEEEESSHHHHHHHHHH
T ss_pred             CC-CCCCCChHHHHHHHHHHhcCCCcEEEEcCCCcHHHHHHHH-HHHHhCC-----------CEEEEecCHHHHHHHHHH
Confidence            56 69999999987655    343 467889999999987532 3333211           199999999999999999


Q ss_pred             HHHHH
Q 043110          130 LQKLL  134 (316)
Q Consensus       130 ~~~~~  134 (316)
                      ++.++
T Consensus        73 l~~~~   77 (664)
T 1c4o_A           73 FRELF   77 (664)
T ss_dssp             HHHHC
T ss_pred             HHHHC
Confidence            99986

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=96.93  E-value=0.003  Score=58.39  Aligned_cols=97  Identities=19%  Similarity=0.178  Sum_probs=55.7

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE  154 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  154 (316)
                      -.++.|+.|+|||...    .+.+..          ...+|++||++++..+.+.+...    +..              
T Consensus       163 v~~I~G~aGsGKTt~I----~~~~~~----------~~~lVlTpT~~aa~~l~~kl~~~----~~~--------------  210 (446)
T 3vkw_A          163 VVLVDGVPGCGKTKEI----LSRVNF----------EEDLILVPGRQAAEMIRRRANAS----GII--------------  210 (446)
T ss_dssp             EEEEEECTTSCHHHHH----HHHCCT----------TTCEEEESCHHHHHHHHHHHTTT----SCC--------------
T ss_pred             EEEEEcCCCCCHHHHH----HHHhcc----------CCeEEEeCCHHHHHHHHHHhhhc----Ccc--------------
Confidence            3789999999999874    222211          12799999999998777665321    000              


Q ss_pred             HHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhc
Q 043110          155 KARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILG  215 (316)
Q Consensus       155 ~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~  215 (316)
                           ...+.-|.|-+.++.   +.........+++|||||-. ++.   ..+..++...+
T Consensus       211 -----~~~~~~V~T~dsfL~---~~~~~~~~~~d~liiDE~sm-~~~---~~l~~l~~~~~  259 (446)
T 3vkw_A          211 -----VATKDNVRTVDSFLM---NYGKGARCQFKRLFIDEGLM-LHT---GCVNFLVEMSL  259 (446)
T ss_dssp             -----CCCTTTEEEHHHHHH---TTTSSCCCCCSEEEEETGGG-SCH---HHHHHHHHHTT
T ss_pred             -----ccccceEEEeHHhhc---CCCCCCCCcCCEEEEeCccc-CCH---HHHHHHHHhCC
Confidence                 011233556554432   21221112478999999984 343   33444555544

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=96.69  E-value=0.0019  Score=50.69  Aligned_cols=19  Identities=26%  Similarity=0.387  Sum_probs=16.6

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .|..+++.+|+|+|||...
T Consensus        35 ~g~~~~l~G~~G~GKTtL~   53 (149)
T 2kjq_A           35 HGQFIYVWGEEGAGKSHLL   53 (149)
T ss_dssp             CCSEEEEESSSTTTTCHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            6788999999999999764

>1pjr_A PCRA; DNA repair, DNA replication, SOS response, helicase, ATP- binding, DNA-binding; 2.50A {Geobacillus stearothermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1qhg_A* 3pjr_A* 2pjr_A* 1qhh_B* 1qhh_D* 1qhh_A* 1qhh_C* 2pjr_B*

Probab=96.69  E-value=0.0054  Score=60.66  Aligned_cols=71  Identities=23%  Similarity=0.183  Sum_probs=53.8

Q ss_pred             CCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           57 EAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        57 ~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      ..+++-|++++..  .+..++|.|+.|||||.+..--+...+.....     ..-.+|+|+.|+..|.++.+++..+.
T Consensus        10 ~~Ln~~Q~~av~~--~~g~~lV~AgAGSGKT~vL~~ri~~ll~~~~~-----~p~~IL~vTFTnkAA~Em~~Rl~~~l   80 (724)
T 1pjr_A           10 AHLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHV-----APWNILAITFTNKAAREMRERVQSLL   80 (724)
T ss_dssp             TTSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCC-----CGGGEEEEESSHHHHHHHHHHHHHHH
T ss_pred             hhCCHHHHHHHhC--CCCCEEEEEcCCCCHHHHHHHHHHHHHHhcCC-----CHHHeEEEeccHHHHHHHHHHHHHHh
Confidence            3689999999876  35689999999999999865545555443111     12349999999999999998888764

>2zpa_A Uncharacterized protein YPFI; RNA modification enzyme, RNA helicase, acetyltransferase, GCN5 acetyltransferase; HET: ACO ADP; 2.35A {Escherichia coli K12}

Probab=96.68  E-value=0.0024  Score=61.98  Aligned_cols=114  Identities=22%  Similarity=0.271  Sum_probs=72.7

Q ss_pred             CCcHHHHHHHHHHhC--CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           58 APTKVQAQAIPVILS--GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~--g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      .+|.-|.+++..+..  ....++.|+-|.|||.+.-+.+.....            .++|.+|+.+-+..+.+.    ..
T Consensus       175 ~~T~dQ~~al~~~~~~~~~~~vlta~RGRGKSa~lG~~~a~~~~------------~~~vtAP~~~a~~~l~~~----~~  238 (671)
T 2zpa_A          175 APQPEQQQLLKQLMTMPPGVAAVTAARGRGKSALAGQLISRIAG------------RAIVTAPAKASTDVLAQF----AG  238 (671)
T ss_dssp             SCCHHHHHHHHHHTTCCSEEEEEEECTTSSHHHHHHHHHHHSSS------------CEEEECSSCCSCHHHHHH----HG
T ss_pred             CCCHHHHHHHHHHHHhhhCeEEEecCCCCCHHHHHHHHHHHHHh------------CcEEECCCHHHHHHHHHH----hh
Confidence            578999999988876  334799999999999765544433221            169999998876543332    21


Q ss_pred             hcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhc
Q 043110          136 RFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILG  215 (316)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~  215 (316)
                      .                          .|-...|..+..   .     ....++||||||=.+    -.+.+..++..  
T Consensus       239 ~--------------------------~i~~~~Pd~~~~---~-----~~~~dlliVDEAAaI----p~pll~~ll~~--  278 (671)
T 2zpa_A          239 E--------------------------KFRFIAPDALLA---S-----DEQADWLVVDEAAAI----PAPLLHQLVSR--  278 (671)
T ss_dssp             G--------------------------GCCBCCHHHHHH---S-----CCCCSEEEEETGGGS----CHHHHHHHHTT--
T ss_pred             C--------------------------CeEEeCchhhhh---C-----cccCCEEEEEchhcC----CHHHHHHHHhh--
Confidence            1                          022335554332   1     135789999999876    33555555542  


Q ss_pred             cCcccccCCCCccccccceEEEEeeecch
Q 043110          216 SRNIASIGEGNEVSNVKRQNLLLSATLNE  244 (316)
Q Consensus       216 ~~~~~~~~~~~~~~~~~~q~i~~SAT~~~  244 (316)
                                       ...++||.|+..
T Consensus       279 -----------------~~~v~~~tTv~G  290 (671)
T 2zpa_A          279 -----------------FPRTLLTTTVQG  290 (671)
T ss_dssp             -----------------SSEEEEEEEBSS
T ss_pred             -----------------CCeEEEEecCCc
Confidence                             234788888753

>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex (helicase/DNA), DNA unwinding, hydrolase/DNA complex; HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19

Probab=96.67  E-value=0.0039  Score=61.14  Aligned_cols=70  Identities=20%  Similarity=0.139  Sum_probs=53.2

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      .+++-|++++..  .+..++|.|+.|||||.+.+--+...+.....     ...++|+|+.|+..+.++.+.+....
T Consensus         2 ~L~~~Q~~av~~--~~~~~lV~AgaGSGKT~~l~~ri~~ll~~~~~-----~~~~IL~lTfT~~Aa~em~~Rl~~~l   71 (673)
T 1uaa_A            2 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGY-----QARHIAAVTFTNKAAREMKERVGQTL   71 (673)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCC-----CGGGEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CCCHHHHHHHhC--CCCCEEEEeCCCCChHHHHHHHHHHHHHhcCC-----CHHHeEEEeccHHHHHHHHHHHHHHc
Confidence            478999999975  36789999999999999865545554443211     12349999999999999999888764

>2b8t_A Thymidine kinase; deoxyribonucleoside kinase, zinc-binding domain, TK1, UU-TK, transferase; HET: THM; 2.00A {Ureaplasma parvum} SCOP: c.37.1.24 g.39.1.14 PDB: 2uz3_A*

Probab=96.58  E-value=0.0026  Score=53.45  Aligned_cols=91  Identities=18%  Similarity=0.223  Sum_probs=50.6

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCCh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR  151 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (316)
                      .|.=.++.+++|+|||.+.+-- +..+..        .+.+++++.|...--   .  ...+....          |...
T Consensus        11 ~G~i~litG~mGsGKTT~ll~~-~~r~~~--------~g~kVli~~~~~d~r---~--~~~i~srl----------G~~~   66 (223)
T 2b8t_A           11 IGWIEFITGPMFAGKTAELIRR-LHRLEY--------ADVKYLVFKPKIDTR---S--IRNIQSRT----------GTSL   66 (223)
T ss_dssp             CCEEEEEECSTTSCHHHHHHHH-HHHHHH--------TTCCEEEEEECCCGG---G--CSSCCCCC----------CCSS
T ss_pred             CcEEEEEECCCCCcHHHHHHHH-HHHHHh--------cCCEEEEEEeccCch---H--HHHHHHhc----------CCCc
Confidence            4556888999999999875443 333332        244588888765310   0  00001110          1100


Q ss_pred             HHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhh
Q 043110          152 SKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRI  198 (316)
Q Consensus       152 ~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l  198 (316)
                                ..+-+.+...+++.+...  ..-...++|||||++.+
T Consensus        67 ----------~~~~~~~~~~i~~~i~~~--~~~~~~dvViIDEaQ~l  101 (223)
T 2b8t_A           67 ----------PSVEVESAPEILNYIMSN--SFNDETKVIGIDEVQFF  101 (223)
T ss_dssp             ----------CCEEESSTHHHHHHHHST--TSCTTCCEEEECSGGGS
T ss_pred             ----------cccccCCHHHHHHHHHHH--hhCCCCCEEEEecCccC
Confidence                      123456666777766542  11235789999999974

>2orw_A Thymidine kinase; TMTK, TP4A, transferase; HET: 4TA; 1.50A {Thermotoga maritima} PDB: 2qpo_A 2qq0_A* 2qqe_A*

Probab=96.48  E-value=0.024  Score=45.87  Aligned_cols=40  Identities=20%  Similarity=0.292  Sum_probs=26.3

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCCh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTS  120 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~  120 (316)
                      .|+-.++.++.|+|||...+- ++.....        .+.+++++.|..
T Consensus         2 ~g~i~vi~G~~gsGKTT~ll~-~~~~~~~--------~g~~v~~~~~~~   41 (184)
T 2orw_A            2 SGKLTVITGPMYSGKTTELLS-FVEIYKL--------GKKKVAVFKPKI   41 (184)
T ss_dssp             CCCEEEEEESTTSSHHHHHHH-HHHHHHH--------TTCEEEEEEEC-
T ss_pred             ccEEEEEECCCCCCHHHHHHH-HHHHHHH--------CCCeEEEEeecc
Confidence            355678999999999987543 3333322        134588888884

>1l8q_A Chromosomal replication initiator protein DNAA; AAA+, helix-turn-helix, nucleotide-binding, DNA binding, REP initiation, DNA binding protein; HET: ADP; 2.70A {Aquifex aeolicus} SCOP: a.4.12.2 c.37.1.20 PDB: 3r8f_A* 2hcb_A*

Probab=96.40  E-value=0.029  Score=49.49  Aligned_cols=18  Identities=28%  Similarity=0.412  Sum_probs=15.6

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      +..+++.||+|+|||...
T Consensus        37 ~~~lll~G~~GtGKT~la   54 (324)
T 1l8q_A           37 YNPIFIYGSVGTGKTHLL   54 (324)
T ss_dssp             CSSEEEECSSSSSHHHHH
T ss_pred             CCeEEEECCCCCcHHHHH
Confidence            457999999999999764

>3te6_A Regulatory protein SIR3; heterochromatin, gene silencing, SIR complex, HMR, HML, TELO AAA+ domain, structural, nucleus, gene RE; 2.80A {Saccharomyces cerevisiae}

Probab=96.38  E-value=0.044  Score=48.46  Aligned_cols=28  Identities=11%  Similarity=0.132  Sum_probs=20.1

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      .+.++++.||+|+|||.+.- .++..+..
T Consensus        44 ~~~~lli~GpPGTGKT~~v~-~v~~~L~~   71 (318)
T 3te6_A           44 QNKLFYITNADDSTKFQLVN-DVMDELIT   71 (318)
T ss_dssp             CCCEEEEECCCSHHHHHHHH-HHHHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHHH-HHHHHHHH
Confidence            34579999999999998753 34455543

>3u4q_A ATP-dependent helicase/nuclease subunit A; helicase, nuclease, double strand DNA repair, protein-DNA CO hydrolase-DNA complex; HET: DNA; 2.80A {Bacillus subtilis} PDB: 3u44_A*

Probab=96.36  E-value=0.0076  Score=63.19  Aligned_cols=73  Identities=26%  Similarity=0.258  Sum_probs=55.6

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      .+|+-|.++|..  .+++++|.|..|||||.+.+--++..+......   ...-+++++++|+..+.++.+.+.....
T Consensus        10 ~~t~eQ~~~i~~--~~~~~~v~a~AGSGKT~vl~~ri~~ll~~~~~~---~~~~~il~~Tft~~aa~e~~~ri~~~l~   82 (1232)
T 3u4q_A           10 TWTDDQWNAIVS--TGQDILVAAAAGSGKTAVLVERMIRKITAEENP---IDVDRLLVVTFTNASAAEMKHRIAEALE   82 (1232)
T ss_dssp             CCCHHHHHHHHC--CSSCEEEEECTTCCHHHHHHHHHHHHHSCSSSC---CCGGGEEEECSSHHHHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHhC--CCCCEEEEecCCCcHHHHHHHHHHHHHhcCCCC---CCccceEEEeccHHHHHHHHHHHHHHHH
Confidence            489999999976  388999999999999998665566655542110   1223599999999999999988877543

>1xx6_A Thymidine kinase; NESG, northeast structural genomics consortium, protein STRU initiative, PSI, structural genomics, DNA synthesis; HET: ADP; 2.00A {Clostridium acetobutylicum} SCOP: c.37.1.24 g.39.1.14

Probab=96.29  E-value=0.022  Score=46.54  Aligned_cols=40  Identities=15%  Similarity=0.141  Sum_probs=26.8

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCCh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTS  120 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~  120 (316)
                      .|+=.++.+++|+|||.+.+- ++.+...        .+.+++++.|..
T Consensus         7 ~g~i~v~~G~mgsGKTT~ll~-~a~r~~~--------~g~kV~v~k~~~   46 (191)
T 1xx6_A            7 HGWVEVIVGPMYSGKSEELIR-RIRRAKI--------AKQKIQVFKPEI   46 (191)
T ss_dssp             CCEEEEEECSTTSSHHHHHHH-HHHHHHH--------TTCCEEEEEEC-
T ss_pred             CCEEEEEECCCCCcHHHHHHH-HHHHHHH--------CCCEEEEEEecc
Confidence            345578899999999987544 3333332        245599998884

>2j9r_A Thymidine kinase; TK1, DNK, lasso, transferase, ATP-binding, deoxyribonucleoside kinase, DNA synthesis, phosphate accept nucleotide-binding; HET: THM; 2.7A {Bacillus anthracis} PDB: 2ja1_A*

Probab=96.09  E-value=0.017  Score=47.90  Aligned_cols=40  Identities=15%  Similarity=0.199  Sum_probs=26.2

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      |+=.++.++.|+|||...+--+......         +.+++++.|...
T Consensus        28 G~l~vitG~MgsGKTT~lL~~a~r~~~~---------g~kVli~k~~~d   67 (214)
T 2j9r_A           28 GWIEVICGSMFSGKSEELIRRVRRTQFA---------KQHAIVFKPCID   67 (214)
T ss_dssp             CEEEEEECSTTSCHHHHHHHHHHHHHHT---------TCCEEEEECC--
T ss_pred             CEEEEEECCCCCcHHHHHHHHHHHHHHC---------CCEEEEEEeccC
Confidence            3446789999999998765444444332         445999998754

>3u61_B DNA polymerase accessory protein 44; AAA+, ATP hydrolase, clamp loader, sliding clamp, primer-TEM DNA, DNA binding protein-DNA complex; HET: DNA ADP 08T; 3.20A {Enterobacteria phage T4} PDB: 3u5z_B* 3u60_B*

Probab=96.09  E-value=0.035  Score=48.85  Aligned_cols=30  Identities=17%  Similarity=0.225  Sum_probs=19.7

Q ss_pred             ceeEEEEecchhhhcCCcHHHHHHHHHHhc
Q 043110          186 NLRWIIFDEADRILELGFGKEIEEILDILG  215 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~~~~~i~~i~~~l~  215 (316)
                      ..++++|||+|.+........+..+++..+
T Consensus       105 ~~~vliiDEi~~l~~~~~~~~L~~~le~~~  134 (324)
T 3u61_B          105 RQKVIVIDEFDRSGLAESQRHLRSFMEAYS  134 (324)
T ss_dssp             CEEEEEEESCCCGGGHHHHHHHHHHHHHHG
T ss_pred             CCeEEEEECCcccCcHHHHHHHHHHHHhCC
Confidence            678999999999862223445555555544

>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=96.04  E-value=0.0012  Score=64.53  Aligned_cols=42  Identities=29%  Similarity=0.304  Sum_probs=28.1

Q ss_pred             eCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          146 MGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       146 ~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                      .|+.+..........+     +||++|++++...        .++|+||+|++++
T Consensus       304 ~G~e~~~~~~~~~~~g-----~tpg~LlDyl~~~--------~llVlDEa~~~l~  345 (661)
T 2d7d_A          304 SGIENYSRHLTLRPPG-----STPYTLLDYFPDD--------FMIVVDESHVTIP  345 (661)
T ss_dssp             TTGGGGHHHHTTCCTT-----CCCBCGGGGSCSS--------CEEEEETHHHHHH
T ss_pred             ccchhHHHHHccccCC-----CCccHHHHHcccC--------cEEEEecHHHHHH
Confidence            3444554444333333     8999999988542        2899999999874

>3h4m_A Proteasome-activating nucleotidase; ATPase, PAN, ATP-binding, nucleotide-binding, HY; HET: ADP; 3.11A {Methanocaldococcus jannaschii}

Probab=96.02  E-value=0.018  Score=49.72  Aligned_cols=54  Identities=17%  Similarity=0.294  Sum_probs=34.0

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHH-HHHHHHH--hCCCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQ-AQAIPVI--LSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q-~~~i~~i--l~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|+++.-.+..++.+.+...    .+.+ ...+..+  ..++.+++.||+|+|||...
T Consensus        12 ~~~~~~~i~G~~~~~~~l~~~~~----~~~~~~~~~~~~~~~~~~~~ll~G~~GtGKT~la   68 (285)
T 3h4m_A           12 PNVRYEDIGGLEKQMQEIREVVE----LPLKHPELFEKVGIEPPKGILLYGPPGTGKTLLA   68 (285)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHTH----HHHHCHHHHHHHCCCCCSEEEEESSSSSSHHHHH
T ss_pred             CCCCHHHhcCHHHHHHHHHHHHH----HHhhCHHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            34678889878888887744321    1111 1122221  34567999999999999764

>1w4r_A Thymidine kinase; type II, human, cytosolic, phosphorylation, transferase; HET: TTP; 1.83A {Homo sapiens} PDB: 1xbt_A* 2wvj_A* 2j87_A*

Probab=96.01  E-value=0.025  Score=46.20  Aligned_cols=39  Identities=13%  Similarity=0.108  Sum_probs=26.6

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCC
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPT  119 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt  119 (316)
                      .|+=.++.++.|+|||.-.+-.+-+....         +.+++++.|.
T Consensus        19 ~g~l~fiyG~MgsGKTt~Ll~~i~n~~~~---------~~kvl~~kp~   57 (195)
T 1w4r_A           19 RGQIQVILGPMFSGKSTELMRRVRRFQIA---------QYKCLVIKYA   57 (195)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHHHHHHHHT---------TCCEEEEEET
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHc---------CCeEEEEccc
Confidence            45668999999999996544433333332         3449999887

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=96.01  E-value=0.015  Score=48.53  Aligned_cols=19  Identities=11%  Similarity=0.155  Sum_probs=16.4

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .+..+++.||+|+|||...
T Consensus        51 ~~~~~ll~G~~G~GKT~la   69 (242)
T 3bos_A           51 GVQAIYLWGPVKSGRTHLI   69 (242)
T ss_dssp             SCSEEEEECSTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4678999999999999864

>2chg_A Replication factor C small subunit; DNA-binding protein, DNA replication, clamp loader, AAA+ ATPase, ATP-binding, nucleotide-binding; HET: ANP; 2.1A {Archaeoglobus fulgidus}

Probab=95.93  E-value=0.18  Score=40.82  Aligned_cols=17  Identities=35%  Similarity=0.532  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCCchHHHH
Q 043110           74 RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~   90 (316)
                      ..+++.||+|+|||...
T Consensus        39 ~~~ll~G~~G~GKT~l~   55 (226)
T 2chg_A           39 PHLLFSGPPGTGKTATA   55 (226)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CeEEEECCCCCCHHHHH
Confidence            35999999999999764

>2z4s_A Chromosomal replication initiator protein DNAA; AAA+ ATPase, domain III (ATPase domain), ATP-binding, cytoplasm, DNA replication; HET: ADP; 3.00A {Thermotoga maritima} PDB: 2z4r_A*

Probab=95.70  E-value=0.09  Score=48.67  Aligned_cols=18  Identities=22%  Similarity=0.307  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      +..+++.||+|+|||...
T Consensus       130 ~~~lll~Gp~G~GKTtLa  147 (440)
T 2z4s_A          130 YNPLFIYGGVGLGKTHLL  147 (440)
T ss_dssp             SCCEEEECSSSSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            357999999999999864

>1d2n_A N-ethylmaleimide-sensitive fusion protein; hexamerization domain, ATPase, transport; HET: ANP; 1.75A {Cricetulus griseus} SCOP: c.37.1.20 PDB: 1nsf_A*

Probab=95.66  E-value=0.33  Score=41.40  Aligned_cols=17  Identities=29%  Similarity=0.366  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCCchHHHH
Q 043110           74 RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~   90 (316)
                      ..+++.||+|+|||...
T Consensus        65 ~~vLl~G~~GtGKT~la   81 (272)
T 1d2n_A           65 VSVLLEGPPHSGKTALA   81 (272)
T ss_dssp             EEEEEECSTTSSHHHHH
T ss_pred             eEEEEECCCCCcHHHHH
Confidence            46999999999999875

>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=95.57  E-value=0.019  Score=56.17  Aligned_cols=65  Identities=26%  Similarity=0.401  Sum_probs=49.0

Q ss_pred             CCcHHHHHHHHHHh----CCC-cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVIL----SGR-DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        58 ~p~~~Q~~~i~~il----~g~-d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      .|+..|..++..+.    .|. ...+.+.||||||++..- ++....  .         .+|||+|+..+|.|+++.++.
T Consensus        12 ~p~~~Q~~~i~~l~~~~~~~~~~~~l~g~~gs~k~~~~a~-~~~~~~--~---------~~lvv~~~~~~A~~l~~el~~   79 (661)
T 2d7d_A           12 QPQGDQPKAIEKLVKGIQEGKKHQTLLGATGTGKTFTVSN-LIKEVN--K---------PTLVIAHNKTLAGQLYSEFKE   79 (661)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHHHH-HHHHHC--C---------CEEEECSSHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEECcCCcHHHHHHHH-HHHHhC--C---------CEEEEECCHHHHHHHHHHHHH
Confidence            58999988887654    343 467889999999986422 233221  1         199999999999999999999


Q ss_pred             HH
Q 043110          133 LL  134 (316)
Q Consensus       133 ~~  134 (316)
                      +.
T Consensus        80 ~~   81 (661)
T 2d7d_A           80 FF   81 (661)
T ss_dssp             HC
T ss_pred             Hc
Confidence            85

>2p65_A Hypothetical protein PF08_0063; CLPB, malaria, structural genomics, structural genomics consortium, SGC, unknown function; 1.70A {Plasmodium falciparum}

Probab=95.46  E-value=0.11  Score=41.09  Aligned_cols=18  Identities=22%  Similarity=0.346  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      +..+++.||+|+|||...
T Consensus        43 ~~~vll~G~~G~GKT~la   60 (187)
T 2p65_A           43 KNNPILLGDPGVGKTAIV   60 (187)
T ss_dssp             SCEEEEESCGGGCHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            457999999999999764

>2orv_A Thymidine kinase; TP4A (P1-(5'-adenosyl)P4-(5'- (2'deoxythymidil))tetraphosphate, transferase; HET: 4TA; 2.30A {Homo sapiens} SCOP: c.37.1.24 g.39.1.14

Probab=95.44  E-value=0.054  Score=45.46  Aligned_cols=41  Identities=12%  Similarity=0.126  Sum_probs=28.1

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      .|+=.++.++.|+|||...+--+......         |.+++++-|...
T Consensus        18 ~g~l~v~~G~MgsGKTT~lL~~~~r~~~~---------g~kvli~kp~~D   58 (234)
T 2orv_A           18 RGQIQVILGPMFSGKSTELMRRVRRFQIA---------QYKCLVIKYAKD   58 (234)
T ss_dssp             CCEEEEEECCTTSCHHHHHHHHHHHHHTT---------TCCEEEEEETTC
T ss_pred             ceEEEEEECCCCCcHHHHHHHHHHHHHHC---------CCeEEEEeecCC
Confidence            45667889999999998755444443322         455899888753

>3kl4_A SRP54, signal recognition 54 kDa protein; signal recognition particle, SRP, SRP54, FFH, signal sequenc peptide; 3.50A {Sulfolobus solfataricus} PDB: 1qzx_A 1qzw_A

Probab=95.43  E-value=0.2  Score=46.14  Aligned_cols=17  Identities=24%  Similarity=0.329  Sum_probs=14.3

Q ss_pred             cEEEEcCCCCchHHHHH
Q 043110           75 DVLVNAATGTGKTVAYL   91 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~   91 (316)
                      -+++.+++|+|||....
T Consensus        99 vI~lvG~~GsGKTTt~~  115 (433)
T 3kl4_A           99 IIMLVGVQGSGKTTTAG  115 (433)
T ss_dssp             EEEECCCTTSCHHHHHH
T ss_pred             EEEEECCCCCCHHHHHH
Confidence            47889999999998753

>2v1u_A Cell division control protein 6 homolog; DNA replication, nucleotide-binding, replication, archaea; HET: ADP; 3.10A {Aeropyrum pernix}

Probab=95.40  E-value=0.13  Score=46.06  Aligned_cols=19  Identities=37%  Similarity=0.461  Sum_probs=16.1

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .+..+++.||+|+|||...
T Consensus        43 ~~~~vll~G~~G~GKT~l~   61 (387)
T 2v1u_A           43 KPSNALLYGLTGTGKTAVA   61 (387)
T ss_dssp             CCCCEEECBCTTSSHHHHH
T ss_pred             CCCcEEEECCCCCCHHHHH
Confidence            3467999999999999864

>3syl_A Protein CBBX; photosynthesis, rubisco activase, AAA+ protein, calvin cycle chaperone; 3.00A {Rhodobacter sphaeroides} PDB: 3syk_A 3zuh_A*

Probab=95.26  E-value=0.083  Score=45.97  Aligned_cols=18  Identities=28%  Similarity=0.313  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      +.++++.||+|+|||...
T Consensus        67 ~~~vll~G~~GtGKT~la   84 (309)
T 3syl_A           67 TLHMSFTGNPGTGKTTVA   84 (309)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            346999999999999875

>1a5t_A Delta prime, HOLB; zinc finger, DNA replication; 2.20A {Escherichia coli K12} SCOP: a.80.1.1 c.37.1.20 PDB: 1jr3_E* 1xxh_E* 1xxi_E* 3glf_E* 3glg_E* 3glh_E* 3gli_E*

Probab=95.24  E-value=0.24  Score=43.89  Aligned_cols=40  Identities=20%  Similarity=0.242  Sum_probs=27.2

Q ss_pred             CcHHHHHHHHHHh----CCC---cEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           59 PTKVQAQAIPVIL----SGR---DVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        59 p~~~Q~~~i~~il----~g~---d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      ..|+|.+++..+.    +|+   -+++.||.|+|||..... +...+.
T Consensus         3 ~~pw~~~~~~~l~~~i~~~~~~~a~L~~G~~G~GKt~~a~~-la~~l~   49 (334)
T 1a5t_A            3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYA-LSRYLL   49 (334)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHH-HHHHHT
T ss_pred             CCCchHHHHHHHHHHHHcCCcceeEEEECCCCchHHHHHHH-HHHHHh
Confidence            3577877765554    444   389999999999987543 444443

>1sxj_E Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=95.22  E-value=0.14  Score=45.41  Aligned_cols=45  Identities=18%  Similarity=0.209  Sum_probs=28.8

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|+++--.+.+.+.|.+.. ...            -...++++.||+|+|||...
T Consensus         9 rP~~~~~~vg~~~~~~~l~~~~-~~~------------~~~~~~ll~Gp~G~GKTtl~   53 (354)
T 1sxj_E            9 RPKSLNALSHNEELTNFLKSLS-DQP------------RDLPHLLLYGPNGTGKKTRC   53 (354)
T ss_dssp             CCCSGGGCCSCHHHHHHHHTTT-TCT------------TCCCCEEEECSTTSSHHHHH
T ss_pred             CCCCHHHhcCCHHHHHHHHHHH-hhC------------CCCCeEEEECCCCCCHHHHH
Confidence            3455777766777777773221 010            12234999999999999864

>1g5t_A COB(I)alamin adenosyltransferase; P-loop protein, cobalamin biosynthesis, RECA fold; HET: ATP; 1.80A {Salmonella typhimurium} SCOP: c.37.1.11 PDB: 1g5r_A* 1g64_A*

Probab=95.15  E-value=0.14  Score=41.84  Aligned_cols=35  Identities=23%  Similarity=0.252  Sum_probs=28.1

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEe
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLV  117 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~  117 (316)
                      ..+++..++|.|||.+++--++..+..         |.+++|+.
T Consensus        29 g~i~v~tG~GkGKTTaA~GlalRA~g~---------G~rV~~vQ   63 (196)
T 1g5t_A           29 GIIIVFTGNGKGKTTAAFGTAARAVGH---------GKNVGVVQ   63 (196)
T ss_dssp             CCEEEEESSSSCHHHHHHHHHHHHHHT---------TCCEEEEE
T ss_pred             ceEEEECCCCCCHHHHHHHHHHHHHHC---------CCeEEEEE
Confidence            479999999999999987777776654         55688884

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=95.08  E-value=0.19  Score=40.68  Aligned_cols=24  Identities=29%  Similarity=0.474  Sum_probs=17.9

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHh
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHL   98 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l   98 (316)
                      +.+++.||+|+|||.... .+...+
T Consensus        55 ~~~~l~G~~GtGKT~la~-~i~~~~   78 (202)
T 2w58_A           55 KGLYLHGSFGVGKTYLLA-AIANEL   78 (202)
T ss_dssp             CEEEEECSTTSSHHHHHH-HHHHHH
T ss_pred             CeEEEECCCCCCHHHHHH-HHHHHH
Confidence            679999999999998643 334444

>2dr3_A UPF0273 protein PH0284; RECA superfamily ATPase, hexamer, structural genomics; HET: ADP; 2.00A {Pyrococcus horikoshii}

Probab=94.98  E-value=0.26  Score=40.96  Aligned_cols=50  Identities=24%  Similarity=0.244  Sum_probs=30.0

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQ  131 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~  131 (316)
                      .|.-+++.|++|+|||...+--+......         +..++++.-. +-..++.+.+.
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~~~~~~~~~~---------~~~v~~~~~e-~~~~~~~~~~~   71 (247)
T 2dr3_A           22 ERNVVLLSGGPGTGKTIFSQQFLWNGLKM---------GEPGIYVALE-EHPVQVRQNMA   71 (247)
T ss_dssp             TTCEEEEEECTTSSHHHHHHHHHHHHHHT---------TCCEEEEESS-SCHHHHHHHHH
T ss_pred             CCcEEEEECCCCCCHHHHHHHHHHHHHhc---------CCeEEEEEcc-CCHHHHHHHHH
Confidence            56678999999999998754333333221         2237777643 33455555544

>3eie_A Vacuolar protein sorting-associated protein 4; AAA ATPase, ATP-binding cassette, ATP-binding, endosome, MEM nucleotide-binding; 2.70A {Saccharomyces cerevisiae} PDB: 3eih_A* 2rko_A 3mhv_C

Probab=94.94  E-value=0.19  Score=44.15  Aligned_cols=51  Identities=18%  Similarity=0.257  Sum_probs=33.1

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHh-----CCCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVIL-----SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il-----~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|+++.-...+++.|.+...    .|..   .|.+.     ..+.+++.||+|+|||...
T Consensus        13 ~~~~~~di~G~~~~~~~l~~~i~----~~~~---~~~~~~~~~~~~~~vLl~GppGtGKT~la   68 (322)
T 3eie_A           13 PNVKWEDVAGLEGAKEALKEAVI----LPVK---FPHLFKGNRKPTSGILLYGPPGTGKSYLA   68 (322)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHTH----HHHH---CGGGCCTTCCCCCEEEEECSSSSCHHHHH
T ss_pred             CCCCHHHhcChHHHHHHHHHHHH----HHHh---CHHHHhcCCCCCCeEEEECCCCCcHHHHH
Confidence            44579999888888888844321    1111   11111     2356999999999999865

>3e2i_A Thymidine kinase; Zn-binding, ATP-binding, DNA synthesis, nucleotide-B transferase; HET: MSE; 2.01A {Staphylococcus aureus}

Probab=94.86  E-value=0.038  Score=45.89  Aligned_cols=41  Identities=15%  Similarity=0.152  Sum_probs=26.5

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      .|.=.++.++.|+|||...+-- +.+...        .+.+++++.|...
T Consensus        27 ~G~I~vitG~M~sGKTT~Llr~-~~r~~~--------~g~kvli~kp~~D   67 (219)
T 3e2i_A           27 SGWIECITGSMFSGKSEELIRR-LRRGIY--------AKQKVVVFKPAID   67 (219)
T ss_dssp             CCEEEEEEECTTSCHHHHHHHH-HHHHHH--------TTCCEEEEEEC--
T ss_pred             CceEEEEECCCCCCHHHHHHHH-HHHHHH--------cCCceEEEEeccC
Confidence            4556789999999999765433 343333        1344899988754

>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase domains, sensor 1, sensor 2, transferase; HET: DNA; 2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*

Probab=94.81  E-value=0.46  Score=38.87  Aligned_cols=16  Identities=31%  Similarity=0.405  Sum_probs=14.2

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      .+++.||+|+|||...
T Consensus        47 ~~ll~G~~G~GKT~l~   62 (250)
T 1njg_A           47 AYLFSGTRGVGKTSIA   62 (250)
T ss_dssp             EEEEECSTTSCHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5899999999999764

>2qby_B CDC6 homolog 3, cell division control protein 6 homolog 3; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=94.58  E-value=0.11  Score=46.72  Aligned_cols=18  Identities=39%  Similarity=0.309  Sum_probs=15.3

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      ++.+++.||+|+|||...
T Consensus        45 ~~~vll~G~~G~GKT~la   62 (384)
T 2qby_B           45 KFSNLFLGLTGTGKTFVS   62 (384)
T ss_dssp             CCEEEEEECTTSSHHHHH
T ss_pred             CCcEEEECCCCCCHHHHH
Confidence            346999999999999865

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=94.55  E-value=1.1  Score=39.39  Aligned_cols=50  Identities=16%  Similarity=0.109  Sum_probs=29.3

Q ss_pred             cccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           32 FASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        32 ~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      +...+|+++--.+..++.+....        + .+...-....++++.||+|+|||...
T Consensus        23 ~~p~~~~~iiG~~~~~~~l~~~l--------~-~~~~~~~~~~~vll~G~~GtGKT~la   72 (338)
T 3pfi_A           23 LRPSNFDGYIGQESIKKNLNVFI--------A-AAKKRNECLDHILFSGPAGLGKTTLA   72 (338)
T ss_dssp             CCCCSGGGCCSCHHHHHHHHHHH--------H-HHHHTTSCCCCEEEECSTTSSHHHHH
T ss_pred             cCCCCHHHhCChHHHHHHHHHHH--------H-HHHhcCCCCCeEEEECcCCCCHHHHH
Confidence            44457887766666666552210        0 00000012347999999999999864

>2qby_A CDC6 homolog 1, cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain, protein-DNA complex; HET: DNA SPD ADP; 3.35A {Sulfolobus solfataricus}

Probab=94.37  E-value=0.69  Score=41.02  Aligned_cols=18  Identities=33%  Similarity=0.556  Sum_probs=15.8

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      +..+++.||+|+|||...
T Consensus        45 ~~~vli~G~~G~GKTtl~   62 (386)
T 2qby_A           45 PNNIFIYGLTGTGKTAVV   62 (386)
T ss_dssp             CCCEEEEECTTSSHHHHH
T ss_pred             CCeEEEECCCCCCHHHHH
Confidence            567999999999999864

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=94.33  E-value=0.16  Score=41.83  Aligned_cols=20  Identities=35%  Similarity=0.471  Sum_probs=16.3

Q ss_pred             CCCcEEEEcCCCCchHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~   91 (316)
                      .|.-+++.+|+|+|||....
T Consensus        22 ~G~~~~i~G~~GsGKTtl~~   41 (235)
T 2w0m_A           22 QGFFIALTGEPGTGKTIFSL   41 (235)
T ss_dssp             TTCEEEEECSTTSSHHHHHH
T ss_pred             CCCEEEEEcCCCCCHHHHHH
Confidence            45678999999999997643

>1sxj_D Activator 1 41 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=94.25  E-value=0.43  Score=42.08  Aligned_cols=17  Identities=35%  Similarity=0.491  Sum_probs=14.8

Q ss_pred             CcEEEEcCCCCchHHHH
Q 043110           74 RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~   90 (316)
                      .++++.||+|+|||...
T Consensus        59 ~~~ll~G~~G~GKT~la   75 (353)
T 1sxj_D           59 PHMLFYGPPGTGKTSTI   75 (353)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            45999999999999764

>2qz4_A Paraplegin; AAA+, SPG7, protease, ADP, structural genomics, structural G consortium, SGC, ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.22A {Homo sapiens}

Probab=94.25  E-value=0.54  Score=39.47  Aligned_cols=53  Identities=17%  Similarity=0.218  Sum_probs=29.2

Q ss_pred             CCcccCCCCHHHHHHHHHHcC-CCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           35 CCFSSLGLDSTLCDQLRERLG-FEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g-~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      .+|+++.-.+.+++.+.+-.. +..|..+....   +...+.+++.||+|+|||...
T Consensus         3 ~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~g---~~~~~~vll~G~~GtGKT~la   56 (262)
T 2qz4_A            3 VSFKDVAGMHEAKLEVREFVDYLKSPERFLQLG---AKVPKGALLLGPPGCGKTLLA   56 (262)
T ss_dssp             CCTTSSCSCHHHHHHHHHHHHHHHCCC---------CCCCCEEEEESCTTSSHHHHH
T ss_pred             CCHHHhCCHHHHHHHHHHHHHHHHCHHHHHHcC---CCCCceEEEECCCCCCHHHHH
Confidence            467777766767666632110 11121111111   123457999999999999764

>3dm5_A SRP54, signal recognition 54 kDa protein; protein-RNA, signal recognition particle, SRP-GTPase, protein targeting, cytoplasm, GTP-binding; HET: GDP; 2.51A {Pyrococcus furiosus}

Probab=94.15  E-value=1.4  Score=40.51  Aligned_cols=51  Identities=25%  Similarity=0.328  Sum_probs=29.4

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEe--CChHHHHHHHHHHHHHHhhc
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLV--PTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~--Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      -+++.+++|+|||....- +...+..        .|.+++++.  |.|.-+   .+.++.++...
T Consensus       102 vIlivG~~G~GKTTt~~k-LA~~l~~--------~G~kVllv~~D~~R~aa---~eqL~~~~~~~  154 (443)
T 3dm5_A          102 ILLMVGIQGSGKTTTVAK-LARYFQK--------RGYKVGVVCSDTWRPGA---YHQLRQLLDRY  154 (443)
T ss_dssp             EEEEECCTTSSHHHHHHH-HHHHHHT--------TTCCEEEEECCCSSTHH---HHHHHHHHGGG
T ss_pred             EEEEECcCCCCHHHHHHH-HHHHHHH--------CCCeEEEEeCCCcchhH---HHHHHHHHHhc
Confidence            478999999999987532 3333333        133465555  444433   44555555443

>1iqp_A RFCS; clamp loader, extended AAA-ATPase domain, complex with ADP, replication; HET: ADP; 2.80A {Pyrococcus furiosus} SCOP: a.80.1.1 c.37.1.20

Probab=94.14  E-value=0.33  Score=42.23  Aligned_cols=16  Identities=38%  Similarity=0.542  Sum_probs=14.5

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      ++++.||+|+|||...
T Consensus        48 ~~ll~G~~G~GKT~la   63 (327)
T 1iqp_A           48 HLLFAGPPGVGKTTAA   63 (327)
T ss_dssp             EEEEESCTTSSHHHHH
T ss_pred             eEEEECcCCCCHHHHH
Confidence            6999999999999864

>2q6t_A DNAB replication FORK helicase; hydrolase; 2.90A {Thermus aquaticus}

Probab=94.14  E-value=0.53  Score=43.42  Aligned_cols=116  Identities=15%  Similarity=0.057  Sum_probs=55.6

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCCh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR  151 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (316)
                      .|.-+++.|++|+|||...+- +.......       .+..++|+..-- -..|+..++...........  ...|..+ 
T Consensus       199 ~G~l~ii~G~pg~GKT~lal~-ia~~~a~~-------~g~~vl~~slE~-~~~~l~~R~~~~~~~i~~~~--l~~g~l~-  266 (444)
T 2q6t_A          199 PGSLNIIAARPAMGKTAFALT-IAQNAALK-------EGVGVGIYSLEM-PAAQLTLRMMCSEARIDMNR--VRLGQLT-  266 (444)
T ss_dssp             TTCEEEEEECTTSCHHHHHHH-HHHHHHHT-------TCCCEEEEESSS-CHHHHHHHHHHHHTTCCTTT--CCGGGCC-
T ss_pred             CCcEEEEEeCCCCCHHHHHHH-HHHHHHHh-------CCCeEEEEECCC-CHHHHHHHHHHHHcCCCHHH--HhCCCCC-
Confidence            344589999999999975443 33333321       123377776532 23455554432222111111  1112222 


Q ss_pred             HHHHHHHh------cCCcEEEe-----CcHHHHHHHhcCCccccCceeEEEEecchhhhcC
Q 043110          152 SKEKARLR------KGISILVA-----TPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL  201 (316)
Q Consensus       152 ~~~~~~l~------~~~~IlV~-----Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~  201 (316)
                      ..++..+.      ....+.+-     |++.+...+....  .-..++++|||..+.+...
T Consensus       267 ~~~~~~~~~a~~~l~~~~l~i~d~~~~s~~~l~~~~~~l~--~~~~~~lIvID~l~~~~~~  325 (444)
T 2q6t_A          267 DRDFSRLVDVASRLSEAPIYIDDTPDLTLMEVRARARRLV--SQNQVGLIIIDYLQLMSGP  325 (444)
T ss_dssp             HHHHHHHHHHHHHHHTSCEEEECCTTCBHHHHHHHHHHHH--HHSCCCEEEEECGGGCBCC
T ss_pred             HHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHH--HHcCCCEEEEcChhhcCCC
Confidence            22222211      12345553     3344444333211  0125789999999998753

>1fnn_A CDC6P, cell division control protein 6; ORC1, AAA protein, DNA replication initation factor, cell cycle control factor; HET: ADP; 2.00A {Pyrobaculum aerophilum} SCOP: a.4.5.11 c.37.1.20

Probab=94.13  E-value=0.19  Score=45.02  Aligned_cols=16  Identities=38%  Similarity=0.474  Sum_probs=14.6

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      .+++.||+|+|||...
T Consensus        46 ~~li~G~~G~GKTtl~   61 (389)
T 1fnn_A           46 RATLLGRPGTGKTVTL   61 (389)
T ss_dssp             EEEEECCTTSSHHHHH
T ss_pred             eEEEECCCCCCHHHHH
Confidence            7999999999999864

>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=94.04  E-value=0.014  Score=57.20  Aligned_cols=27  Identities=22%  Similarity=0.258  Sum_probs=21.3

Q ss_pred             eCcHHHHHHHhcCCccccCceeEEEEecchhhhcC
Q 043110          167 ATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL  201 (316)
Q Consensus       167 ~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~  201 (316)
                      +||++|++++..        -.++|+||+|++.+.
T Consensus       314 ~tp~~LlDyl~~--------~~llVlDEah~~~~~  340 (664)
T 1c4o_A          314 EPPYTLLDYFPE--------DFLVFLDESHVTVPQ  340 (664)
T ss_dssp             SCCCCGGGGSCT--------TCEEEEETHHHHHHH
T ss_pred             CCchHHHHHHhh--------ccEEEEecccccHHH
Confidence            789999888753        238999999998753

>4b4t_J 26S protease regulatory subunit 8 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=94.04  E-value=0.2  Score=45.60  Aligned_cols=55  Identities=18%  Similarity=0.324  Sum_probs=35.2

Q ss_pred             ccCCcccCCCCHHHHHHHHHHc--CCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERL--GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~--g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|++.|=-++.++.|++..  .+.+|-.++...+   ...+.+++.||+|+|||+.+
T Consensus       143 p~v~~~dIgGl~~~k~~l~e~v~~Pl~~pe~f~~~gi---~~prGvLL~GPPGTGKTllA  199 (405)
T 4b4t_J          143 PDSTYDMVGGLTKQIKEIKEVIELPVKHPELFESLGI---AQPKGVILYGPPGTGKTLLA  199 (405)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCHHHHHHHTC---CCCCCEEEESCSSSSHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCceEEeCCCCCCHHHHH
Confidence            3468999987777777774432  1223333332221   23467999999999999874

>3vfd_A Spastin; ATPase, microtubule severing, hydrolase; 3.30A {Homo sapiens}

Probab=94.02  E-value=0.28  Score=44.41  Aligned_cols=18  Identities=33%  Similarity=0.525  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      .+.+++.||+|+|||...
T Consensus       148 ~~~vLL~GppGtGKT~la  165 (389)
T 3vfd_A          148 ARGLLLFGPPGNGKTMLA  165 (389)
T ss_dssp             CSEEEEESSTTSCHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            468999999999999864

>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A {Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A 2r6e_A 2vyf_A 2vye_A

Probab=93.98  E-value=0.89  Score=42.05  Aligned_cols=130  Identities=15%  Similarity=0.080  Sum_probs=61.6

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCCh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR  151 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (316)
                      .|.-+++.|++|+|||...+--+.......        |..++|+..--. ..|+..++...........  ...|... 
T Consensus       202 ~G~liiI~G~pG~GKTtl~l~ia~~~~~~~--------g~~Vl~~s~E~s-~~~l~~r~~~~~~~~~~~~--l~~g~l~-  269 (454)
T 2r6a_A          202 RSDLIIVAARPSVGKTAFALNIAQNVATKT--------NENVAIFSLEMS-AQQLVMRMLCAEGNINAQN--LRTGKLT-  269 (454)
T ss_dssp             TTCEEEEECCTTSCHHHHHHHHHHHHHHHS--------SCCEEEEESSSC-HHHHHHHHHHHHHTCCHHH--HHTSCCC-
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHhC--------CCcEEEEECCCC-HHHHHHHHHHHHcCCCHHH--HhcCCCC-
Confidence            455699999999999976543333332221        223777764322 3454544322111111000  0111122 


Q ss_pred             HHHHHHHh------cCCcEEEe-----CcHHHHHHHhcCCccccCceeEEEEecchhhhcCC-----cHHHHHHHHHHhc
Q 043110          152 SKEKARLR------KGISILVA-----TPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELG-----FGKEIEEILDILG  215 (316)
Q Consensus       152 ~~~~~~l~------~~~~IlV~-----Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~-----~~~~i~~i~~~l~  215 (316)
                      ..++..+.      ...++.+.     |++.+...+....  .-..++++|||+.+.+....     ....+..+.+.|.
T Consensus       270 ~~~~~~~~~a~~~l~~~~l~i~d~~~~s~~~i~~~~~~l~--~~~~~~livID~l~~~~~~~~~~~~~~~~i~~i~~~Lk  347 (454)
T 2r6a_A          270 PEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLK--QESGLGMIVIDYLQLIQGSGRSKENRQQEVSEISRSLK  347 (454)
T ss_dssp             HHHHHHHHHHHHHHHSSCEEEECCTTCCHHHHHHHHHHHH--TTTCCCEEEEECGGGSCCSCC----CHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCEEEECCCCCCHHHHHHHHHHHH--HHcCCCEEEEccHHHhccCCCCCCCHHHHHHHHHHHHH
Confidence            22222211      12345554     3344444333211  11257899999999987532     3344555554443

>1sxj_C Activator 1 40 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=93.64  E-value=0.75  Score=40.56  Aligned_cols=29  Identities=21%  Similarity=0.418  Sum_probs=19.1

Q ss_pred             ceeEEEEecchhhhcCCcHHHHHHHHHHhc
Q 043110          186 NLRWIIFDEADRILELGFGKEIEEILDILG  215 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~~~~~i~~i~~~l~  215 (316)
                      ..+++|+||+|.|... ....+..+++..+
T Consensus       110 ~~~viiiDe~~~l~~~-~~~~L~~~le~~~  138 (340)
T 1sxj_C          110 GFKLIILDEADAMTNA-AQNALRRVIERYT  138 (340)
T ss_dssp             SCEEEEETTGGGSCHH-HHHHHHHHHHHTT
T ss_pred             CceEEEEeCCCCCCHH-HHHHHHHHHhcCC
Confidence            4789999999987542 3344555555543

>1n0w_A DNA repair protein RAD51 homolog 1; DNA repair, homologous recombination, breast cancer susceptibility, RECA-like ATPase, protein complex; HET: DNA MSE; 1.70A {Homo sapiens} SCOP: c.37.1.11

Probab=93.54  E-value=0.4  Score=39.73  Aligned_cols=21  Identities=24%  Similarity=0.126  Sum_probs=17.2

Q ss_pred             CCCcEEEEcCCCCchHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~l   92 (316)
                      .|.-+.+.+|+|+|||.....
T Consensus        23 ~G~~~~i~G~~GsGKTtl~~~   43 (243)
T 1n0w_A           23 TGSITEMFGEFRTGKTQICHT   43 (243)
T ss_dssp             TTSEEEEECCTTSSHHHHHHH
T ss_pred             CCeEEEEECCCCCcHHHHHHH
Confidence            456799999999999987544

>2qp9_X Vacuolar protein sorting-associated protein 4; ATPase domain, beta domain, C-terminal helix, ATP-binding, E nucleotide-binding; 2.90A {Saccharomyces cerevisiae} PDB: 2qpa_A*

Probab=93.40  E-value=0.26  Score=44.13  Aligned_cols=51  Identities=18%  Similarity=0.245  Sum_probs=30.4

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHh-----CCCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVIL-----SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il-----~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|++++-...+++.|.+...    .|.   -.|.+.     ..+.+++.||+|+|||...
T Consensus        46 ~~~~~~di~G~~~~~~~l~~~v~----~~~---~~~~~~~~~~~~~~~iLL~GppGtGKT~la  101 (355)
T 2qp9_X           46 PNVKWEDVAGLEGAKEALKEAVI----LPV---KFPHLFKGNRKPTSGILLYGPPGTGKSYLA  101 (355)
T ss_dssp             -CCCGGGSCCGGGHHHHHHHHTH----HHH---HCGGGGCSSCCCCCCEEEECSTTSCHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHH----HHH---hCHHHHhcCCCCCceEEEECCCCCcHHHHH
Confidence            34678888766666666633211    010   011111     2356999999999999875

>3pvs_A Replication-associated recombination protein A; maintenance of genome stability Pro recombination; 2.50A {Escherichia coli}

Probab=93.39  E-value=0.13  Score=47.81  Aligned_cols=17  Identities=29%  Similarity=0.444  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCCchHHHH
Q 043110           74 RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~   90 (316)
                      ..+++.||+|+|||...
T Consensus        51 ~~vLL~GppGtGKTtlA   67 (447)
T 3pvs_A           51 HSMILWGPPGTGKTTLA   67 (447)
T ss_dssp             CEEEEECSTTSSHHHHH
T ss_pred             cEEEEECCCCCcHHHHH
Confidence            36999999999999864

>1sxj_B Activator 1 37 kDa subunit; clamp loader, processivity clamp, DNA sliding clamp, AAA+ at polymerase, DNA-binding protein; HET: AGS ADP; 2.85A {Saccharomyces cerevisiae} SCOP: a.80.1.1 c.37.1.20

Probab=92.97  E-value=0.56  Score=40.64  Aligned_cols=16  Identities=25%  Similarity=0.563  Sum_probs=14.2

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      ++++.||.|+|||...
T Consensus        44 ~~ll~G~~G~GKt~la   59 (323)
T 1sxj_B           44 HMIISGMPGIGKTTSV   59 (323)
T ss_dssp             CEEEECSTTSSHHHHH
T ss_pred             eEEEECcCCCCHHHHH
Confidence            5999999999999764

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=92.58  E-value=0.65  Score=40.59  Aligned_cols=16  Identities=13%  Similarity=0.077  Sum_probs=14.1

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      ..++.||.|+|||...
T Consensus        20 ~~Lf~Gp~G~GKtt~a   35 (305)
T 2gno_A           20 SILINGEDLSYPREVS   35 (305)
T ss_dssp             EEEEECSSSSHHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            5899999999998765

>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein; HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A* 1e32_A* 1s3s_A*

Probab=92.24  E-value=0.43  Score=44.71  Aligned_cols=55  Identities=22%  Similarity=0.340  Sum_probs=30.1

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHH--hCCCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVI--LSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~i--l~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|++++=....++.|.+....  |... .+.+..+  ...+.+++.||+|+|||+..
T Consensus       199 ~~~~~~~i~G~~~~~~~l~~~i~~--~l~~-~~~~~~~g~~~~~~vLL~GppGtGKT~lA  255 (489)
T 3hu3_A          199 NEVGYDDIGGCRKQLAQIKEMVEL--PLRH-PALFKAIGVKPPRGILLYGPPGTGKTLIA  255 (489)
T ss_dssp             TCCCGGGCCSCHHHHHHHHHHTHH--HHHC-HHHHHHHTCCCCCEEEEECSTTSSHHHHH
T ss_pred             CCCCHHHcCCHHHHHHHHHHHHHH--HhhC-HHHHHhcCCCCCCcEEEECcCCCCHHHHH
Confidence            345677776555555555343211  1000 1112222  23457999999999999864

>3cmu_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 4.20A {Escherichia coli}

Probab=92.21  E-value=0.28  Score=53.38  Aligned_cols=47  Identities=23%  Similarity=0.302  Sum_probs=32.4

Q ss_pred             HHHHhC------CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHH
Q 043110           67 IPVILS------GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSEL  122 (316)
Q Consensus        67 i~~il~------g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L  122 (316)
                      +..++.      |+.+++.+|+|+|||....--+.+....         |.+++++.....+
T Consensus      1415 LD~lLG~GGi~~g~~vll~GppGtGKT~LA~ala~ea~~~---------G~~v~Fi~~e~~~ 1467 (2050)
T 3cmu_A         1415 LDIALGAGGLPMGRIVEIYGPESSGKTTLTLQVIAAAQRE---------GKTCAFIDAEHAL 1467 (2050)
T ss_dssp             HHHHHSSSSEETTSEEEEECCTTSSHHHHHHHHHHHHHTT---------TCCEEEECTTSCC
T ss_pred             HHHhcCCCCccCCeEEEEECCCCCCHHHHHHHHHHHHHHc---------CCcEEEEEccccc
Confidence            566665      6789999999999998865444443322         4458888766444

>1cr0_A DNA primase/helicase; RECA-type protein fold, transferase; HET: DNA; 2.30A {Enterobacteria phage T7} SCOP: c.37.1.11 PDB: 1cr1_A* 1cr2_A* 1cr4_A* 1e0j_A* 1e0k_A*

Probab=92.00  E-value=0.56  Score=40.47  Aligned_cols=21  Identities=24%  Similarity=0.460  Sum_probs=17.2

Q ss_pred             CCCcEEEEcCCCCchHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~l   92 (316)
                      .|.-+++.|++|+|||.....
T Consensus        34 ~G~~~~i~G~~G~GKTTl~~~   54 (296)
T 1cr0_A           34 GGEVIMVTSGSGMGKSTFVRQ   54 (296)
T ss_dssp             TTCEEEEEESTTSSHHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHHH
Confidence            567799999999999976543

>4a1f_A DNAB helicase, replicative DNA helicase; hydrolase, DNA replication, ATPase; HET: FLC; 2.50A {Helicobacter pylori}

Probab=91.47  E-value=1.2  Score=39.45  Aligned_cols=115  Identities=13%  Similarity=0.067  Sum_probs=55.8

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCCh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR  151 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~  151 (316)
                      .|.=+++.|++|+|||...+- +...+..        .+..++|++.- .-..|+..++...........   +..|.-.
T Consensus        45 ~G~LiiIaG~pG~GKTt~al~-ia~~~a~--------~g~~Vl~fSlE-ms~~ql~~Rlls~~~~v~~~~---l~~g~Ls  111 (338)
T 4a1f_A           45 KGSLVIIGARPSMGKTSLMMN-MVLSALN--------DDRGVAVFSLE-MSAEQLALRALSDLTSINMHD---LESGRLD  111 (338)
T ss_dssp             TTCEEEEEECTTSCHHHHHHH-HHHHHHH--------TTCEEEEEESS-SCHHHHHHHHHHHHHCCCHHH---HHHTCCC
T ss_pred             CCcEEEEEeCCCCCHHHHHHH-HHHHHHH--------cCCeEEEEeCC-CCHHHHHHHHHHHhhCCCHHH---HhcCCCC
Confidence            445599999999999976543 3333332        13447777653 334555555433322211100   1112222


Q ss_pred             HHHHHHHh------cCCcEEE-eCc----HHHHHHHhcCCccccCceeEEEEecchhhhc
Q 043110          152 SKEKARLR------KGISILV-ATP----GHLLDHLKHTSSFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       152 ~~~~~~l~------~~~~IlV-~Tp----~~l~~~l~~~~~~~~~~l~~lViDEad~l~~  200 (316)
                      ..++..+.      ...++.| .+|    ..+...++.... ....++++|||-.+.|..
T Consensus       112 ~~e~~~l~~a~~~l~~~~l~I~d~~~~si~~i~~~ir~l~~-~~gg~~lIVIDyLqlm~~  170 (338)
T 4a1f_A          112 DDQWENLAKCFDHLSQKKLFFYDKSYVRIEQIRLQLRKLKS-QHKELGIAFIDYLQLMSG  170 (338)
T ss_dssp             HHHHHHHHHHHHHHHHSCEEEECCTTCCHHHHHHHHHHHHH-HCTTEEEEEEEEEECCCT
T ss_pred             HHHHHHHHHHHHHHhcCCeEEeCCCCCcHHHHHHHHHHHHH-hcCCCCEEEEechHHhcC
Confidence            22222221      1234544 444    334333332100 001689999999997754

>1w5s_A Origin recognition complex subunit 2 ORC2; replication, CDC6, DNA replication initiation, DNA BIND protein, AAA+ ATPase; HET: ADP; 2.4A {Aeropyrum pernix} SCOP: a.4.5.11 c.37.1.20 PDB: 1w5t_A*

Probab=91.28  E-value=1.3  Score=39.86  Aligned_cols=17  Identities=24%  Similarity=0.305  Sum_probs=14.3

Q ss_pred             CcEEE--EcCCCCchHHHH
Q 043110           74 RDVLV--NAATGTGKTVAY   90 (316)
Q Consensus        74 ~d~li--~a~TGsGKT~~~   90 (316)
                      ..+++  .|+.|+|||...
T Consensus        51 ~~~li~i~G~~G~GKT~L~   69 (412)
T 1w5s_A           51 VNMIYGSIGRVGIGKTTLA   69 (412)
T ss_dssp             EEEEEECTTCCSSSHHHHH
T ss_pred             CEEEEeCcCcCCCCHHHHH
Confidence            35888  899999999864

>2zr9_A Protein RECA, recombinase A; recombination, RECA mutants, DNA-repair, ATP-binding, DNA DA recombination, DNA repair, DNA-binding; HET: DTP; 2.50A {Mycobacterium smegmatis str} PDB: 2zr0_A* 2zra_A* 2zrb_A 2zrm_A* 1ubc_A* 1ubf_A* 1ubg_A* 1ube_A* 2g88_A* 2odw_A* 2oe2_A 2oep_A* 2oes_A 2ofo_A 2zr7_A 2odn_A* 2zrn_A 2zro_A* 2zrp_A* 2zre_A* ...

Probab=91.13  E-value=0.46  Score=42.42  Aligned_cols=39  Identities=23%  Similarity=0.335  Sum_probs=25.2

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCC
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPT  119 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt  119 (316)
                      .|.-+++.+++|+|||...+--+......         +..++|+.-.
T Consensus        60 ~G~iv~I~G~pGsGKTtLal~la~~~~~~---------g~~vlyi~~E   98 (349)
T 2zr9_A           60 RGRVIEIYGPESSGKTTVALHAVANAQAA---------GGIAAFIDAE   98 (349)
T ss_dssp             TTSEEEEEESTTSSHHHHHHHHHHHHHHT---------TCCEEEEESS
T ss_pred             CCeEEEEECCCCCCHHHHHHHHHHHHHhC---------CCeEEEEECC
Confidence            35669999999999998754433333322         3347777644

>3bh0_A DNAB-like replicative helicase; ATPase, replication; 2.35A {Bacillus phage SPP1}

Probab=91.11  E-value=1.2  Score=38.85  Aligned_cols=52  Identities=17%  Similarity=-0.050  Sum_probs=31.3

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .|.-+++.|++|+|||...+--+.+....         +..++|++-- +-..|+..++...
T Consensus        67 ~G~l~li~G~pG~GKTtl~l~ia~~~a~~---------g~~vl~~slE-~s~~~l~~R~~~~  118 (315)
T 3bh0_A           67 RRNFVLIAARPSMGKTAFALKQAKNMSDN---------DDVVNLHSLE-MGKKENIKRLIVT  118 (315)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHTT---------TCEEEEEESS-SCHHHHHHHHHHH
T ss_pred             CCcEEEEEeCCCCCHHHHHHHHHHHHHHc---------CCeEEEEECC-CCHHHHHHHHHHH
Confidence            45569999999999997544333333222         2347777644 3455555555443

>3m6a_A ATP-dependent protease LA 1; alpha, beta, ATP-binding, hydrolase, nucleotide-binding, Pro serine protease, stress response; HET: ADP; 3.40A {Bacillus subtilis} PDB: 1x37_A

Probab=91.06  E-value=0.47  Score=45.07  Aligned_cols=19  Identities=26%  Similarity=0.338  Sum_probs=16.5

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .|..+++.+|+|+|||...
T Consensus       107 ~g~~vll~Gp~GtGKTtla  125 (543)
T 3m6a_A          107 KGPILCLAGPPGVGKTSLA  125 (543)
T ss_dssp             CSCEEEEESSSSSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            4678999999999999764

>3co5_A Putative two-component system transcriptional RES regulator; structural genomics, APC89341.1; 2.40A {Neisseria gonorrhoeae}

Probab=90.76  E-value=0.21  Score=38.27  Aligned_cols=21  Identities=10%  Similarity=0.077  Sum_probs=17.4

Q ss_pred             HhCCCcEEEEcCCCCchHHHH
Q 043110           70 ILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        70 il~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+.++++.+++|+|||..+
T Consensus        24 ~~~~~~vll~G~~GtGKt~lA   44 (143)
T 3co5_A           24 AKRTSPVFLTGEAGSPFETVA   44 (143)
T ss_dssp             HTCSSCEEEEEETTCCHHHHH
T ss_pred             hCCCCcEEEECCCCccHHHHH
Confidence            346678999999999999763

>2l8b_A Protein TRAI, DNA helicase I; RECD, hydrolase; NMR {Escherichia coli}

Probab=90.68  E-value=0.32  Score=39.13  Aligned_cols=59  Identities=14%  Similarity=0.165  Sum_probs=43.0

Q ss_pred             CcHHHHHHHHHHhCCC--cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH
Q 043110           59 PTKVQAQAIPVILSGR--DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL  125 (316)
Q Consensus        59 p~~~Q~~~i~~il~g~--d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q  125 (316)
                      ..+-|..++..++...  -.++.++-|++|+...+-.++.....        .|.++.+|+|+..-...
T Consensus        35 ~~~~~~~a~~~l~~s~~~~~iv~g~ggs~~~~~~~a~L~~~a~~--------~Gr~V~vLAp~~~s~~~   95 (189)
T 2l8b_A           35 RTAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMARE--------QGREVQIIAADRRSQMN   95 (189)
T ss_dssp             CHHHHHHHHHHHHHHSCCEECCBCSSCSHHHHHHHHHHHHHHHH--------TTCCEEEECSTTHHHHH
T ss_pred             cCccchhHHHHHhccCCceEEEecccchHHHHHHHHHHHHHHHh--------cCeEEEEEcCchHHHHH
Confidence            3577899998887544  37889999999999865555444433        35569999999876543

>3n70_A Transport activator; sigma-54, ntpase, PSI, MCSG, structural genomics, center for structural genomics; 2.80A {Escherichia coli}

Probab=90.63  E-value=0.24  Score=37.92  Aligned_cols=20  Identities=25%  Similarity=0.307  Sum_probs=17.2

Q ss_pred             hCCCcEEEEcCCCCchHHHH
Q 043110           71 LSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        71 l~g~d~li~a~TGsGKT~~~   90 (316)
                      ..+.++++.+++|+|||..+
T Consensus        22 ~~~~~vll~G~~GtGKt~lA   41 (145)
T 3n70_A           22 ETDIAVWLYGAPGTGRMTGA   41 (145)
T ss_dssp             TCCSCEEEESSTTSSHHHHH
T ss_pred             CCCCCEEEECCCCCCHHHHH
Confidence            46678999999999999874

>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B* 3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*

Probab=90.07  E-value=2.9  Score=36.92  Aligned_cols=16  Identities=31%  Similarity=0.405  Sum_probs=14.0

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      .+++.||.|+|||...
T Consensus        40 ~~ll~G~~G~GKT~la   55 (373)
T 1jr3_A           40 AYLFSGTRGVGKTSIA   55 (373)
T ss_dssp             EEEEESCTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3799999999999865

>2z43_A DNA repair and recombination protein RADA; archaea, filament, DNA binding, molecular SWI RECA, DMC1; HET: DNA; 1.93A {Sulfolobus solfataricus} PDB: 2bke_A* 2dfl_A* 2zub_A* 2zuc_A* 2zud_A*

Probab=90.04  E-value=0.94  Score=39.80  Aligned_cols=63  Identities=14%  Similarity=0.064  Sum_probs=33.4

Q ss_pred             HHHHHhC-----CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHH-HHHHHHHHH
Q 043110           66 AIPVILS-----GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSEL-CLLVYEILQ  131 (316)
Q Consensus        66 ~i~~il~-----g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L-~~Q~~~~~~  131 (316)
                      .++.++.     |.-+++.+++|+|||...+--+.+ ......  ..+.+..++|+.-...+ ..++.+.++
T Consensus        95 ~LD~~L~GGl~~G~i~~i~G~~GsGKT~la~~la~~-~~~~~~--~gg~~~~vlyi~~e~~~~~~~l~~~~~  163 (324)
T 2z43_A           95 ALDGLLAGGIETRTMTEFFGEFGSGKTQLCHQLSVN-VQLPPE--KGGLSGKAVYIDTEGTFRWERIENMAK  163 (324)
T ss_dssp             HHHHHTTTSEETTSEEEEEESTTSSHHHHHHHHHHH-TTSCGG--GTCCSCEEEEEESSSCCCHHHHHHHHH
T ss_pred             hHHHhcCCCCCCCcEEEEECCCCCCHhHHHHHHHHH-Hhcccc--cCCCCCeEEEEECCCCCCHHHHHHHHH
Confidence            3555553     456899999999999865433332 211000  00113457888754432 344444443

>3lda_A DNA repair protein RAD51; DNA binding protein, ATP-binding, DNA damage, DNA recombinat repair, nucleotide-binding; HET: DNA; 2.50A {Saccharomyces cerevisiae} PDB: 1szp_A*

Probab=89.22  E-value=4  Score=37.03  Aligned_cols=19  Identities=21%  Similarity=0.081  Sum_probs=15.7

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 043110           73 GRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~   91 (316)
                      |.-+.+.+|+|+|||....
T Consensus       178 Gei~~I~G~sGsGKTTLl~  196 (400)
T 3lda_A          178 GSITELFGEFRTGKSQLCH  196 (400)
T ss_dssp             TSEEEEEESTTSSHHHHHH
T ss_pred             CcEEEEEcCCCCChHHHHH
Confidence            3468999999999998654

>3hr8_A Protein RECA; alpha and beta proteins (A/B, A+B), ATP-binding, cytoplasm, damage, DNA recombination, DNA repair, DNA-binding; 1.95A {Thermotoga maritima}

Probab=89.13  E-value=0.72  Score=41.28  Aligned_cols=41  Identities=27%  Similarity=0.255  Sum_probs=26.3

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSEL  122 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L  122 (316)
                      |.-+++.+|+|+|||... +.++..+..        .+..++++..-..+
T Consensus        61 G~i~~I~GppGsGKSTLa-l~la~~~~~--------~gg~VlyId~E~s~  101 (356)
T 3hr8_A           61 GRIVEIFGQESSGKTTLA-LHAIAEAQK--------MGGVAAFIDAEHAL  101 (356)
T ss_dssp             TEEEEEEESTTSSHHHHH-HHHHHHHHH--------TTCCEEEEESSCCC
T ss_pred             CcEEEEECCCCCCHHHHH-HHHHHHHHh--------cCCeEEEEeccccc
Confidence            456899999999999754 444444333        13347888765443

>1xp8_A RECA protein, recombinase A; recombination, radioresistance, DNA-repair, ATPase, DNA-BIND protein, DNA binding protein; HET: AGS; 2.50A {Deinococcus radiodurans} SCOP: c.37.1.11 d.48.1.1

Probab=88.89  E-value=0.81  Score=41.10  Aligned_cols=39  Identities=23%  Similarity=0.255  Sum_probs=25.0

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCCh
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTS  120 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~  120 (316)
                      |.-+++.+++|+|||...+ .++..+...        +..++|+..-.
T Consensus        74 G~li~I~G~pGsGKTtlal-~la~~~~~~--------g~~vlyi~~E~  112 (366)
T 1xp8_A           74 GRITEIYGPESGGKTTLAL-AIVAQAQKA--------GGTCAFIDAEH  112 (366)
T ss_dssp             TSEEEEEESTTSSHHHHHH-HHHHHHHHT--------TCCEEEEESSC
T ss_pred             CcEEEEEcCCCCChHHHHH-HHHHHHHHC--------CCeEEEEECCC
Confidence            4568999999999997654 344333331        23477777543

>4b4t_M 26S protease regulatory subunit 6A; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=88.48  E-value=0.22  Score=45.94  Aligned_cols=55  Identities=22%  Similarity=0.306  Sum_probs=37.3

Q ss_pred             ccCCcccCCCCHHHHHHHHHHc--CCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERL--GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~--g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|++.+-.++.++.|.+..  .+.+|-.++...+   ...+.+++.||+|+|||+.+
T Consensus       176 p~~t~~digGl~~~k~~l~e~v~~pl~~pe~f~~~g~---~~prGvLLyGPPGTGKTllA  232 (434)
T 4b4t_M          176 PTETYSDVGGLDKQIEELVEAIVLPMKRADKFKDMGI---RAPKGALMYGPPGTGKTLLA  232 (434)
T ss_dssp             CSCCGGGSCSCHHHHHHHHHHTHHHHHCSHHHHHHCC---CCCCEEEEESCTTSSHHHHH
T ss_pred             CCCChHhcCcHHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeeEEECcCCCCHHHHH
Confidence            4468999998888888885432  2234444443322   12467999999999999874

>3nwn_A Kinesin-like protein KIF9; motor domain, ADP, structural genomics, structural consortium, SGC, contractIle protein; HET: ADP; 2.00A {Homo sapiens}

Probab=88.27  E-value=0.34  Score=43.48  Aligned_cols=25  Identities=28%  Similarity=0.519  Sum_probs=20.8

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  +++.++||||||...
T Consensus        96 lv~~~l~G~N~tifAYGQTGSGKTyTM  122 (359)
T 3nwn_A           96 VVSQALDGYNGTIMCYGQTGAGKTYTM  122 (359)
T ss_dssp             HHHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhCCCCEEEEEeCCCCCCccEEe
Confidence            4556678988  899999999999874

>3io5_A Recombination and repair protein; storage dimer, inactive conformation, RECA like core domain, binding, DNA damage, DNA recombination; 2.40A {Enterobacteria phage T4}

Probab=88.14  E-value=0.71  Score=40.66  Aligned_cols=42  Identities=7%  Similarity=0.022  Sum_probs=27.8

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      -+.+.+|+|+|||...+-.+.+....       +.+.+++|+..-..+.
T Consensus        30 iteI~G~pGsGKTtL~Lq~~~~~~~~-------g~g~~vlyId~E~s~~   71 (333)
T 3io5_A           30 LLILAGPSKSFKSNFGLTMVSSYMRQ-------YPDAVCLFYDSEFGIT   71 (333)
T ss_dssp             EEEEEESSSSSHHHHHHHHHHHHHHH-------CTTCEEEEEESSCCCC
T ss_pred             eEEEECCCCCCHHHHHHHHHHHHHhc-------CCCceEEEEeccchhh
Confidence            58999999999998754433333322       1245689988766553

>1e9r_A Conjugal transfer protein TRWB; coupling protein, bacterial conjugation, F1-ATPase-like quaternary structure, ring helicases; 2.4A {Escherichia coli} SCOP: c.37.1.11 PDB: 1e9s_A 1gki_A* 1gl7_A* 1gl6_A*

Probab=87.98  E-value=0.69  Score=42.38  Aligned_cols=26  Identities=42%  Similarity=0.507  Sum_probs=19.4

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHh
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHL   98 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l   98 (316)
                      ...++++.|+||||||... -+++..+
T Consensus        52 ~~~h~~i~G~tGsGKs~~~-~~li~~~   77 (437)
T 1e9r_A           52 EPRHLLVNGATGTGKSVLL-RELAYTG   77 (437)
T ss_dssp             GGGCEEEEECTTSSHHHHH-HHHHHHH
T ss_pred             CcceEEEECCCCCCHHHHH-HHHHHHH
Confidence            4568999999999999974 3344443

>1v5w_A DMC1, meiotic recombination protein DMC1/LIM15 homolog; DNA-binding protein, ring protein, octamer, AAA ATPase; 3.20A {Homo sapiens} SCOP: c.37.1.11 PDB: 2zjb_A

Probab=87.87  E-value=2.6  Score=37.29  Aligned_cols=51  Identities=12%  Similarity=-0.025  Sum_probs=28.7

Q ss_pred             HHHHhC-----CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCCh
Q 043110           67 IPVILS-----GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTS  120 (316)
Q Consensus        67 i~~il~-----g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~  120 (316)
                      +..++.     |.-+++.+++|+|||...+--+......   ....+.+..++|+.-..
T Consensus       111 LD~~LgGGl~~G~i~~I~G~~GsGKTtla~~la~~~~~~---~~~gg~~~~vlyi~~E~  166 (343)
T 1v5w_A          111 FDKLLGGGIESMAITEAFGEFRTGKTQLSHTLCVTAQLP---GAGGYPGGKIIFIDTEN  166 (343)
T ss_dssp             HHHHTTSSBCSSEEEEEECCTTCTHHHHHHHHHHHTTSC---BTTTBCCCEEEEEESSS
T ss_pred             HHHHhcCCCCCCeEEEEECCCCCCHHHHHHHHHHHHhcc---cccCCCCCeEEEEECCC
Confidence            555553     3458999999999998654333221111   00011244688887554

>1bg2_A Kinesin; motor protein, ATPase, microtubule associated; HET: ADP; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 2p4n_K* 1mkj_A* 2kin_A* 3kin_A*

Probab=87.54  E-value=0.43  Score=42.18  Aligned_cols=25  Identities=24%  Similarity=0.432  Sum_probs=20.4

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..++||||||...
T Consensus        69 lv~~~l~G~n~tifAYGqTGSGKTyTm   95 (325)
T 1bg2_A           69 IVKDVLEGYNGTIFAYGQTSSGKTHTM   95 (325)
T ss_dssp             HHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             hHHHHhCCCeEEEEEECCCCCCCceEe
Confidence            3455678988  799999999999884

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=87.11  E-value=5.7  Score=31.72  Aligned_cols=71  Identities=15%  Similarity=0.134  Sum_probs=47.7

Q ss_pred             eEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHH---Hh-cCCcEEEeCcHHHHHHHhcCCccccCce
Q 043110          112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKAR---LR-KGISILVATPGHLLDHLKHTSSFLHTNL  187 (316)
Q Consensus       112 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~l  187 (316)
                      ++||.+++++-+..+.+.+...+     ..+..++|+....+....   +. ...+|+|+|.     .+.  .++++.++
T Consensus        56 ~~lVF~~~~~~~~~l~~~L~~~g-----~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~-----~~~--~Gldi~~v  123 (191)
T 2p6n_A           56 PVLIFAEKKADVDAIHEYLLLKG-----VEAVAIHGGKDQEERTKAIEAFREGKKDVLVATD-----VAS--KGLDFPAI  123 (191)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHT-----CCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECH-----HHH--TTCCCCCC
T ss_pred             CEEEEECCHHHHHHHHHHHHHcC-----CcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcC-----chh--cCCCcccC
Confidence            59999999999999988887642     445567777665443332   22 3578999992     222  45566778


Q ss_pred             eEEEEec
Q 043110          188 RWIIFDE  194 (316)
Q Consensus       188 ~~lViDE  194 (316)
                      +++|.-+
T Consensus       124 ~~VI~~d  130 (191)
T 2p6n_A          124 QHVINYD  130 (191)
T ss_dssp             SEEEESS
T ss_pred             CEEEEeC
Confidence            8777643

>2i1q_A DNA repair and recombination protein RADA; ATPase, recombinase, ATP complex, calcium stimulation, RECA, DMC1; HET: DNA ANP; 1.90A {Methanococcus voltae} SCOP: a.60.4.1 c.37.1.11 PDB: 1xu4_A* 2b21_A* 2fpk_A* 2fpl_A* 2fpm_A* 1t4g_A* 3fyh_A* 2f1j_A* 2f1i_A* 2f1h_A* 3ntu_A* 3ewa_A* 3ew9_A* 3etl_A* 4dc9_A* 2gdj_A*

Probab=87.04  E-value=2.3  Score=37.05  Aligned_cols=27  Identities=19%  Similarity=0.196  Sum_probs=19.5

Q ss_pred             HHHHHhC-----CCcEEEEcCCCCchHHHHHH
Q 043110           66 AIPVILS-----GRDVLVNAATGTGKTVAYLA   92 (316)
Q Consensus        66 ~i~~il~-----g~d~li~a~TGsGKT~~~~l   92 (316)
                      .++.++.     |.-+++.+++|+|||...+-
T Consensus        86 ~LD~~l~GGl~~g~i~~i~G~~gsGKT~la~~  117 (322)
T 2i1q_A           86 ELDSVLGGGLESQSVTEFAGVFGSGKTQIMHQ  117 (322)
T ss_dssp             HHHHHTTSSEETTEEEEEEESTTSSHHHHHHH
T ss_pred             hHHHhcCCCccCCeEEEEECCCCCCHHHHHHH
Confidence            3555553     34589999999999986543

>3dc4_A Kinesin-like protein NOD; catalytic domain, ATPase, microtubule, ADP, nucleotide-binding protein, ATP-binding, coiled coil, motor protein; HET: ADP; 1.90A {Drosophila melanogaster} PDB: 3dcb_A* 3dco_N* 3pxn_A*

Probab=86.75  E-value=0.43  Score=42.53  Aligned_cols=24  Identities=33%  Similarity=0.526  Sum_probs=19.6

Q ss_pred             HHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           67 IPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        67 i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      +..++.|.|  ++..++||||||...
T Consensus        87 v~~~l~G~N~tifAYGQTGSGKTyTM  112 (344)
T 3dc4_A           87 VDKLLEGFQCTALAYGQTGTGKSYSM  112 (344)
T ss_dssp             HHHHHHTCCEEEEEESSTTSSHHHHH
T ss_pred             hhHhhCCCceEEEEecCCCCCCCeEE
Confidence            445568887  789999999999874

>2vvg_A Kinesin-2; motor protein, nucleotide-binding, microtubule, ATP-binding; HET: ADP; 1.60A {Giardia intestinalis}

Probab=86.63  E-value=0.51  Score=42.13  Aligned_cols=24  Identities=33%  Similarity=0.559  Sum_probs=19.7

Q ss_pred             HHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           67 IPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        67 i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      +..++.|.|  ++..|+||||||...
T Consensus        82 v~~~l~G~n~tifAYGqTGSGKTyTm  107 (350)
T 2vvg_A           82 IDAVLEGFNSTIFAYGQTGAGKTWTM  107 (350)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhCCCceeEEeecCCCCCCCEEe
Confidence            345568887  789999999999874

>2y65_A Kinesin, kinesin heavy chain; motor protein; HET: ADP; 2.20A {Drosophila melanogaster} PDB: 2y5w_A*

Probab=86.61  E-value=0.51  Score=42.40  Aligned_cols=24  Identities=25%  Similarity=0.483  Sum_probs=19.9

Q ss_pred             HHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           67 IPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        67 i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      +..++.|.|  ++..|+||||||...
T Consensus        77 v~~~l~G~n~tifAYGqTGSGKTyTm  102 (365)
T 2y65_A           77 VTDVLAGYNGTIFAYGQTSSGKTHTM  102 (365)
T ss_dssp             HHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhCCCceEEEeecCCCCCCceEE
Confidence            445668987  789999999999884

>3lre_A Kinesin-like protein KIF18A; motor protein, nucleotide binding, microtubule binding, ATP- cell projection, cytoskeleton, glycoprotein, microtubule; HET: ADP; 2.20A {Homo sapiens} SCOP: c.37.1.0

Probab=86.59  E-value=0.52  Score=42.20  Aligned_cols=24  Identities=42%  Similarity=0.600  Sum_probs=19.9

Q ss_pred             HHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           67 IPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        67 i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      +..++.|.|  ++..++||||||...
T Consensus        98 v~~~l~G~n~tifAYGqTGSGKTyTm  123 (355)
T 3lre_A           98 LRSFLNGYNCTVLAYGATGAGKTHTM  123 (355)
T ss_dssp             HHHHTTTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHHhCCCceEEEEeCCCCCCceeee
Confidence            455668988  799999999999874

>1goj_A Kinesin, kinesin heavy chain; motor protein, ATPase; HET: ADP; 2.3A {Neurospora crassa} SCOP: c.37.1.9

Probab=86.49  E-value=0.52  Score=42.19  Aligned_cols=24  Identities=33%  Similarity=0.558  Sum_probs=19.9

Q ss_pred             HHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           67 IPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        67 i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      +..++.|.|  ++..|+||||||...
T Consensus        73 v~~~l~G~n~tifAYGqTGSGKTyTm   98 (355)
T 1goj_A           73 VDDILNGYNGTVFAYGQTGAGKSYTM   98 (355)
T ss_dssp             HHHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhCCCcceEEEECCCCCCcceEe
Confidence            445678987  789999999999874

>4a14_A Kinesin, kinesin-like protein KIF7; motor protein, motor domain; HET: ADP; 1.60A {Homo sapiens} SCOP: c.37.1.0 PDB: 2xt3_A*

Probab=86.46  E-value=0.53  Score=41.96  Aligned_cols=25  Identities=28%  Similarity=0.489  Sum_probs=20.3

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..++||||||...
T Consensus        75 lv~~~l~G~n~tifAYGqTGSGKTyTm  101 (344)
T 4a14_A           75 LLEAFFEGFNATVFAYGQTGSGKTYTM  101 (344)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHHhhcCeeEEEecccCCCceEee
Confidence            3455668988  789999999999874

>2h58_A Kinesin-like protein KIFC3 variant; motor domain, ADP, structural genomics, structur Al genomics consortium, SGC; HET: ADP; 1.85A {Homo sapiens}

Probab=86.40  E-value=0.54  Score=41.63  Aligned_cols=26  Identities=23%  Similarity=0.437  Sum_probs=21.6

Q ss_pred             HHHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           65 QAIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        65 ~~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      ..+..++.|.|  ++..++||||||...
T Consensus        71 ~lv~~~l~G~n~tifAYGqTGSGKTyTm   98 (330)
T 2h58_A           71 ALVTSCIDGFNVCIFAYGQTGAGKTYTM   98 (330)
T ss_dssp             HHHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHHhCCCEEEEEeECCCCCCCcEEE
Confidence            35666789998  789999999999875

>3b6u_A Kinesin-like protein KIF3B; structural genomics consortium, motor domain, ADP, SGC, ATP-binding, coiled coil, microtubule, motor protein; HET: ADP; 1.80A {Homo sapiens} PDB: 3b6v_A*

Probab=86.27  E-value=0.51  Score=42.48  Aligned_cols=25  Identities=32%  Similarity=0.539  Sum_probs=20.3

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..++||||||...
T Consensus        93 lv~~~l~G~n~tifAYGqTGSGKTyTM  119 (372)
T 3b6u_A           93 LVDSVLQGFNGTIFAYGQTGTGKTYTM  119 (372)
T ss_dssp             HHHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhCCCeeeEEeecCCCCCCCEeE
Confidence            3455678987  789999999999874

>2zfi_A Kinesin-like protein KIF1A, kinesin heavy chain isoform 5C; alpha and beta protein, enzyme, ATPase, P-loop, motor protein, ATP-binding, coiled coil; HET: ADP; 1.55A {Mus musculus} SCOP: c.37.1.9 PDB: 1vfw_A* 1vfx_A* 1vfz_A* 1vfv_A* 2zfj_A* 2zfk_A* 2zfl_A* 2zfm_A* 1i5s_A* 1i6i_A* 2hxf_C* 1ia0_K* 2hxh_C*

Probab=86.26  E-value=0.54  Score=42.25  Aligned_cols=25  Identities=20%  Similarity=0.437  Sum_probs=20.4

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..|+||||||...
T Consensus        81 lv~~~l~G~N~tifAYGqTGSGKTyTm  107 (366)
T 2zfi_A           81 MLQHAFEGYNVCIFAYGQTGAGKSYTM  107 (366)
T ss_dssp             HHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcCCeeEEEEeCCCCCCCceEe
Confidence            3455678988  789999999999874

>1v8k_A Kinesin-like protein KIF2C; microtubule destabilizer, structural P; HET: ANP; 2.25A {Mus musculus} SCOP: c.37.1.9 PDB: 1v8j_A* 2gry_A*

Probab=86.20  E-value=0.54  Score=42.85  Aligned_cols=25  Identities=28%  Similarity=0.485  Sum_probs=20.3

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..|+||||||.+.
T Consensus       146 lV~~~l~G~N~tifAYGQTGSGKTyTM  172 (410)
T 1v8k_A          146 LVQTIFEGGKATCFAYGQTGSGKTHTM  172 (410)
T ss_dssp             HHHHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhcCCceeEEeecCCCCCCCeEe
Confidence            3455678887  789999999999884

>1qvr_A CLPB protein; coiled coil, AAA ATPase, chaperone; HET: ANP; 3.00A {Thermus thermophilus} SCOP: a.174.1.1 c.37.1.20 c.37.1.20

Probab=86.18  E-value=1.9  Score=43.29  Aligned_cols=17  Identities=24%  Similarity=0.378  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCCchHHHH
Q 043110           74 RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~   90 (316)
                      .++++.||+|+|||...
T Consensus       192 ~~vlL~G~pG~GKT~la  208 (854)
T 1qvr_A          192 NNPVLIGEPGVGKTAIV  208 (854)
T ss_dssp             CCCEEEECTTSCHHHHH
T ss_pred             CceEEEcCCCCCHHHHH
Confidence            47999999999999764

>4etp_A Kinesin-like protein KAR3; kinesin motor protein, kinesin motor homology domain, karyog mitosis, microtubules; HET: ADP EBC; 2.30A {Saccharomyces cerevisiae}

Probab=86.17  E-value=0.55  Score=42.77  Aligned_cols=25  Identities=28%  Similarity=0.506  Sum_probs=21.4

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..|+||||||...
T Consensus       132 lv~~~l~G~N~tifAYGqTGSGKTyTM  158 (403)
T 4etp_A          132 LVQSSLDGYNVAIFAYGQTGSGKTFTM  158 (403)
T ss_dssp             HHHHHHTTCCEEEEEESCTTSSHHHHH
T ss_pred             HHHHHhCCcceEEEEECCCCCCCceEe
Confidence            5667789998  789999999999885

>3gbj_A KIF13B protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, ATP-binding, microtubule, motor protein; HET: ADP; 2.10A {Homo sapiens} SCOP: c.37.1.9

Probab=86.07  E-value=0.54  Score=42.05  Aligned_cols=25  Identities=20%  Similarity=0.449  Sum_probs=20.6

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..++||||||...
T Consensus        84 lv~~~l~G~n~tifAYGqTGSGKTyTm  110 (354)
T 3gbj_A           84 ILQNAFDGYNACIFAYGQTGSGKSYTM  110 (354)
T ss_dssp             HHHHHHTTCCEEEEEEECTTSSHHHHH
T ss_pred             HHHHHhCCceeEEEeeCCCCCCCceEE
Confidence            3455678988  789999999999885

>3hws_A ATP-dependent CLP protease ATP-binding subunit CL; CLPXP, AAA+ molecular machine, hexamer, asymmetric,, ATP-BIN chaperone, metal-binding; HET: ADP; 3.25A {Escherichia coli} PDB: 3hte_A

Probab=86.03  E-value=1.2  Score=39.74  Aligned_cols=19  Identities=32%  Similarity=0.518  Sum_probs=16.3

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .+..+++.+|+|+|||..+
T Consensus        50 ~~~~vll~GppGtGKT~la   68 (363)
T 3hws_A           50 GKSNILLIGPTGSGKTLLA   68 (363)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCCeEEEECCCCCCHHHHH
Confidence            4567999999999999865

>3t0q_A AGR253WP; kinesin, alpha and beta proteins, P-loop containing nucleosi triphosphate hydrolases, microtubule motor protein; HET: ADP; 2.35A {Ashbya gossypii}

Probab=85.94  E-value=0.57  Score=41.83  Aligned_cols=25  Identities=28%  Similarity=0.490  Sum_probs=21.6

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..++||||||...
T Consensus        77 lv~~~l~G~n~tifAYGqTGSGKTyTm  103 (349)
T 3t0q_A           77 LVQSSLDGYNVCIFAYGQTGSGKTYTM  103 (349)
T ss_dssp             HHHGGGTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHCCcceeEEEeCCCCCCCceEe
Confidence            5677789998  789999999999885

>1t5c_A CENP-E protein, centromeric protein E; kinesin motor-domain-ADP complex, stranded beta-sheet core with solvent exposed alpha-helices; HET: ADP PIN; 2.50A {Homo sapiens}

Probab=85.89  E-value=0.55  Score=41.90  Aligned_cols=25  Identities=24%  Similarity=0.413  Sum_probs=20.4

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..++||||||...
T Consensus        69 lv~~~l~G~n~tifAYGqTGSGKTyTM   95 (349)
T 1t5c_A           69 IIDSAIQGYNGTIFAYGQTASGKTYTM   95 (349)
T ss_dssp             HHHHHHTTCCEEEEEEESTTSSHHHHH
T ss_pred             HHHHHHcCCccceeeecCCCCCCCeEE
Confidence            3455678987  789999999999885

>1x88_A Kinesin-like protein KIF11; switch II, motor domain, NECK linker, cell cycle; HET: ADP NAT; 1.80A {Homo sapiens} SCOP: c.37.1.9 PDB: 3hqd_A* 3ken_A* 2pg2_A* 1yrs_A* 2fme_A* 2g1q_A* 2gm1_A* 1ii6_A* 2uyi_A* 2uym_A* 2wog_A* 2x2r_A* 2x7c_A* 2x7d_A* 2x7e_A* 2xae_A* 3k3b_A* 3k5e_A* 3l9h_A* 1q0b_A* ...

Probab=85.88  E-value=0.53  Score=42.22  Aligned_cols=25  Identities=28%  Similarity=0.526  Sum_probs=20.5

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..++||||||...
T Consensus        80 lv~~~l~G~n~tifAYGqTGSGKTyTM  106 (359)
T 1x88_A           80 ILDEVIMGYNCTIFAYGQTGTGKTFTM  106 (359)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hHHHHhCCCceEEEEeCCCCCCCceEE
Confidence            4555678987  789999999999874

>2qgz_A Helicase loader, putative primosome component; structural genomics, PSI-2, protein structure initiative; 2.40A {Streptococcus pyogenes serotype M3}

Probab=85.80  E-value=1.5  Score=38.17  Aligned_cols=26  Identities=15%  Similarity=0.324  Sum_probs=19.1

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      ++++++.||+|+|||.... .+...+.
T Consensus       152 ~~~lll~G~~GtGKT~La~-aia~~~~  177 (308)
T 2qgz_A          152 QKGLYLYGDMGIGKSYLLA-AMAHELS  177 (308)
T ss_dssp             CCEEEEECSTTSSHHHHHH-HHHHHHH
T ss_pred             CceEEEECCCCCCHHHHHH-HHHHHHH
Confidence            5789999999999997653 3444443

>2heh_A KIF2C protein; kinesin, motor domain, ADP, structural genomics, structural genomics consortium, SGC, structural protein; HET: ADP; 2.15A {Homo sapiens} PDB: 3edl_D*

Probab=85.65  E-value=0.58  Score=42.32  Aligned_cols=25  Identities=28%  Similarity=0.485  Sum_probs=20.4

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..++||||||...
T Consensus       126 lv~~~l~G~N~tifAYGQTGSGKTyTM  152 (387)
T 2heh_A          126 LVQTIFEGGKATCFAYGQTGSGKTHTM  152 (387)
T ss_dssp             HHHHHHTTCEEEEEEESCTTSSHHHHH
T ss_pred             HHHHHhcCCceEEEEecCCCCCCCeEe
Confidence            3455678987  789999999999885

>3nbx_X ATPase RAVA; AAA+ ATPase, alpha-beta-alpha structure, rossman fold, hydro; HET: ADP; 2.91A {Escherichia coli}

Probab=85.55  E-value=1.1  Score=42.01  Aligned_cols=36  Identities=19%  Similarity=0.300  Sum_probs=26.1

Q ss_pred             CCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           55 GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        55 g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      .+-.-...=..++-.+..+.++++.||+|+|||...
T Consensus        23 ~ivGq~~~i~~l~~al~~~~~VLL~GpPGtGKT~LA   58 (500)
T 3nbx_X           23 GLYERSHAIRLCLLAALSGESVFLLGPPGIAKSLIA   58 (500)
T ss_dssp             TCSSCHHHHHHHHHHHHHTCEEEEECCSSSSHHHHH
T ss_pred             hhHHHHHHHHHHHHHHhcCCeeEeecCchHHHHHHH
Confidence            343334444555666778899999999999999763

>3cmw_A Protein RECA, recombinase A; homologous recombination, recombination/DNA complex; HET: DNA ADP; 2.80A {Escherichia coli} PDB: 3cmt_A* 3cmx_A* 3cmv_A*

Probab=85.39  E-value=1.3  Score=47.67  Aligned_cols=99  Identities=19%  Similarity=0.215  Sum_probs=57.5

Q ss_pred             HHHHHhC------CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCC
Q 043110           66 AIPVILS------GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRW  139 (316)
Q Consensus        66 ~i~~il~------g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~  139 (316)
                      .++.++.      |+-+.+.+|.|||||...+- ++....+        .|-.|+++.+-.+|....   +++++-... 
T Consensus      1418 ~lD~~lg~gG~prg~~iei~g~~~sGkttl~~~-~~a~~~~--------~g~~~~~i~~e~~~~~~~---~~~~Gv~~~- 1484 (1706)
T 3cmw_A         1418 SLDIALGAGGLPMGRIVEIYGPESSGKTTLTLQ-VIAAAQR--------EGKTCAFIDAEHALDPIY---ARKLGVDID- 1484 (1706)
T ss_dssp             HHHHHTSSSSEETTSEEEEECSTTSSHHHHHHH-HHHHHHH--------TTCCEEEECTTSCCCHHH---HHHTTCCGG-
T ss_pred             HHHHhcCCCCCCCCCEEEEEcCCCCCHHHHHHH-HHHHHHh--------cCCeEEEEecCCCCCHHH---HHHcCCCHH-
Confidence            4555554      46699999999999987644 4433333        244599998887776443   444432221 


Q ss_pred             ceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCC-ccccCceeEEEEecchhhhc
Q 043110          140 IVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTS-SFLHTNLRWIIFDEADRILE  200 (316)
Q Consensus       140 ~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~-~~~~~~l~~lViDEad~l~~  200 (316)
                                             +++|.-|+.-.+++.... .+.-..++.+|||.+..|..
T Consensus      1485 -----------------------~l~~~~p~~~e~~l~~~~~~~~s~~~~~vvvDsv~al~~ 1523 (1706)
T 3cmw_A         1485 -----------------------NLLCSQPDTGEQALEICDALARSGAVDVIVVDSVAALTP 1523 (1706)
T ss_dssp             -----------------------GCEEECCSSHHHHHHHHHHHHHHTCCSEEEESCSTTCCC
T ss_pred             -----------------------HeEEeCCCcHHHHHHHHHHHHHcCCCCEEEEccHHhCCc
Confidence                                   255666643222221100 01113578999999988764

>3cob_A Kinesin heavy chain-like protein; motor, switch II, loop L11, conformation, nucleotide, ATP-binding, microtubule, motor protein; HET: ADP; 2.20A {Solanum tuberosum} SCOP: c.37.1.9 PDB: 3cnz_A* 1sdm_A* 3h4s_A*

Probab=85.33  E-value=0.51  Score=42.43  Aligned_cols=25  Identities=24%  Similarity=0.484  Sum_probs=21.0

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..|+||||||...
T Consensus        71 lv~~~l~G~n~tifAYGqTGSGKTyTM   97 (369)
T 3cob_A           71 LVQSAVDGYNVCIFAYGQTGSGKTFTI   97 (369)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hhHhhhcCCceEEEEECCCCCCCeEee
Confidence            5566779988  788999999999874

>1f9v_A Kinesin-like protein KAR3; kinesin-related protein, motor protein, microtubinding proteinbule, contractIle protein; HET: ADP; 1.30A {Saccharomyces cerevisiae} SCOP: c.37.1.9 PDB: 1f9t_A* 1f9w_A* 1f9u_A* 3kar_A*

Probab=85.27  E-value=0.58  Score=41.73  Aligned_cols=25  Identities=28%  Similarity=0.506  Sum_probs=21.1

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..++||||||...
T Consensus        76 lv~~~l~G~n~tifAYGqTGSGKTyTM  102 (347)
T 1f9v_A           76 LVQSSLDGYNVCIFAYGQTGSGKTFTM  102 (347)
T ss_dssp             HHGGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             HHHHhcCCceeEEEEECCCCCCCcEec
Confidence            5566778988  789999999999875

>3u06_A Protein claret segregational; motor domain, stalk rotation, power stroke, kinesin-14, MICR binding, NCD, transport, molecular motor; HET: ADP GOL; 2.35A {Drosophila melanogaster} PDB: 2ncd_A* 1n6m_A* 1cz7_A* 3l1c_A*

Probab=85.16  E-value=0.58  Score=42.74  Aligned_cols=25  Identities=32%  Similarity=0.515  Sum_probs=21.4

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..|+||||||...
T Consensus       130 lv~~~l~G~n~tifAYGqTGSGKTyTM  156 (412)
T 3u06_A          130 LIQSALDGYNICIFAYGQTGSGKTYTM  156 (412)
T ss_dssp             HHHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHHHHCCCceEEEEecCCCCCCeeEe
Confidence            5667789998  799999999999874

>2x8a_A Nuclear valosin-containing protein-like; nuclear protein; 2.60A {Homo sapiens}

Probab=85.11  E-value=0.17  Score=43.49  Aligned_cols=54  Identities=17%  Similarity=0.297  Sum_probs=28.8

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHH-HHHHHHHh--CCCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQ-AQAIPVIL--SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q-~~~i~~il--~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|++++-.+++++.|.+..    ..|+. ..++..+-  -.+.+++.+|+|+|||...
T Consensus         5 ~~~~~~di~g~~~~~~~l~~~i----~~~~~~~~~l~~~~l~~~~GvlL~Gp~GtGKTtLa   61 (274)
T 2x8a_A            5 PNVTWADIGALEDIREELTMAI----LAPVRNPDQFKALGLVTPAGVLLAGPPGCGKTLLA   61 (274)
T ss_dssp             -------CCHHHHHHHHHHHHH----THHHHSHHHHHHTTCCCCSEEEEESSTTSCHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHH----HHHhhCHHHHHHcCCCCCCeEEEECCCCCcHHHHH
Confidence            3467999988888888884432    12222 22232221  1234999999999999764

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=85.10  E-value=3.6  Score=31.76  Aligned_cols=72  Identities=17%  Similarity=0.101  Sum_probs=48.1

Q ss_pred             eEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHH---HHh-cCCcEEEeCcHHHHHHHhcCCccccCce
Q 043110          112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA---RLR-KGISILVATPGHLLDHLKHTSSFLHTNL  187 (316)
Q Consensus       112 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~l  187 (316)
                      ++||.++++.-+..+.+.+...     ...+..++|+....+...   .+. ...+|+|+|.-     +.  .++++.++
T Consensus        37 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~--~Gld~~~~  104 (163)
T 2hjv_A           37 SCIIFCRTKEHVNQLTDELDDL-----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATDV-----AA--RGIDIENI  104 (163)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECGG-----GT--TTCCCSCC
T ss_pred             cEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECCh-----hh--cCCchhcC
Confidence            4999999999999988887764     245566777766544332   233 34689999931     11  45666778


Q ss_pred             eEEEEecc
Q 043110          188 RWIIFDEA  195 (316)
Q Consensus       188 ~~lViDEa  195 (316)
                      +++|.-+.
T Consensus       105 ~~Vi~~~~  112 (163)
T 2hjv_A          105 SLVINYDL  112 (163)
T ss_dssp             SEEEESSC
T ss_pred             CEEEEeCC
Confidence            88876443

>2wbe_C Bipolar kinesin KRP-130; EG5, KLP61F, tubulin, mitosis, GTP-binding, motor protein, cell division, cell cycle, microtubule, ATP-binding; HET: GTP ANP GDP TA1; 9.40A {Drosophila melanogaster}

Probab=85.10  E-value=0.57  Score=42.21  Aligned_cols=25  Identities=40%  Similarity=0.562  Sum_probs=20.1

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..++||||||...
T Consensus        92 lv~~~l~G~n~tifAYGqTGSGKTyTm  118 (373)
T 2wbe_C           92 LIEEVLNGYNCTVFAYGQTGTGKTHTM  118 (373)
T ss_dssp             HHHHHHHTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhCCceEEEEeecCCCCCcceec
Confidence            3445668887  799999999999874

>1u0j_A DNA replication protein; AAA+ protein, P-loop atpases, helicase; HET: DNA ADP; 2.10A {Adeno-associated virus - 2} SCOP: c.37.1.20 PDB: 1s9h_A

Probab=84.80  E-value=2.3  Score=36.29  Aligned_cols=44  Identities=18%  Similarity=0.161  Sum_probs=31.4

Q ss_pred             HHHHHHHHHHcCCCCCcHHH-HHHHHHHhCCC-----cEEEEcCCCCchHHHHH
Q 043110           44 STLCDQLRERLGFEAPTKVQ-AQAIPVILSGR-----DVLVNAATGTGKTVAYL   91 (316)
Q Consensus        44 ~~l~~~l~~~~g~~~p~~~Q-~~~i~~il~g~-----d~li~a~TGsGKT~~~~   91 (316)
                      ..+.+.| +..|++   +++ ..++..++.|+     .+++.||.|+|||+.+.
T Consensus        73 n~i~~~l-~~qg~~---~~~~~~~l~~~l~~~~~~~n~~~l~GppgtGKt~~a~  122 (267)
T 1u0j_A           73 NRIYKIL-ELNGYD---PQYAASVFLGWATKKFGKRNTIWLFGPATTGKTNIAE  122 (267)
T ss_dssp             CHHHHHH-HHTTCC---HHHHHHHHHHHHTTCSTTCCEEEEECSTTSSHHHHHH
T ss_pred             HHHHHHH-HHcCCC---HHHHHHHHHHHHhCCCCCCcEEEEECCCCCCHHHHHH
Confidence            3677777 556776   566 34456666654     39999999999998764

>2owm_A Nckin3-434, related to kinesin-like protein KIF1C; motor domain, ADP, NECK linker, motor PR; HET: ADP; 3.25A {Neurospora crassa}

Probab=84.70  E-value=0.7  Score=42.64  Aligned_cols=24  Identities=21%  Similarity=0.418  Sum_probs=19.9

Q ss_pred             HHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           67 IPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        67 i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      +..++.|.|  ++..|+||||||...
T Consensus       129 v~~~l~GyN~tIfAYGQTGSGKTyTM  154 (443)
T 2owm_A          129 LDHNFEGYHTCIFAYGQTGSGKSYTM  154 (443)
T ss_dssp             HHHHHTTCCEEEEEESSTTSSHHHHH
T ss_pred             HHHhhcCCceEEEEeCCCCCCCCEEe
Confidence            445568988  799999999999875

>3hjh_A Transcription-repair-coupling factor; MFD, mutation frequency decline, ATP-binding, DNA DAMA repair, DNA-binding, helicase, hydrolase; 1.95A {Escherichia coli} PDB: 2b2n_A* 4dfc_A

Probab=84.68  E-value=1.8  Score=40.36  Aligned_cols=51  Identities=14%  Similarity=0.214  Sum_probs=37.7

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      .|....+.+-||||||++.. .++.   ...        ..+|||+|+...|.|+++.++.+.
T Consensus        13 ~~~~~~l~g~~gs~ka~~~a-~l~~---~~~--------~p~lvv~~~~~~A~~l~~~l~~~~   63 (483)
T 3hjh_A           13 AGEQRLLGELTGAACATLVA-EIAE---RHA--------GPVVLIAPDMQNALRLHDEISQFT   63 (483)
T ss_dssp             TTCEEEEECCCTTHHHHHHH-HHHH---HSS--------SCEEEEESSHHHHHHHHHHHHHTC
T ss_pred             CCCeEEEeCCCchHHHHHHH-HHHH---HhC--------CCEEEEeCCHHHHHHHHHHHHhhC
Confidence            45668999999999997632 1222   211        128999999999999999998875

>3bfn_A Kinesin-like protein KIF22; limited proteolysis, structural genomics consortium domain, ADP, SGC, ATP-binding, DNA-binding, microtubule, MO protein; HET: ADP; 2.30A {Homo sapiens}

Probab=84.67  E-value=0.56  Score=42.47  Aligned_cols=23  Identities=39%  Similarity=0.605  Sum_probs=19.0

Q ss_pred             HHHhCCCc--EEEEcCCCCchHHHH
Q 043110           68 PVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        68 ~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      ..++.|.|  ++..|+||||||...
T Consensus        92 ~~~l~G~N~tifAYGqTGSGKTyTM  116 (388)
T 3bfn_A           92 RHLLEGQNASVLAYGPTGAGKTHTM  116 (388)
T ss_dssp             HHHTTTCCEEEEEESCTTSSHHHHH
T ss_pred             HHhhcCceeeEeeecCCCCCCCeEe
Confidence            34568887  789999999999875

>1w36_B RECB, exodeoxyribonuclease V beta chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} SCOP: c.37.1.19 c.37.1.19 c.52.1.24 PDB: 3k70_B*

Probab=84.61  E-value=2.1  Score=44.59  Aligned_cols=61  Identities=21%  Similarity=0.174  Sum_probs=43.0

Q ss_pred             cEEEEcCCCCchHHHHHHHHHHHhhhcCCC---CCCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           75 DVLVNAATGTGKTVAYLAPIINHLQSYSPR---IDRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        75 d~li~a~TGsGKT~~~~lp~l~~l~~~~~~---~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      ..+|.|..|||||.+..--++..+......   .....--++|+|+=|+.-+.++.+++.....
T Consensus        18 ~~lV~AsAGSGKT~~L~~r~lrLll~~g~~~~~~~~~~~~~ILvvTFT~aAA~EMr~RI~~~L~   81 (1180)
T 1w36_B           18 ERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNIH   81 (1180)
T ss_dssp             CEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHhcCCcccccCCCCCHHHEEEEeccHHHHHHHHHHHHHHHH
Confidence            459999999999998766667766532100   0001123599999999999999988877654

>4ag6_A VIRB4 ATPase, type IV secretory pathway VIRB4 components-like P; hydrolase, type IV secretion, conjugation; 2.35A {Thermoanaerobacter pseudethanolicus} PDB: 4ag5_A

Probab=84.30  E-value=1.1  Score=40.29  Aligned_cols=31  Identities=10%  Similarity=-0.007  Sum_probs=23.3

Q ss_pred             eeEEEEecchhhhcC---CcHHHHHHHHHHhccC
Q 043110          187 LRWIIFDEADRILEL---GFGKEIEEILDILGSR  217 (316)
Q Consensus       187 l~~lViDEad~l~~~---~~~~~i~~i~~~l~~~  217 (316)
                      -.++|+||||.++..   .+...+..+++..++.
T Consensus       263 ~~~i~iDEa~~~~~~~~~~~~~~l~~~~~~~Rk~  296 (392)
T 4ag6_A          263 RTVLVVDEAWMLVDPQTPQAIAFLRDTSKRIRKY  296 (392)
T ss_dssp             TCEEEETTGGGGCCTTCTHHHHHHHHHHHHGGGG
T ss_pred             cEEEEEecHHHHhCcCchHHHHHHHHHHHHhhhh
Confidence            468999999999963   3556777888777653

>2rep_A Kinesin-like protein KIFC1; structural genomics consortium, motor domain, ADP, binding, cell cycle, cell division, endosome, microtubule; HET: ADP; 2.60A {Homo sapiens}

Probab=83.96  E-value=0.64  Score=41.93  Aligned_cols=25  Identities=28%  Similarity=0.481  Sum_probs=20.7

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..++.|.|  ++..++||||||...
T Consensus       107 lv~~~l~G~N~tifAYGqTGSGKTyTM  133 (376)
T 2rep_A          107 LVQSALDGYPVCIFAYGQTGSGKTFTM  133 (376)
T ss_dssp             HHHGGGGTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhcCCCceEEEEeCCCCCCCceEe
Confidence            4556678987  789999999999874

>3cf0_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD, CDC48, ATP-binding, lipid-binding, nucle binding, nucleus, phosphoprotein, transport; HET: ADP; 3.00A {Mus musculus}

Probab=83.49  E-value=0.56  Score=40.73  Aligned_cols=56  Identities=18%  Similarity=0.329  Sum_probs=32.8

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHH-HhCCCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPV-ILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~-il~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|++++-.+.+++.|.+...+  |.......... +..++.+++.||+|+|||...
T Consensus        10 ~~~~~~di~G~~~~~~~l~~~v~~--~~~~~~~~~~~~~~~~~~vLL~Gp~GtGKT~la   66 (301)
T 3cf0_A           10 PQVTWEDIGGLEDVKRELQELVQY--PVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLA   66 (301)
T ss_dssp             CCCCGGGSCSCHHHHHHHHHHHHH--HHHCHHHHHHHCCCCCSEEEEECSSSSSHHHHH
T ss_pred             CCCCHHHhCCHHHHHHHHHHHHHH--HhhCHHHHHHcCCCCCceEEEECCCCcCHHHHH
Confidence            345788888777777777432110  10000110111 234567999999999999864

>2zts_A Putative uncharacterized protein PH0186; KAIC like protein, ATP-binding, nucleotide-binding, ATP- binding protein; HET: ADP; 2.07A {Pyrococcus horikoshii}

Probab=83.40  E-value=1.4  Score=36.44  Aligned_cols=52  Identities=25%  Similarity=0.279  Sum_probs=30.1

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      .|.-+++.|++|+|||...+--+.+.....        +..++|++-. +-..++.+.+..
T Consensus        29 ~G~l~~i~G~pG~GKT~l~l~~~~~~~~~~--------~~~v~~~s~E-~~~~~~~~~~~~   80 (251)
T 2zts_A           29 EGTTVLLTGGTGTGKTTFAAQFIYKGAEEY--------GEPGVFVTLE-ERARDLRREMAS   80 (251)
T ss_dssp             TTCEEEEECCTTSSHHHHHHHHHHHHHHHH--------CCCEEEEESS-SCHHHHHHHHHT
T ss_pred             CCeEEEEEeCCCCCHHHHHHHHHHHHHHhc--------CCCceeeccc-CCHHHHHHHHHH
Confidence            345699999999999976543333333332        2227777643 334555555443

>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=83.37  E-value=9  Score=29.80  Aligned_cols=72  Identities=8%  Similarity=-0.047  Sum_probs=48.8

Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHH---Hh-cCCcEEEeCcHHHHHHHhcCCccccC
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKAR---LR-KGISILVATPGHLLDHLKHTSSFLHT  185 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~  185 (316)
                      +.++||.++++..+..+++.+...     ...+..++|+.........   +. ...+|+|+|.-       -..++++.
T Consensus        34 ~~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~-------~~~Gid~~  101 (175)
T 2rb4_A           34 IGQAIIFCQTRRNAKWLTVEMIQD-----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNV-------CARGIDVK  101 (175)
T ss_dssp             CSEEEEECSCHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCS-------CCTTTCCT
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecc-------hhcCCCcc
Confidence            346999999999999888877653     2455667777665544332   33 34789999931       12456677


Q ss_pred             ceeEEEEe
Q 043110          186 NLRWIIFD  193 (316)
Q Consensus       186 ~l~~lViD  193 (316)
                      .++++|.-
T Consensus       102 ~~~~Vi~~  109 (175)
T 2rb4_A          102 QVTIVVNF  109 (175)
T ss_dssp             TEEEEEES
T ss_pred             cCCEEEEe
Confidence            88888853

>2fna_A Conserved hypothetical protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE ADP; 2.00A {Sulfolobus solfataricus} SCOP: a.4.5.11 c.37.1.20

Probab=83.34  E-value=21  Score=30.68  Aligned_cols=17  Identities=29%  Similarity=0.180  Sum_probs=14.9

Q ss_pred             CcEEEEcCCCCchHHHH
Q 043110           74 RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~   90 (316)
                      ..+++.|+.|+|||...
T Consensus        31 ~~v~i~G~~G~GKT~L~   47 (357)
T 2fna_A           31 PITLVLGLRRTGKSSII   47 (357)
T ss_dssp             SEEEEEESTTSSHHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            57999999999999763

>1xwi_A SKD1 protein; VPS4B, AAA ATPase, protein transport; 2.80A {Homo sapiens}

Probab=83.16  E-value=1.5  Score=38.41  Aligned_cols=50  Identities=20%  Similarity=0.274  Sum_probs=31.9

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHh-----CCCcEEEEcCCCCchHHHH
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVIL-----SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il-----~g~d~li~a~TGsGKT~~~   90 (316)
                      ..+|++++=...+++.|.+...    .|.+   .|.+.     ..+.+++.||+|+|||...
T Consensus         8 ~~~~~di~G~~~~k~~l~~~v~----~p~~---~~~~~~~~~~~~~~iLL~GppGtGKT~la   62 (322)
T 1xwi_A            8 NVKWSDVAGLEGAKEALKEAVI----LPIK---FPHLFTGKRTPWRGILLFGPPGTGKSYLA   62 (322)
T ss_dssp             CCCGGGSCSCHHHHHHHHHHHH----HHHH---CGGGSCTTCCCCSEEEEESSSSSCHHHHH
T ss_pred             CCCHHHhcCHHHHHHHHHHHHH----HHHh---CHHHHhCCCCCCceEEEECCCCccHHHHH
Confidence            4579999877887777743211    0111   11222     2357999999999999864

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=83.09  E-value=1.3  Score=34.66  Aligned_cols=18  Identities=22%  Similarity=0.337  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      +..+++.||+|+|||...
T Consensus        43 ~~~~ll~G~~G~GKT~l~   60 (195)
T 1jbk_A           43 KNNPVLIGEPGVGKTAIV   60 (195)
T ss_dssp             SCEEEEECCTTSCHHHHH
T ss_pred             CCceEEECCCCCCHHHHH
Confidence            457999999999999864

>1ls1_A Signal recognition particle protein; FFH, SRP54, SRP, GTPase, ultrahigh resolution, protein transport; 1.10A {Thermus aquaticus} SCOP: a.24.13.1 c.37.1.10 PDB: 1jpn_B* 1jpj_A* 1ry1_U* 2j45_A* 1o87_A* 2c04_A* 2j46_A* 1rj9_B* 2c03_A* 2j7p_A* 1okk_A* 2cnw_A* 1ng1_A* 2xkv_A 3ng1_A 1ffh_A 2ng1_A*

Probab=82.76  E-value=16  Score=31.44  Aligned_cols=18  Identities=22%  Similarity=0.231  Sum_probs=14.1

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      ++-+.+.+++|+|||...
T Consensus        98 ~~~i~i~g~~G~GKTT~~  115 (295)
T 1ls1_A           98 RNLWFLVGLQGSGKTTTA  115 (295)
T ss_dssp             SEEEEEECCTTTTHHHHH
T ss_pred             CeEEEEECCCCCCHHHHH
Confidence            345677899999999764

>1tue_A Replication protein E1; helicase, replication, E1E2 complex, AAA+ protein; 2.10A {Human papillomavirus type 18} SCOP: c.37.1.20

Probab=82.27  E-value=2.3  Score=34.89  Aligned_cols=50  Identities=18%  Similarity=0.185  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHcCCCCCcHHHHHHHHHHhCC----CcEEEEcCCCCchHHHHHHHHHHH
Q 043110           44 STLCDQLRERLGFEAPTKVQAQAIPVILSG----RDVLVNAATGTGKTVAYLAPIINH   97 (316)
Q Consensus        44 ~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g----~d~li~a~TGsGKT~~~~lp~l~~   97 (316)
                      ..+.+.| +-.|++ +-.+ ...+..++.+    ..+++.+|.|+|||..+ ..++..
T Consensus        28 ~~I~~~l-~yq~~~-~~~f-~~~l~~~~~~iPkkn~ili~GPPGtGKTt~a-~ala~~   81 (212)
T 1tue_A           28 RPIVQFL-RYQQIE-FITF-LGALKSFLKGTPKKNCLVFCGPANTGKSYFG-MSFIHF   81 (212)
T ss_dssp             HHHHHHH-HHTTCC-HHHH-HHHHHHHHHTCTTCSEEEEESCGGGCHHHHH-HHHHHH
T ss_pred             HHHHHHH-HHcCcC-HHHH-HHHHHHHHhcCCcccEEEEECCCCCCHHHHH-HHHHHH
Confidence            4667777 333443 4444 4555555554    24999999999999765 334443

>3b85_A Phosphate starvation-inducible protein; PHOH2, ATPase, PFAM: PF02562, ST genomics, PSI-2, protein structure initiative; 2.35A {Corynebacterium glutamicum atcc 13032}

Probab=82.03  E-value=1.6  Score=35.69  Aligned_cols=32  Identities=25%  Similarity=0.154  Sum_probs=26.4

Q ss_pred             CcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           59 PTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        59 p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      -+.-|..++..+..|.-+.+.+|+|+|||...
T Consensus         8 k~~g~~~~l~~i~~Ge~~~liG~nGsGKSTLl   39 (208)
T 3b85_A            8 KTLGQKHYVDAIDTNTIVFGLGPAGSGKTYLA   39 (208)
T ss_dssp             CSHHHHHHHHHHHHCSEEEEECCTTSSTTHHH
T ss_pred             CCHhHHHHHHhccCCCEEEEECCCCCCHHHHH
Confidence            34456778888888988999999999999864

>4b4t_H 26S protease regulatory subunit 7 homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=82.00  E-value=0.64  Score=43.03  Aligned_cols=54  Identities=24%  Similarity=0.390  Sum_probs=34.9

Q ss_pred             cCCcccCCCCHHHHHHHHHHcC--CCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           34 SCCFSSLGLDSTLCDQLRERLG--FEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g--~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      .-+|++.+=.+++++.|.+..-  +.+|-.++..-   +...+.+++.||+|+|||+.+
T Consensus       205 ~vt~~DIgGl~~~k~~L~e~V~~pl~~pe~f~~~G---i~pprGILLyGPPGTGKTlLA  260 (467)
T 4b4t_H          205 DVTYSDVGGCKDQIEKLREVVELPLLSPERFATLG---IDPPKGILLYGPPGTGKTLCA  260 (467)
T ss_dssp             SCCCSSCTTCHHHHHHHHHHTHHHHHCHHHHHHHT---CCCCSEEEECSCTTSSHHHHH
T ss_pred             CCCHHHhccHHHHHHHHHHHHHHHhcCHHHHHHCC---CCCCCceEeeCCCCCcHHHHH
Confidence            3689999988888888855321  22222222211   123467999999999999864

>1ofh_A ATP-dependent HSL protease ATP-binding subunit HSLU; chaperone, hydrolase, ATP-binding; HET: ADP; 2.5A {Haemophilus influenzae} SCOP: c.37.1.20 PDB: 1ofi_A*

Probab=81.88  E-value=2.4  Score=36.28  Aligned_cols=18  Identities=33%  Similarity=0.492  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      +..+++.||+|+|||...
T Consensus        50 ~~~vll~G~~GtGKT~la   67 (310)
T 1ofh_A           50 PKNILMIGPTGVGKTEIA   67 (310)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             CceEEEECCCCCCHHHHH
Confidence            568999999999999764

>2bjv_A PSP operon transcriptional activator; AAA, transcription activation, gene regulation, sigma54 activator, enhancer binding protein, PSPF; 1.7A {Escherichia coli} PDB: 2bjw_A 2c96_A* 2c98_A* 2c99_A* 2c9c_A* 2vii_A*

Probab=81.85  E-value=1.3  Score=37.33  Aligned_cols=19  Identities=32%  Similarity=0.450  Sum_probs=16.4

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .+..+++.|++|+|||...
T Consensus        28 ~~~~vll~G~~GtGKt~la   46 (265)
T 2bjv_A           28 LDKPVLIIGERGTGKELIA   46 (265)
T ss_dssp             SCSCEEEECCTTSCHHHHH
T ss_pred             CCCCEEEECCCCCcHHHHH
Confidence            5678999999999999764

>1kgd_A CASK, peripheral plasma membrane CASK; maguk, guanylate kinase like domain, protein binding; 1.31A {Homo sapiens} SCOP: c.37.1.1

Probab=81.63  E-value=0.79  Score=36.37  Aligned_cols=19  Identities=16%  Similarity=0.284  Sum_probs=16.3

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .|+-+++.||+|+|||...
T Consensus         4 ~g~~i~i~GpsGsGKSTL~   22 (180)
T 1kgd_A            4 MRKTLVLLGAHGVGRRHIK   22 (180)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5677899999999999864

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=81.55  E-value=13  Score=28.58  Aligned_cols=72  Identities=14%  Similarity=0.086  Sum_probs=47.7

Q ss_pred             eeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHH---HHh-cCCcEEEeCcHHHHHHHhcCCccccCc
Q 043110          111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA---RLR-KGISILVATPGHLLDHLKHTSSFLHTN  186 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~  186 (316)
                      .++||.+++++-+..+.+.+...     ...+..++|+........   .+. ...+|+|+|.-     +.  .++++.+
T Consensus        31 ~~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~--~G~d~~~   98 (165)
T 1fuk_A           31 TQAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDL-----LA--RGIDVQQ   98 (165)
T ss_dssp             SCEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGG-----GT--TTCCCCS
T ss_pred             CCEEEEECCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcCh-----hh--cCCCccc
Confidence            35999999999999888887663     244556777766544332   222 34789999931     11  4556677


Q ss_pred             eeEEEEec
Q 043110          187 LRWIIFDE  194 (316)
Q Consensus       187 l~~lViDE  194 (316)
                      ++++|.-+
T Consensus        99 ~~~Vi~~~  106 (165)
T 1fuk_A           99 VSLVINYD  106 (165)
T ss_dssp             CSEEEESS
T ss_pred             CCEEEEeC
Confidence            88877644

>4b4t_L 26S protease subunit RPT4; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=81.40  E-value=0.67  Score=42.67  Aligned_cols=55  Identities=27%  Similarity=0.376  Sum_probs=34.2

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcC--CCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLG--FEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g--~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|++.+=.++.++.|.+..-  +.+|--++...+   ...+-+++.||+|+|||+.+
T Consensus       176 p~v~~~digGl~~~k~~l~e~v~~pl~~p~~f~~~g~---~~prGvLL~GPPGtGKTllA  232 (437)
T 4b4t_L          176 GEITFDGIGGLTEQIRELREVIELPLKNPEIFQRVGI---KPPKGVLLYGPPGTGKTLLA  232 (437)
T ss_dssp             CSSCSGGGCSCHHHHHHHHHHHHHHHHCHHHHHHHCC---CCCCEEEEESCTTSSHHHHH
T ss_pred             CCCChhHhCChHHHHHHHHHHHHHHHhCHHHHHhCCC---CCCCeEEEECCCCCcHHHHH
Confidence            34579999877777777744321  222322222211   13367999999999999874

>2oap_1 GSPE-2, type II secretion system protein; hexameric ATPase, hydrolase; HET: ANP; 2.95A {Archaeoglobus fulgidus} PDB: 2oaq_1

Probab=81.30  E-value=0.83  Score=43.03  Aligned_cols=21  Identities=29%  Similarity=0.308  Sum_probs=18.0

Q ss_pred             HHhCCCcEEEEcCCCCchHHH
Q 043110           69 VILSGRDVLVNAATGTGKTVA   89 (316)
Q Consensus        69 ~il~g~d~li~a~TGsGKT~~   89 (316)
                      .+..|..+++.||||||||..
T Consensus       256 ~v~~g~~i~I~GptGSGKTTl  276 (511)
T 2oap_1          256 AIEHKFSAIVVGETASGKTTT  276 (511)
T ss_dssp             HHHTTCCEEEEESTTSSHHHH
T ss_pred             HHhCCCEEEEECCCCCCHHHH
Confidence            345788999999999999976

>2r44_A Uncharacterized protein; putative ATPase, structural genomics, joint center for struc genomics, JCSG; HET: MSE PG4; 2.00A {Cytophaga hutchinsonii atcc 33406}

Probab=81.04  E-value=0.84  Score=39.99  Aligned_cols=26  Identities=23%  Similarity=0.399  Sum_probs=20.2

Q ss_pred             HHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           65 QAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        65 ~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      .+.-.+..+.++++.||+|+|||...
T Consensus        38 ~l~~~l~~~~~vll~G~pGtGKT~la   63 (331)
T 2r44_A           38 RLLIGICTGGHILLEGVPGLAKTLSV   63 (331)
T ss_dssp             HHHHHHHHTCCEEEESCCCHHHHHHH
T ss_pred             HHHHHHHcCCeEEEECCCCCcHHHHH
Confidence            33344556889999999999999764

>1lv7_A FTSH; alpha/beta domain, four helix bundle, hydrolase; 1.50A {Escherichia coli} SCOP: c.37.1.20

Probab=80.65  E-value=2  Score=36.01  Aligned_cols=55  Identities=20%  Similarity=0.255  Sum_probs=30.8

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcC-CCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLG-FEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g-~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      ...+|+++.-.+.+.+.+.+... +..|..++...   ....+.+++.||+|+|||...
T Consensus         7 ~~~~~~~i~G~~~~~~~l~~~~~~~~~~~~~~~~~---~~~~~~vll~G~~GtGKT~la   62 (257)
T 1lv7_A            7 IKTTFADVAGCDEAKEEVAELVEYLREPSRFQKLG---GKIPKGVLMVGPPGTGKTLLA   62 (257)
T ss_dssp             SCCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHH
T ss_pred             CCCCHHHhcCcHHHHHHHHHHHHHHhCHHHHHHcC---CCCCCeEEEECcCCCCHHHHH
Confidence            34678888877777776633211 11111111100   012346999999999999764

>2gza_A Type IV secretion system protein VIRB11; ATPase, hydrolase; 2.60A {Brucella suis}

Probab=80.40  E-value=0.94  Score=40.54  Aligned_cols=20  Identities=35%  Similarity=0.511  Sum_probs=17.7

Q ss_pred             HhCCCcEEEEcCCCCchHHH
Q 043110           70 ILSGRDVLVNAATGTGKTVA   89 (316)
Q Consensus        70 il~g~d~li~a~TGsGKT~~   89 (316)
                      +..|..+++.+|||||||..
T Consensus       172 i~~G~~i~ivG~sGsGKSTl  191 (361)
T 2gza_A          172 VQLERVIVVAGETGSGKTTL  191 (361)
T ss_dssp             HHTTCCEEEEESSSSCHHHH
T ss_pred             HhcCCEEEEECCCCCCHHHH
Confidence            45788999999999999975

>4b4t_K 26S protease regulatory subunit 6B homolog; hydrolase, AAA-atpases, protein degradation, ubiquitin-prote pathway; 7.40A {Saccharomyces cerevisiae}

Probab=80.29  E-value=0.82  Score=41.99  Aligned_cols=54  Identities=22%  Similarity=0.283  Sum_probs=33.4

Q ss_pred             cCCcccCCCCHHHHHHHHHHc--CCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           34 SCCFSSLGLDSTLCDQLRERL--GFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~--g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      ..+|++.|=-.++++.|.+..  .+.+|--++..-   +...+-+++.||+|+|||+.+
T Consensus       168 ~v~~~digGl~~~k~~l~e~v~~pl~~p~~~~~~g---~~~prGiLL~GPPGtGKT~la  223 (428)
T 4b4t_K          168 DVTYADVGGLDMQKQEIREAVELPLVQADLYEQIG---IDPPRGVLLYGPPGTGKTMLV  223 (428)
T ss_dssp             SCCGGGSCSCHHHHHHHHHHHHHHHHCHHHHHHHC---CCCCCEEEEESCTTTTHHHHH
T ss_pred             CCCHHHhccHHHHHHHHHHHHHHHHhCHHHHHhCC---CCCCceEEEECCCCCCHHHHH
Confidence            358999987777777774432  122222222211   123356999999999999874

>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=80.21  E-value=12  Score=30.33  Aligned_cols=69  Identities=16%  Similarity=0.126  Sum_probs=46.9

Q ss_pred             eEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHH---Hhc-CCcEEEeCcHHHHHHHhcCCccccCce
Q 043110          112 FALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKAR---LRK-GISILVATPGHLLDHLKHTSSFLHTNL  187 (316)
Q Consensus       112 ~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~~l  187 (316)
                      ++||.++++.-+..+.+.+...+     ..+..++|+.........   +.. ..+|+|+|.-     +.  .++++.++
T Consensus        33 ~~lVF~~~~~~~~~l~~~L~~~~-----~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~-----~~--~Gidi~~v  100 (212)
T 3eaq_A           33 RAMVFTRTKAETEEIAQGLLRLG-----HPAQALHGDLSQGERERVLGAFRQGEVRVLVATDV-----AA--RGLDIPQV  100 (212)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHT-----CCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTT-----TT--CSSSCCCB
T ss_pred             eEEEEeCCHHHHHHHHHHHHHcC-----CCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecCh-----hh--cCCCCccC
Confidence            49999999999999888887642     445667777665544332   333 4689999931     11  45666778


Q ss_pred             eEEEE
Q 043110          188 RWIIF  192 (316)
Q Consensus       188 ~~lVi  192 (316)
                      +++|.
T Consensus       101 ~~Vi~  105 (212)
T 3eaq_A          101 DLVVH  105 (212)
T ss_dssp             SEEEE
T ss_pred             cEEEE
Confidence            87764

>1lvg_A Guanylate kinase, GMP kinase; transferase; HET: ADP 5GP; 2.10A {Mus musculus} SCOP: c.37.1.1

Probab=80.05  E-value=0.95  Score=36.59  Aligned_cols=19  Identities=26%  Similarity=0.532  Sum_probs=15.3

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .|+-+.+.||+|+|||...
T Consensus         3 ~g~~i~lvGpsGaGKSTLl   21 (198)
T 1lvg_A            3 GPRPVVLSGPSGAGKSTLL   21 (198)
T ss_dssp             --CCEEEECCTTSSHHHHH
T ss_pred             CCCEEEEECCCCCCHHHHH
Confidence            5677999999999999864

---

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	316
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	3e-39
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	2e-38
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	2e-37
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	3e-35
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	3e-34
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	8e-34
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	7e-33
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	2e-29
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	2e-27
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	2e-25
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	5e-25
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	2e-19
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	4e-13
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	1e-12
d2fz4a1	206	c.37.1.19 (A:24-229) DNA repair protein RAD25 {Arc	3e-04
d1yksa1	140	c.37.1.14 (A:185-324) YFV helicase domain {Yellow	4e-04

>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 =  135 bits (341), Expect = 3e-39
 Identities = 63/225 (28%), Positives = 111/225 (49%), Gaps = 27/225 (12%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGR-DVLVNAATGTGKTVAYLAPII 95
           F+ L L   + + +R   GFE PT +Q + IP+ L+   +++  A TG+GKT ++  P+I
Sbjct: 6   FNELNLSDNILNAIRN-KGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLI 64

Query: 96  NHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK 155
             +   +       G  A++L PT EL + V + ++ L       +    + GG     +
Sbjct: 65  ELVNENN-------GIEAIILTPTRELAIQVADEIESLKGNKNLKI--AKIYGGKAIYPQ 115

Query: 156 ARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILG 215
            +  K  +I+V TPG +LDH+   +  L  N+++ I DEAD +L +GF K++E+IL+   
Sbjct: 116 IKALKNANIVVGTPGRILDHINRGTLNLK-NVKYFILDEADEMLNMGFIKDVEKILNACN 174

Query: 216 SRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                            ++ LL SAT+  ++ +L K  +     I
Sbjct: 175 K---------------DKRILLFSATMPREILNLAKKYMGDYSFI 204

>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 =  133 bits (336), Expect = 2e-38
 Identities = 64/242 (26%), Positives = 110/242 (45%), Gaps = 24/242 (9%)

Query: 19  DKMSKKKETVKEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLV 78
           D    + ET +E+  +  F ++GL   L   +    GFE P+ +Q +AI  I+ GRDV+ 
Sbjct: 1   DMTKVEFETSEEVDVTPTFDTMGLREDLLRGIYA-YGFEKPSAIQQRAIKQIIKGRDVIA 59

Query: 79  NAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFR 138
            + +GTGKT  +   ++  L            T AL+L PT EL + + + L  L   + 
Sbjct: 60  QSQSGTGKTATFSISVLQCLDIQVR------ETQALILAPTRELAVQIQKGLLALG-DYM 112

Query: 139 WIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRI 198
            +     +GG N  ++  +L  G  ++  TPG + D      S     ++ ++ DEAD +
Sbjct: 113 NVQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDM-IRRRSLRTRAIKMLVLDEADEM 171

Query: 199 LELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPV 258
           L  GF ++I ++   L                   Q +L+SATL  ++  +T   +  P+
Sbjct: 172 LNKGFKEQIYDVYRYLPP---------------ATQVVLISATLPHEILEMTNKFMTDPI 216

Query: 259 LI 260
            I
Sbjct: 217 RI 218

>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 =  130 bits (328), Expect = 2e-37
 Identities = 61/224 (27%), Positives = 95/224 (42%), Gaps = 23/224 (10%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F  + L  +L   +    GFE P+ +Q +AI   + G DV+  A +GTGKT  +   I+ 
Sbjct: 14  FDDMNLSESLLRGIYA-YGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQ 72

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            ++           T ALVL PT EL   + +++  L           + G   R++ + 
Sbjct: 73  QIEL------DLKATQALVLAPTRELAQQIQKVVMALGDYMGASCHACIGGTNVRAEVQK 126

Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS 216
              +   I+V TPG + D L           +  + DEAD +L  GF  +I +I   L S
Sbjct: 127 LQMEAPHIIVGTPGRVFDMLNRRYLSPKYI-KMFVLDEADEMLSRGFKDQIYDIFQKLNS 185

Query: 217 RNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                            Q +LLSAT+   V  +TK  +  P+ I
Sbjct: 186 ---------------NTQVVLLSATMPSDVLEVTKKFMRDPIRI 214

>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 =  125 bits (315), Expect = 3e-35
 Identities = 70/227 (30%), Positives = 113/227 (49%), Gaps = 17/227 (7%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F  L LD T+ + +     ++ PT +Q  AIP IL  RD++  A TG+GKT A+L PIIN
Sbjct: 23  FDELKLDPTIRNNILL-ASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIIN 81

Query: 97  HLQSYSP---RIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSK 153
           HL        R  +++    L+L PT EL + +     +       +    V GG +   
Sbjct: 82  HLVCQDLNQQRYSKTAYPKCLILAPTRELAIQILSE-SQKFSLNTPLRSCVVYGGADTHS 140

Query: 154 EKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDI 213
           +   ++ G  +LVATPG L+D ++     L    ++I+ DEADR+L++GF  +I +I++ 
Sbjct: 141 QIREVQMGCHLLVATPGRLVDFIEKNKISLEFC-KYIVLDEADRMLDMGFEPQIRKIIEE 199

Query: 214 LGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                       N  S + RQ L+ SAT  +++  L    L   + +
Sbjct: 200 S-----------NMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFM 235

>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 =  122 bits (306), Expect = 3e-34
 Identities = 68/224 (30%), Positives = 102/224 (45%), Gaps = 23/224 (10%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F    L   L   + E +G+E P+ +Q ++IP+ LSGRD+L  A  GTGK+ AYL P++ 
Sbjct: 5   FEDYCLKRELLMGIFE-MGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLE 63

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
                     +     A+V+VPT EL L V +I  ++             GG N   +  
Sbjct: 64  R------LDLKKDNIQAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIM 117

Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS 216
           RL   + +++ATPG +LD           +++ I+ DEAD++L   F + +E+I+  L  
Sbjct: 118 RLDDTVHVVIATPGRILDL-IKKGVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPK 176

Query: 217 RNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                           RQ LL SAT    V       LE P  I
Sbjct: 177 ---------------NRQILLYSATFPLSVQKFMNSHLEKPYEI 205

>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 =  121 bits (304), Expect = 8e-34
 Identities = 63/224 (28%), Positives = 96/224 (42%), Gaps = 25/224 (11%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F  + LD  L   +    GFE P+ +Q +AI  I+ G DVL  A +GTGKT  +    + 
Sbjct: 12  FDDMELDENLLRGVFG-YGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQ 70

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            + +            AL+L PT EL L + +++  L       V   +   G    E A
Sbjct: 71  RIDT------SVKAPQALMLAPTRELALQIQKVVMALAFHMDIKVHACIG--GTSFVEDA 122

Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS 216
              +   I+V TPG + D+++          +  I DEAD +L  GF ++I +I  +L  
Sbjct: 123 EGLRDAQIVVGTPGRVFDNIQRRRFRTDKI-KMFILDEADEMLSSGFKEQIYQIFTLLPP 181

Query: 217 RNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                            Q +LLSAT+   V  +T   +  PV I
Sbjct: 182 ---------------TTQVVLLSATMPNDVLEVTTKFMRNPVRI 210

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 207

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  118 bits (296), Expect = 7e-33
 Identities = 50/225 (22%), Positives = 101/225 (44%), Gaps = 23/225 (10%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F    L   L   + +  GFE P++VQ + IP  + G DVL  A +G GKT  ++   + 
Sbjct: 3   FRDFLLKPELLRAIVD-CGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQ 61

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            L+  + ++        LV+  T EL   + +  ++       +      GG +  K++ 
Sbjct: 62  QLEPVTGQV------SVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEE 115

Query: 157 RLRK-GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILG 215
            L+K    I+V TPG +L   ++ S  L     +I+ +    + +L   ++++EI  +  
Sbjct: 116 VLKKNCPHIVVGTPGRILALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTP 175

Query: 216 SRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                           ++Q ++ SATL++++  + +  ++ P+ I
Sbjct: 176 H---------------EKQVMMFSATLSKEIRPVCRKFMQDPMEI 205

>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 =  109 bits (273), Expect = 2e-29
 Identities = 67/228 (29%), Positives = 94/228 (41%), Gaps = 24/228 (10%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F    L   L   + E  GFE P+ +Q +AIPV ++GRD+L  A  GTGKT A++ P + 
Sbjct: 3   FEDFYLKRELLMGIFE-AGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLE 61

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            ++    +I           +  +    L    + + L +   I      GG N   +  
Sbjct: 62  KVKPKLNKIQALI-------MVPTRELALQTSQVVRTLGKHCGISCMVTTGGTNLRDDIL 114

Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS 216
           RL + + ILV TPG +LD      + L       I DEAD++L   F   IE+IL  L  
Sbjct: 115 RLNETVHILVGTPGRVLDLASRKVADLSDC-SLFIMDEADKMLSRDFKTIIEQILSFLPP 173

Query: 217 RNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLDE 264
                            Q+LL SAT    V       L  P  I L E
Sbjct: 174 ---------------THQSLLFSATFPLTVKEFMVKHLHKPYEINLME 206

>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 =  103 bits (258), Expect = 2e-27
 Identities = 43/226 (19%), Positives = 69/226 (30%), Gaps = 31/226 (13%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
              L L+S     L+E  G++     Q + I  +LSGRD LV   TG GK++ Y  P + 
Sbjct: 4   AEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALL 63

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
                            +V+ P   L     + LQ        +                
Sbjct: 64  LNG------------LTVVVSPLISLMKDQVDQLQANGVAAACL-NSTQTREQQLEVMTG 110

Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELG--FGKEIEEILDIL 214
                I +L   P  L+            N   +  DEA  I + G  F  E   +  + 
Sbjct: 111 CRTGQIRLLYIAPERLMLDNFLEHLAHW-NPVLLAVDEAHCISQWGHDFRPEYAALGQLR 169

Query: 215 GSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNH--LTKISLETPV 258
                                + L+AT ++      +  + L  P+
Sbjct: 170 QRFP-------------TLPFMALTATADDTTRQDIVRLLGLNDPL 202

>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 = 99.0 bits (245), Expect = 2e-25
 Identities = 50/224 (22%), Positives = 94/224 (41%), Gaps = 20/224 (8%)

Query: 37  FSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIIN 96
           F+       + + ++  L F  PT++Q + IP  L G  ++  + TGTGKT AY   ++ 
Sbjct: 3   FTRFPFQPFIIEAIKT-LRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAY---LLP 58

Query: 97  HLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKA 156
            ++   P                +         + K   + R IV   ++GG ++ K   
Sbjct: 59  IMEKIKPERAEVQAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALE 118

Query: 157 RLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGS 216
           +L     I++ TPG + D ++  +         ++ DEAD +L++GF  ++++I   +  
Sbjct: 119 KLNVQPHIVIGTPGRINDFIREQALD-VHTAHILVVDEADLMLDMGFITDVDQIAARMPK 177

Query: 217 RNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI 260
                            Q L+ SAT+ EK+    K  +E P  +
Sbjct: 178 ---------------DLQMLVFSATIPEKLKPFLKKYMENPTFV 206

>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 = 98.4 bits (244), Expect = 5e-25
 Identities = 37/199 (18%), Positives = 68/199 (34%), Gaps = 23/199 (11%)

Query: 53  RLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF 112
           R     P  +Q      IL        A TG GKT   LA  +                 
Sbjct: 38  RKCVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKG---------KR 88

Query: 113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKAR-----LRKGISILVA 167
             V+ PTS L +   E ++K   +        +     R  ++ +       +   I++ 
Sbjct: 89  CYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVIT 148

Query: 168 TPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNE 227
           T   L  H +        +  +I  D+ D IL+    K ++++L +LG      +   + 
Sbjct: 149 TTQFLSKHYRELG-----HFDFIFVDDVDAILK--ASKNVDKLLHLLGFH--YDLKTKSW 199

Query: 228 VSNVKRQNLLLSATLNEKV 246
           V   +   ++ +AT  +  
Sbjct: 200 VGEARGCLMVSTATAKKGK 218

>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 = 82.3 bits (202), Expect = 2e-19
 Identities = 37/202 (18%), Positives = 72/202 (35%), Gaps = 28/202 (13%)

Query: 41  GLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQS 100
            + S     L+E  G E     QA+A+  + SG+++L+   T  GKT+     ++     
Sbjct: 9   SISSYAVGILKEE-GIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK 67

Query: 101 YSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRK 160
               +          +VP   L    YE  +K       I    +  G   S+++     
Sbjct: 68  GGKSL---------YVVPLRALAGEKYESFKKWEKIGLRI---GISTGDYESRDEH--LG 113

Query: 161 GISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIA 220
              I+V T       +++ +S++      ++ DE   +     G  +E ++  +      
Sbjct: 114 DCDIIVTTSEKADSLIRNRASWIKAV-SCLVVDEIHLLDSEKRGATLEILVTKMRRM--- 169

Query: 221 SIGEGNEVSNVKRQNLLLSATL 242
                    N   + + LSAT 
Sbjct: 170 ---------NKALRVIGLSATA 182

>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 = 66.5 bits (161), Expect = 4e-13
 Identities = 28/182 (15%), Positives = 45/182 (24%), Gaps = 37/182 (20%)

Query: 69  VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE 128
           +    R  +++   G GKT  YL  I+        R         L+L PT  +   + E
Sbjct: 5   IFRKKRLTIMDLHPGAGKTKRYLPAIVREAIKRGLRT--------LILAPTRVVAAEMEE 56

Query: 129 ILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLR 188
            L+ L  R++         G                 +         L         N  
Sbjct: 57  ALRGLPIRYQTPAIRAEHTGREIVD------------LMCHATFTMRLLSPIRV--PNYN 102

Query: 189 WIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNH 248
            II DEA              I   +                     + ++AT     + 
Sbjct: 103 LIIMDEAHFTDPASIA-ARGYISTRVEMGE--------------AAGIFMTATPPGSRDP 147

Query: 249 LT 250
             
Sbjct: 148 FP 149

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 63.3 bits (152), Expect = 1e-12
 Identities = 36/216 (16%), Positives = 67/216 (31%), Gaps = 30/216 (13%)

Query: 59  PTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVP 118
           P   Q           + L+   TG GKT+  +      L           G   L+L P
Sbjct: 10  PRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRL--------TKYGGKVLMLAP 60

Query: 119 TSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKH 178
           T  L L   E  ++L +     +           + KA       ++VATP  + + L  
Sbjct: 61  TKPLVLQHAESFRRLFNLPPEKIVALTGEKSPEERSKA--WARAKVIVATPQTIENDLLA 118

Query: 179 TSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLL 238
                  ++  I+FDEA R +       I                            + L
Sbjct: 119 G-RISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKN---------------PLVIGL 162

Query: 239 SATLNEKVNHLTKISLETPVLIGLDEKKFPEDKSNV 274
           +A+       + ++ +    +  ++ +   E+  +V
Sbjct: 163 TASPGSTPEKIMEV-INNLGIEHIEYR--SENSPDV 195

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]} 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: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

 Score = 39.1 bits (90), Expect = 3e-04
 Identities = 30/180 (16%), Positives = 49/180 (27%), Gaps = 49/180 (27%)

Query: 63  QAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSEL 122
           Q +A+   L  +   +   TG+GKT   +A I                T  L++VPT  L
Sbjct: 75  QEKALERWLVDKRGCIVLPTGSGKTHVAMAAINEL------------STPTLIVVPTLAL 122

Query: 123 CLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSF 182
                E L      +     G +      +                     D     +  
Sbjct: 123 AEQWKERLGIFGEEYVGEFSGRIKELKPLTVST-----------------YDSAYVNAEK 165

Query: 183 LHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATL 242
           L      +IFDE   +      +   +I  +  +                   L L+AT 
Sbjct: 166 LGNRFMLLIFDEVHHLP----AESYVQIAQMSIAPFR----------------LGLTATF 205

>d1yksa1 c.37.1.14 (A:185-324) YFV helicase domain {Yellow fever virus [TaxId: 11089]} Length = 140

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

 Score = 37.7 bits (86), Expect = 4e-04
 Identities = 27/173 (15%), Positives = 44/173 (25%), Gaps = 37/173 (21%)

Query: 69  VILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE 128
           ++  G   +++   G GKT  +L  I+                  LVL PT  +   + E
Sbjct: 3   MLKKGMTTVLDFHPGAGKTRRFLPQILAECARR--------RLRTLVLAPTRVVLSEMKE 54

Query: 129 ILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLR 188
               L  +F          G                       L   +         N  
Sbjct: 55  AFHGLDVKFHTQAFSAHGSGREVIDAM------------CHATLTYRMLE--PTRVVNWE 100

Query: 189 WIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSAT 241
            II DEA  +                   N ++              +L++AT
Sbjct: 101 VIIMDEAHFL--DPASIAARGWAAHRARANESAT-------------ILMTAT 138

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	316
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	100.0
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	100.0
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	100.0
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	100.0
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	100.0
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	100.0
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.97
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.96
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.96
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.93
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.83
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.81
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.8
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.75
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.74
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	99.74
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	99.63
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	99.19
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	99.11
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	99.06
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	99.03
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	98.4
d1uaaa1	306	DEXX box DNA helicase {Escherichia coli, RepD [Tax	97.87
d1pjra1	318	DEXX box DNA helicase {Bacillus stearothermophilus	97.56
g1qhh.1	623	DEXX box DNA helicase {Bacillus stearothermophilus	97.15
d1a5ta2	207	delta prime subunit of DNA polymerase III, N-domai	96.9
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	96.8
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	96.65
d1sxje2	252	Replication factor C5 {Baker's yeast (Saccharomyce	96.61
d1sxjb2	224	Replication factor C4 {Baker's yeast (Saccharomyce	96.58
d1sxjd2	237	Replication factor C2 {Baker's yeast (Saccharomyce	96.55
d1ls1a2	207	GTPase domain of the signal sequence recognition p	96.47
d1sxjc2	227	Replication factor C3 {Baker's yeast (Saccharomyce	96.4
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	96.37
d1t5la1	413	Nucleotide excision repair enzyme UvrB {Bacillus c	96.27
d1iqpa2	231	Replication factor C {Archaeon Pyrococcus furiosus	95.91
d1ixza_	247	AAA domain of cell division protein FtsH {Thermus	95.69
d1d2na_	246	Hexamerization domain of N-ethylmalemide-sensitive	95.64
d2qy9a2	211	GTPase domain of the signal recognition particle r	95.53
d1vmaa2	213	GTPase domain of the signal recognition particle r	95.48
d1okkd2	207	GTPase domain of the signal recognition particle r	95.3
d1j8yf2	211	GTPase domain of the signal sequence recognition p	94.46
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	94.19
d2b8ta1	139	Thymidine kinase, TK1, N-terminal domain {Ureaplas	93.71
d1g6oa_	323	Hexameric traffic ATPase, HP0525 {Helicobacter pyl	93.68
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	93.53
d1c4oa1	408	Nucleotide excision repair enzyme UvrB {Thermus th	93.37
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	93.16
d1w36b1	485	Exodeoxyribonuclease V beta chain (RecB), N-termin	92.89
d1w5sa2	287	CDC6-like protein APE0152, N-terminal domain {Aero	92.4
d1um8a_	364	ClpX {Helicobacter pylori [TaxId: 210]}	92.39
d1tf7a2	242	Circadian clock protein KaiC {Synechococcus sp. st	92.11
d1e9ra_	433	Bacterial conjugative coupling protein TrwB {Esche	91.78
d2i3ba1	189	Cancer-related NTPase, C1orf57 {Human (Homo sapien	91.63
d1in4a2	238	Holliday junction helicase RuvB {Thermotoga mariti	91.25
d1g41a_	443	HslU {Haemophilus influenzae [TaxId: 727]}	91.21
d1ofha_	309	HslU {Haemophilus influenzae [TaxId: 727]}	91.18
d1p9ra_	401	Extracellular secretion NTPase EpsE {Vibrio choler	91.13
d1xbta1	133	Thymidine kinase, TK1, N-terminal domain {Human (H	91.03
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	90.72
d1xx6a1	141	Thymidine kinase, TK1, N-terminal domain {Clostrid	90.15
d1qvra2	387	ClpB, AAA+ modules {Thermus thermophilus [TaxId: 2	89.45
d1mo6a1	269	RecA protein, ATPase-domain {Mycobacterium tubercu	88.89
d1jbka_	195	ClpB, AAA+ modules {Escherichia coli [TaxId: 562]}	88.69
d1lv7a_	256	AAA domain of cell division protein FtsH {Escheric	88.25
d1bg2a_	323	Kinesin {Human (Homo sapiens) [TaxId: 9606]}	88.1
d1kaga_	169	Shikimate kinase (AroK) {Escherichia coli [TaxId:	87.9
d1sxja2	253	Replication factor C1 {Baker's yeast (Saccharomyce	87.8
d1fnna2	276	CDC6, N-domain {Archaeon Pyrobaculum aerophilum [T	86.97
d1ixsb2	239	Holliday junction helicase RuvB {Thermus thermophi	86.48
d1y63a_	174	Probable kinase LmjF30.1890 {Leishmania major [Tax	85.72
d1v8ka_	362	Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090	85.72
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	85.67
d1zp6a1	176	Hypothetical protein Atu3015 {Agrobacterium tumefa	85.5
d1goja_	354	Kinesin {Neurospora crassa [TaxId: 5141]}	85.47
d1ly1a_	152	Polynucleotide kinase, kinase domain {Bacteriophag	85.39
d1r6bx2	268	ClpA, an Hsp100 chaperone, AAA+ modules {Escherich	85.32
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	85.08
d1sdma_	364	Kinesin heavy chain-like protein {Potato (Solanum	85.06
d2zfia1	349	Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090	84.87
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	84.65
d1x88a1	345	Kinesin {Human (Homo sapiens), mitotic kinesin eg5	84.4
d2ncda_	368	Kinesin motor Ncd (non-claret disjunctional) {Frui	84.34
d1lw7a2	192	Transcriptional regulator NadR, ribosylnicotinamid	84.26
d2bdta1	176	Hypothetical protein BH3686 {Bacillus halodurans [	83.84
d1gvnb_	273	Plasmid maintenance system epsilon/zeta, toxin zet	83.73
d1rkba_	173	Adenylate kinase {Human (Homo sapiens), isoenzyme	83.18
d1f9va_	342	Kinesin motor Ncd (non-claret disjunctional) {Bake	82.59
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	82.46
d1cr2a_	277	Gene 4 protein (g4p, DNA primase), helicase domain	82.43
d1nlfa_	274	Hexameric replicative helicase repA {Escherichia c	81.86
d1tf7a1	242	Circadian clock protein KaiC {Synechococcus sp. st	81.37
d1viaa_	161	Shikimate kinase (AroK) {Campylobacter jejuni [Tax	80.99
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	80.51
d1qhxa_	178	Chloramphenicol phosphotransferase {Streptomyces v	80.1

>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=100.00  E-value=5.5e-49  Score=334.47  Aligned_cols=211  Identities=29%  Similarity=0.485  Sum_probs=192.1

Q ss_pred             ccccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCC
Q 043110           29 KEIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRS  108 (316)
Q Consensus        29 ~~~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~  108 (316)
                      ++.....+|+++||+++++++| +++||..|||+|+++||.+++|+|++++||||||||+||++|+++.+...      .
T Consensus        11 ~~~~~~~sF~~l~L~~~l~~~L-~~~g~~~pt~IQ~~aIp~il~g~dvi~~a~TGSGKTlayllPil~~l~~~------~   83 (222)
T d2j0sa1          11 EEVDVTPTFDTMGLREDLLRGI-YAYGFEKPSAIQQRAIKQIIKGRDVIAQSQSGTGKTATFSISVLQCLDIQ------V   83 (222)
T ss_dssp             TTCCCCCSGGGGCCCHHHHHHH-HHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHTCCTT------S
T ss_pred             CCCCCCCCHHHCCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHHCCCCeEEEcCcchhhhhhhccccccccccc------c
Confidence            3455667899999999999999 66799999999999999999999999999999999999999999988653      2


Q ss_pred             CCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCcee
Q 043110          109 SGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLR  188 (316)
Q Consensus       109 ~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~  188 (316)
                      ..++++|++||+|||.|+++.++.++.... ..+...+||.....+...+..+++|+|+|||++.+++.. ....+++++
T Consensus        84 ~~~~~lil~PtreLa~Qi~~~~~~l~~~~~-i~~~~~~g~~~~~~~~~~l~~~~~Ilv~TPgrl~~~~~~-~~~~~~~l~  161 (222)
T d2j0sa1          84 RETQALILAPTRELAVQIQKGLLALGDYMN-VQCHACIGGTNVGEDIRKLDYGQHVVAGTPGRVFDMIRR-RSLRTRAIK  161 (222)
T ss_dssp             CSCCEEEECSSHHHHHHHHHHHHHHTTTTT-CCEEEECTTSCHHHHHHHHHHCCSEEEECHHHHHHHHHT-TSSCCTTCC
T ss_pred             cCceeEEecchHHHHHHHHHHHHHHhCccc-eeEEEEeecccchhhHHHhccCCeEEeCCCCcHHhcccc-cccccccce
Confidence            467799999999999999999999987644 677788899999888888999999999999999999877 566778999


Q ss_pred             EEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcC
Q 043110          189 WIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD  263 (316)
Q Consensus       189 ~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~  263 (316)
                      ++|+||||+|++.+|.+++..|++.+++               .+|+++||||+|+++.++++.+|++|+.|.+.
T Consensus       162 ~lVlDEaD~ll~~~f~~~i~~I~~~l~~---------------~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V~  221 (222)
T d2j0sa1         162 MLVLDEADEMLNKGFKEQIYDVYRYLPP---------------ATQVVLISATLPHEILEMTNKFMTDPIRILVK  221 (222)
T ss_dssp             EEEEETHHHHTSTTTHHHHHHHHTTSCT---------------TCEEEEEESCCCHHHHTTGGGTCSSCEEECCC
T ss_pred             eeeecchhHhhhcCcHHHHHHHHHhCCC---------------CCEEEEEEEeCCHHHHHHHHHHCCCCEEEEEe
Confidence            9999999999999999999999999987               89999999999999999999999999998764

>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=100.00  E-value=4.2e-48  Score=326.20  Aligned_cols=205  Identities=34%  Similarity=0.500  Sum_probs=188.8

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      .++|++++|+++++++| .++||.+|||+|++|||.+++|+|++++||||||||++|++|+++++...      ..++++
T Consensus         2 ~~~F~~l~L~~~l~~~l-~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllP~l~~~~~~------~~~~~~   74 (206)
T d1veca_           2 GNEFEDYCLKRELLMGI-FEMGWEKPSPIQEESIPIALSGRDILARAKNGTGKSGAYLIPLLERLDLK------KDNIQA   74 (206)
T ss_dssp             CSSGGGSCCCHHHHHHH-HTTTCCSCCHHHHHHHHHHHTTCCEEEECCSSSTTHHHHHHHHHHHCCTT------SCSCCE
T ss_pred             CCChhccCcCHHHHHHH-HHCCCCCCCHHHHHHHHHHHcCCCEEeeccCccccccccccchhhccccc------ccCcce
Confidence            46899999999999999 77899999999999999999999999999999999999999999987642      346789


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      ||++||++|+.|+++.+..+.............|+.....+...+..+++|+|+||+++.+++.. +...+++++++|+|
T Consensus        75 lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~ivv~TPgrl~~~~~~-~~~~~~~l~~lVlD  153 (206)
T d1veca_          75 MVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVVIATPGRILDLIKK-GVAKVDHVQMIVLD  153 (206)
T ss_dssp             EEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHT-TCSCCTTCCEEEEE
T ss_pred             EEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHHHhccCeEEeCCccccccccc-hhccccccceEEEe
Confidence            99999999999999999998877666777788888888888888889999999999999999886 55677899999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEE
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIG  261 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~  261 (316)
                      |||.|++.+|..++..|++.+++               ++|+++||||+|+++.++++.+|++|+.|.
T Consensus       154 EaD~ll~~~f~~~i~~I~~~~~~---------------~~Q~~l~SAT~~~~v~~l~~~~l~~P~~I~  206 (206)
T d1veca_         154 EADKLLSQDFVQIMEDIILTLPK---------------NRQILLYSATFPLSVQKFMNSHLEKPYEIN  206 (206)
T ss_dssp             THHHHTSTTTHHHHHHHHHHSCT---------------TCEEEEEESCCCHHHHHHHHHHCSSCEEEC
T ss_pred             ccccccccchHHHHHHHHHhCCC---------------CCEEEEEEecCCHHHHHHHHHHCCCCEEEC
Confidence            99999999999999999999988               899999999999999999999999999873

>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=100.00  E-value=5.4e-47  Score=319.61  Aligned_cols=205  Identities=25%  Similarity=0.443  Sum_probs=185.5

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      ..|++++|+++++++| .++||.+|||+|+++||.+++|+|++++||||||||++|++|+++.+...      ..+++++
T Consensus         1 s~F~dl~L~~~l~~~l-~~~g~~~pt~iQ~~aip~il~g~dvl~~A~TGsGKTla~~lp~l~~~~~~------~~~~~~l   73 (207)
T d1t6na_           1 SGFRDFLLKPELLRAI-VDCGFEHPSEVQHECIPQAILGMDVLCQAKSGMGKTAVFVLATLQQLEPV------TGQVSVL   73 (207)
T ss_dssp             CCSTTSCCCHHHHHHH-HHTTCCCCCHHHHHHHHHHHTTCCEEEECCTTSCHHHHHHHHHHHHCCCC------TTCCCEE
T ss_pred             CCccccCcCHHHHHHH-HHCCCCCCCHHHHHHHHHHHcCCCeEEEeccccccccccccceeeeeccc------CCCceEE
Confidence            3699999999999999 66899999999999999999999999999999999999999999987542      3467899


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHH-hcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARL-RKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l-~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      |++||++|+.|+++.++.++.........+..|+.....+...+ ..+++|+|+||+++.+++.+ +.+.+++++++|+|
T Consensus        74 il~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~-~~~~l~~l~~lVlD  152 (207)
T d1t6na_          74 VMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN-KSLNLKHIKHFILD  152 (207)
T ss_dssp             EECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEE
T ss_pred             EEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccC-Cceeccccceeehh
Confidence            99999999999999999999887777778888888887777666 45789999999999999987 56678999999999


Q ss_pred             cchhhhcC-CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEc
Q 043110          194 EADRILEL-GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGL  262 (316)
Q Consensus       194 Ead~l~~~-~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~  262 (316)
                      |||.|++. +|...+..|++.+++               .+|+++||||+|+++.++++.+|++|+.|.+
T Consensus       153 EaD~ll~~~~~~~~i~~I~~~~~~---------------~~Q~il~SAT~~~~v~~l~~~~l~~P~~I~V  207 (207)
T d1t6na_         153 ECDKMLEQLDMRRDVQEIFRMTPH---------------EKQVMMFSATLSKEIRPVCRKFMQDPMEIFV  207 (207)
T ss_dssp             SHHHHHSSHHHHHHHHHHHHTSCS---------------SSEEEEEESCCCTTTHHHHHTTCSSCEEEEC
T ss_pred             hhhhhhhcCCcHHHHHHHHHhCCC---------------CCEEEEEeeeCCHHHHHHHHHHCCCCEEEeC
Confidence            99999985 899999999999887               8999999999999999999999999998864

>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=100.00  E-value=2.6e-46  Score=317.49  Aligned_cols=205  Identities=31%  Similarity=0.452  Sum_probs=178.8

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      .+|++++|++.++++| +++||.+|||+|++|||.++.|+|++++||||||||++|++|+++.+..      ...++++|
T Consensus        12 ~sF~~l~L~~~l~~~L-~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKTlayllp~l~~i~~------~~~~~~al   84 (218)
T d2g9na1          12 DSFDDMNLSESLLRGI-YAYGFEKPSAIQQRAILPCIKGYDVIAQAQSGTGKTATFAISILQQIEL------DLKATQAL   84 (218)
T ss_dssp             CCGGGSCCCHHHHHHH-HHHTCCSCCHHHHHHHHHHHHTCCEEEECCTTSSHHHHHHHHHHHHCCT------TCCSCCEE
T ss_pred             CCHHHCCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHHcCCCEEEEcccchhhhhhhhhhhhheecc------cccCccEE
Confidence            5899999999999999 6789999999999999999999999999999999999999999999854      23578899


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH-HHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE-KARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      |++||++||.|+++.+..+...... ......++...... .......++|+|+||+++.+++.+ ....+++++++|+|
T Consensus        85 il~Pt~eL~~Q~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~-~~~~~~~l~~lVlD  162 (218)
T d2g9na1          85 VLAPTRELAQQIQKVVMALGDYMGA-SCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNR-RYLSPKYIKMFVLD  162 (218)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTTTTC-CEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHT-TSSCSTTCCEEEEE
T ss_pred             EEcccchhhhhHHHHHhhhccccce-eEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhc-CCcccccceEEEee
Confidence            9999999999999999999887654 44444444433322 223345689999999999999986 55677899999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcC
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD  263 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~  263 (316)
                      |||+|++.+|.+.+..|++.+++               ++|++++|||+|+++.++++.++++|+.|.+.
T Consensus       163 EaD~ll~~~f~~~~~~Il~~~~~---------------~~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v~  217 (218)
T d2g9na1         163 EADEMLSRGFKDQIYDIFQKLNS---------------NTQVVLLSATMPSDVLEVTKKFMRDPIRILVK  217 (218)
T ss_dssp             SHHHHHHTTCHHHHHHHHHHSCT---------------TCEEEEEESCCCHHHHHHHHHHCSSCEEEECC
T ss_pred             ecchhhcCchHHHHHHHHHhCCC---------------CCeEEEEEecCCHHHHHHHHHHCCCCEEEEEe
Confidence            99999999999999999999987               89999999999999999999999999999764

>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=100.00  E-value=2.7e-45  Score=310.02  Aligned_cols=204  Identities=31%  Similarity=0.506  Sum_probs=174.7

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      ..+|++++|+++++++| +++||.+|||+|+++||.++.|+|++++||||||||++|++|+++.+..      ...++++
T Consensus         9 ~~sF~~l~l~~~l~~~L-~~~g~~~pt~iQ~~aip~il~g~dvl~~a~TGsGKT~a~~lp~i~~l~~------~~~~~~~   81 (212)
T d1qdea_           9 VYKFDDMELDENLLRGV-FGYGFEEPSAIQQRAIMPIIEGHDVLAQAQSGTGKTGTFSIAALQRIDT------SVKAPQA   81 (212)
T ss_dssp             CCCGGGGTCCHHHHHHH-HHHTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHCCT------TCCSCCE
T ss_pred             ccChhhCCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHHcCCCEEeecccccchhhhhHhhhHhhhhc------cCCCcce
Confidence            46799999999999999 6689999999999999999999999999999999999999999999854      2347889


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEe
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFD  193 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViD  193 (316)
                      +|++||++|+.|++..+..+..... .......++.....+...+ ++++|+|+||+++..++.. +...+++++++|+|
T Consensus        82 lil~pt~el~~q~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-~~~~IvI~TP~~l~~~~~~-~~~~l~~l~~lVlD  158 (212)
T d1qdea_          82 LMLAPTRELALQIQKVVMALAFHMD-IKVHACIGGTSFVEDAEGL-RDAQIVVGTPGRVFDNIQR-RRFRTDKIKMFILD  158 (212)
T ss_dssp             EEECSSHHHHHHHHHHHHHHTTTSC-CCEEEECC----------C-TTCSEEEECHHHHHHHHHT-TSSCCTTCCEEEEE
T ss_pred             EEEcccHHHhhhhhhhhcccccccc-cceeeEeeccchhHHHHHh-cCCcEEEECCCcccccccc-CceecCcceEEeeh
Confidence            9999999999999999988876544 4555555665555554443 4689999999999999887 56678899999999


Q ss_pred             cchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEc
Q 043110          194 EADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGL  262 (316)
Q Consensus       194 Ead~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~  262 (316)
                      |||.|++.+|.+++..|++.+++               .+|+++||||+|+++.++++.+|++|+.|.+
T Consensus       159 Ead~lld~~f~~~v~~I~~~~~~---------------~~Q~vl~SAT~~~~v~~l~~~~l~~Pv~i~v  212 (212)
T d1qdea_         159 EADEMLSSGFKEQIYQIFTLLPP---------------TTQVVLLSATMPNDVLEVTTKFMRNPVRILV  212 (212)
T ss_dssp             THHHHHHTTCHHHHHHHHHHSCT---------------TCEEEEEESSCCHHHHHHHHHHCSSCEEEC-
T ss_pred             hhhhhcccchHHHHHHHHHhCCC---------------CCeEEEEEeeCCHHHHHHHHHHCCCCEEEeC
Confidence            99999999999999999999987               8999999999999999999999999998864

>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=100.00  E-value=2.7e-45  Score=315.44  Aligned_cols=217  Identities=32%  Similarity=0.518  Sum_probs=190.1

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCC---CCCCC
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPR---IDRSS  109 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~---~~~~~  109 (316)
                      .-.+|++++|+++++++| .++||.+|+|+|++|||.+++|+|++++||||||||++|++|+++++......   .....
T Consensus        19 ~~~~F~~l~l~~~l~~~L-~~~g~~~pt~iQ~~~ip~il~g~dvvi~a~TGsGKTlayllp~l~~l~~~~~~~~~~~~~~   97 (238)
T d1wrba1          19 VIENFDELKLDPTIRNNI-LLASYQRPTPIQKNAIPAILEHRDIMACAQTGSGKTAAFLIPIINHLVCQDLNQQRYSKTA   97 (238)
T ss_dssp             CCCSSGGGSCCCSTTTTT-TTTTCCSCCHHHHHHHHHHHTTCCEEEECCTTSSHHHHHHHHHHHHHHTTCC------CCB
T ss_pred             ccCCHHHCCCCHHHHHHH-HHCCCCCCCHHHHHHhhhhhCCCCEEEECCCCCCcceeeHHHHHHHHHhcccccccccCCC
Confidence            346899999999999999 67899999999999999999999999999999999999999999998765432   22345


Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeE
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRW  189 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~  189 (316)
                      ++++||++||++||.|+++.+..++...+ .......|+.....+.+....+++|+||||++|.+++.. ....+.++++
T Consensus        98 ~~~alil~pt~el~~q~~~~~~~~~~~~~-~~~~~~~g~~~~~~~~~~~~~~~~ivV~TP~~l~~~~~~-~~~~l~~v~~  175 (238)
T d1wrba1          98 YPKCLILAPTRELAIQILSESQKFSLNTP-LRSCVVYGGADTHSQIREVQMGCHLLVATPGRLVDFIEK-NKISLEFCKY  175 (238)
T ss_dssp             CCSEEEECSSHHHHHHHHHHHHHHHTTSS-CCEEEECSSSCSHHHHHHHSSCCSEEEECHHHHHHHHHT-TSBCCTTCCE
T ss_pred             CceEEEeccchhhhcchheeeeecccCCC-cEEEEEeccchhhHHHhhcccCCceeecCHHHHHhHHcc-Cceeccccce
Confidence            78899999999999999999999887654 666777888888888888889999999999999999987 4566789999


Q ss_pred             EEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcC
Q 043110          190 IIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD  263 (316)
Q Consensus       190 lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~  263 (316)
                      +|+||||.|++.+|.+++..|++.+...           ...++|++++|||+|+++.++++.+|++|++|.++
T Consensus       176 lViDEaD~ll~~~f~~~i~~Il~~~~~~-----------~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~vg  238 (238)
T d1wrba1         176 IVLDEADRMLDMGFEPQIRKIIEESNMP-----------SGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG  238 (238)
T ss_dssp             EEEETHHHHHHTTCHHHHHHHHHSSCCC-----------CGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC
T ss_pred             eeeehhhhhhhhccHHHHHHHHHHhcCC-----------CCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEeC
Confidence            9999999999999999999999876431           22368999999999999999999999999998763

>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=100.00  E-value=5.3e-44  Score=301.59  Aligned_cols=204  Identities=30%  Similarity=0.542  Sum_probs=182.4

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCC-cEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGR-DVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~-d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ..+|++++|+++++++| .++||.+|+|+|+++||.+++|+ |++++||||+|||++|++|+++....       ..+++
T Consensus         3 ~msf~~l~l~~~l~~~l-~~~g~~~pt~iQ~~~ip~~l~g~~d~iv~a~TGsGKT~~~~l~~~~~~~~-------~~~~~   74 (208)
T d1hv8a1           3 YMNFNELNLSDNILNAI-RNKGFEKPTDIQMKVIPLFLNDEYNIVAQARTGSGKTASFAIPLIELVNE-------NNGIE   74 (208)
T ss_dssp             CCCGGGSSCCHHHHHHH-HHHTCCSCCHHHHHHHHHHHHTCSEEEEECCSSSSHHHHHHHHHHHHSCS-------SSSCC
T ss_pred             ccCHHHcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHHcCCCCeeeechhcccccceeeccccccccc-------ccCcc
Confidence            46899999999999999 66899999999999999999885 99999999999999999999987543       45788


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEE
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIF  192 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lVi  192 (316)
                      +||++||++||.|+++.+..+..... ..+....|+.....+...+ ++++|+||||++|.+++.+ +.+.+++++++|+
T Consensus        75 ~lil~pt~~l~~q~~~~~~~~~~~~~-~~v~~~~g~~~~~~~~~~l-~~~~IlV~TP~~l~~~l~~-~~~~~~~l~~lVi  151 (208)
T d1hv8a1          75 AIILTPTRELAIQVADEIESLKGNKN-LKIAKIYGGKAIYPQIKAL-KNANIVVGTPGRILDHINR-GTLNLKNVKYFIL  151 (208)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHCSSC-CCEEEECTTSCHHHHHHHH-HTCSEEEECHHHHHHHHHT-TCSCTTSCCEEEE
T ss_pred             eEEEeeccccchhhhhhhhhhcccCC-eEEEEeeCCCChHHHHHhc-CCCCEEEEChHHHHHHHHc-CCCCcccCcEEEE
Confidence            99999999999999999999987654 5566777777777776655 4789999999999999976 5567899999999


Q ss_pred             ecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcC
Q 043110          193 DEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD  263 (316)
Q Consensus       193 DEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~  263 (316)
                      ||||+|++.++..++..|++.+++               ++|++++|||+|+++.++++.+|+||..|.+.
T Consensus       152 DEad~l~~~~~~~~i~~I~~~~~~---------------~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~~~  207 (208)
T d1hv8a1         152 DEADEMLNMGFIKDVEKILNACNK---------------DKRILLFSATMPREILNLAKKYMGDYSFIKAK  207 (208)
T ss_dssp             ETHHHHHTTTTHHHHHHHHHTSCS---------------SCEEEEECSSCCHHHHHHHHHHCCSEEEEECC
T ss_pred             EChHHhhcCCChHHHHHHHHhCCC---------------CCeEEEEEccCCHHHHHHHHHHCCCCeEEEEE
Confidence            999999999999999999999887               89999999999999999999999999999764

>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=100.00  E-value=4.6e-44  Score=301.62  Aligned_cols=205  Identities=34%  Similarity=0.487  Sum_probs=187.7

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      .+|++++|++.++++| +++||.+|||+|+++||.+++|+|++++||||||||++|++|+++.+...      ..+.+++
T Consensus         1 ~sF~~l~L~~~l~~~L-~~~g~~~pt~iQ~~aip~il~g~dvi~~a~tGsGKTlay~lp~i~~~~~~------~~~~~~~   73 (206)
T d1s2ma1           1 NTFEDFYLKRELLMGI-FEAGFEKPSPIQEEAIPVAITGRDILARAKNGTGKTAAFVIPTLEKVKPK------LNKIQAL   73 (206)
T ss_dssp             CCGGGGCCCHHHHHHH-HHTTCCSCCHHHHHHHHHHHHTCCEEEECCTTSCHHHHHHHHHHHHCCTT------SCSCCEE
T ss_pred             CChHHcCCCHHHHHHH-HHCCCCCCCHHHHHHHHHHHcCCCEEEecCCcchhhhhhccccccccccc------cccccce
Confidence            4799999999999999 67899999999999999999999999999999999999999999987653      2356799


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEec
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDE  194 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDE  194 (316)
                      +++|+++++.|....+..+.... ...+....|+.....+...+..+++|+|+||++|.+++.. ....+.+++++|+||
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l~~~~~Ili~TP~~l~~~l~~-~~~~l~~l~~lV~DE  151 (206)
T d1s2ma1          74 IMVPTRELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRLNETVHILVGTPGRVLDLASR-KVADLSDCSLFIMDE  151 (206)
T ss_dssp             EECSSHHHHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHTTSCCSEEEECHHHHHHHHHT-TCSCCTTCCEEEEES
T ss_pred             eeccchhhhhhhhhhhhhccccc-CeeEEeecCccchhhHHHHhcccceEEEECCccccccccc-ceeecccceEEEeec
Confidence            99999999999999988887654 4777888889988888888889999999999999999987 566788999999999


Q ss_pred             chhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEcC
Q 043110          195 ADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGLD  263 (316)
Q Consensus       195 ad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~~  263 (316)
                      ||.|++.+|.+++..|++.+++               .+|+++||||+|+++.++++.+|++|+.|.+.
T Consensus       152 aD~l~~~~f~~~v~~I~~~l~~---------------~~Q~il~SATl~~~v~~~~~~~l~~P~~I~~~  205 (206)
T d1s2ma1         152 ADKMLSRDFKTIIEQILSFLPP---------------THQSLLFSATFPLTVKEFMVKHLHKPYEINLM  205 (206)
T ss_dssp             HHHHSSHHHHHHHHHHHTTSCS---------------SCEEEEEESCCCHHHHHHHHHHCSSCEEESCC
T ss_pred             hhhhhhhhhHHHHHHHHHhCCC---------------CCEEEEEEEeCCHHHHHHHHHHCCCCEEEEee
Confidence            9999999999999999999987               89999999999999999999999999999875

>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=100.00  E-value=3.6e-42  Score=290.70  Aligned_cols=205  Identities=28%  Similarity=0.480  Sum_probs=177.7

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEE
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFAL  114 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~l  114 (316)
                      ++|+++||+++++++| +++||.+|||+|++|||.+++|+|++++||||||||++|++|+++.+...      ......+
T Consensus         1 t~F~~l~L~~~l~~~l-~~~g~~~pt~iQ~~aip~~l~G~dvii~a~TGSGKTlayllp~l~~~~~~------~~~~~~~   73 (209)
T d1q0ua_           1 TQFTRFPFQPFIIEAI-KTLRFYKPTEIQERIIPGALRGESMVGQSQTGTGKTHAYLLPIMEKIKPE------RAEVQAV   73 (209)
T ss_dssp             CCGGGSCCCHHHHHHH-HHTTCCSCCHHHHHHHHHHHHTCCEEEECCSSHHHHHHHHHHHHHHCCTT------SCSCCEE
T ss_pred             CccccCCcCHHHHHHH-HHCCCCCCCHHHHHHHHHHHCCCCeEeecccccccceeeeeeeccccccc------ccccccc
Confidence            4799999999999999 67899999999999999999999999999999999999999999987653      2345689


Q ss_pred             EEeCChHHHHHHHHHHHHHHhhcC---CceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEE
Q 043110          115 VLVPTSELCLLVYEILQKLLHRFR---WIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWII  191 (316)
Q Consensus       115 il~Pt~~L~~Q~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lV  191 (316)
                      +++|+++++.+.+..+........   .....+..++.+...+......+++|+|+||+++..++.+ ....+.+++++|
T Consensus        74 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ilv~TP~~l~~~~~~-~~~~~~~l~~lV  152 (209)
T d1q0ua_          74 ITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNVQPHIVIGTPGRINDFIRE-QALDVHTAHILV  152 (209)
T ss_dssp             EECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCCSSCCSEEEECHHHHHHHHHT-TCCCGGGCCEEE
T ss_pred             ccccccchhHHHHHHHHhhhccccccccccccccccchhhHHHHHHhccCceEEEecCchhhhhhhh-hccccccceEEE
Confidence            999999999999998887765542   2233444555555555555667899999999999999887 455668999999


Q ss_pred             EecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEEEc
Q 043110          192 FDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLIGL  262 (316)
Q Consensus       192 iDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i~~  262 (316)
                      +||||.+++++|..++..|+..+++               ++|++++|||+|+++.++++.+|++|+.|.+
T Consensus       153 iDEad~ll~~~f~~~v~~I~~~~~~---------------~~Q~il~SATl~~~v~~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         153 VDEADLMLDMGFITDVDQIAARMPK---------------DLQMLVFSATIPEKLKPFLKKYMENPTFVHV  208 (209)
T ss_dssp             ECSHHHHHHTTCHHHHHHHHHTSCT---------------TCEEEEEESCCCGGGHHHHHHHCSSCEEEEC
T ss_pred             EeecccccccccHHHHHHHHHHCCC---------------CCEEEEEEccCCHHHHHHHHHHCCCCEEEEe
Confidence            9999999999999999999999887               8999999999999999999999999999875

>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=99.97  E-value=9.8e-32  Score=225.70  Aligned_cols=189  Identities=23%  Similarity=0.270  Sum_probs=141.8

Q ss_pred             CcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEE
Q 043110           36 CFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALV  115 (316)
Q Consensus        36 ~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~li  115 (316)
                      ..+.++|++.+.+.|++.|||+.++|+|.++++.+++|+|+++++|||+|||++|.+|++...            .++++
T Consensus         3 ~~e~~~l~~~~~~~l~~~fg~~~~rp~Q~~ai~~~l~g~~vlv~apTGsGKT~~~~~~~~~~~------------~~~~~   70 (206)
T d1oywa2           3 QAEVLNLESGAKQVLQETFGYQQFRPGQEEIIDTVLSGRDCLVVMPTGGGKSLCYQIPALLLN------------GLTVV   70 (206)
T ss_dssp             CCCCSSHHHHHHHHHHHTTCCSSCCTTHHHHHHHHHTTCCEEEECSCHHHHHHHHHHHHHHSS------------SEEEE
T ss_pred             chhhCCCCHHHHHHHHHhcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCCCcchhhhhhhhcc------------CceEE
Confidence            467889999999999888899999999999999999999999999999999999999987543            34999


Q ss_pred             EeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCCh----HHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEE
Q 043110          116 LVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNR----SKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWII  191 (316)
Q Consensus       116 l~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lV  191 (316)
                      ++|+++|+.|+.+.++.++..     ..........    ...........+|+++||.++...... ......+++++|
T Consensus        71 v~P~~~L~~q~~~~l~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~-~~~~~~~v~~lv  144 (206)
T d1oywa2          71 VSPLISLMKDQVDQLQANGVA-----AACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFL-EHLAHWNPVLLA  144 (206)
T ss_dssp             ECSCHHHHHHHHHHHHHTTCC-----EEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHH-HHHTTSCEEEEE
T ss_pred             eccchhhhhhHHHHHHhhccc-----ccccccccccccchhHHHHHhcCCceEEEEechhhhchhhc-ccchhheeeeee
Confidence            999999999999988876532     1122222222    122223345578999999987554332 223456899999


Q ss_pred             EecchhhhcCCc--HHHH---HHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHH-HHHH-hcCCCE
Q 043110          192 FDEADRILELGF--GKEI---EEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNH-LTKI-SLETPV  258 (316)
Q Consensus       192 iDEad~l~~~~~--~~~i---~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~-~~~~-~l~~p~  258 (316)
                      +||||++.++++  ...+   ..+...++                ++|++++|||+++.+.+ +.+. .+.+|+
T Consensus       145 iDEaH~~~~~~~~~~~~~~~~~~l~~~~~----------------~~~ii~lSATl~~~v~~di~~~L~l~~p~  202 (206)
T d1oywa2         145 VDEAHCISQWGHDFRPEYAALGQLRQRFP----------------TLPFMALTATADDTTRQDIVRLLGLNDPL  202 (206)
T ss_dssp             ESSGGGGCTTSSCCCHHHHGGGGHHHHCT----------------TSCEEEEESCCCHHHHHHHHHHHTCCSCE
T ss_pred             eeeeeeeeccccchHHHHHHHHHHHHhCC----------------CCceEEEEeCCCHHHHHHHHHHcCCCCCc
Confidence            999999988753  2322   23333332                68999999999998865 4444 589995

>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=99.96  E-value=2.9e-29  Score=215.08  Aligned_cols=197  Identities=21%  Similarity=0.268  Sum_probs=140.4

Q ss_pred             ccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCee
Q 043110           33 ASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTF  112 (316)
Q Consensus        33 ~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~  112 (316)
                      ..+.|.+..+.+.+.+.+ ++ ++.+|+++|+++++.++.|+|+++.||||+|||++++++++.....         +.+
T Consensus        20 ~~~~~~~~~~~~~~~~~~-~~-~~~~p~~~Q~~~i~~~l~g~~~~i~apTGsGKT~~~~~~~~~~~~~---------~~r   88 (237)
T d1gkub1          20 SLCLFPEDFLLKEFVEFF-RK-CVGEPRAIQKMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALK---------GKR   88 (237)
T ss_dssp             CCSCCTTHHHHHHHHHHH-HT-TTCSCCHHHHHHHHHHHTTCCEECCCCBTSCSHHHHHHHHHHHHTT---------SCC
T ss_pred             ccccCccchhHHHHHHHH-Hh-ccCCCCHHHHHHHHHHHCCCCEEEEecCCChHHHHHHHHHHHHHHh---------cCe
Confidence            345566666666676666 44 7889999999999999999999999999999999999998877654         456


Q ss_pred             EEEEeCChHHHHHHHHHHHHHHhhcCCce---eEEeeCCCChHHHHHHH--hcCCcEEEeCcHHHHHHHhcCCccccCce
Q 043110          113 ALVLVPTSELCLLVYEILQKLLHRFRWIV---PGYVMGGGNRSKEKARL--RKGISILVATPGHLLDHLKHTSSFLHTNL  187 (316)
Q Consensus       113 ~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~l--~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l  187 (316)
                      +||++||++|+.|+++.+++++...+...   .....++.........+  ...++|+|+||++|.+.+.     .++++
T Consensus        89 vliv~Pt~~La~Q~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~~~-----~~~~~  163 (237)
T d1gkub1          89 CYVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKHYR-----ELGHF  163 (237)
T ss_dssp             EEEEESCHHHHHHHHHHHHHHHTTTCCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHCST-----TSCCC
T ss_pred             EEEEeccHHHHHHHHHHHHHHHHHcCCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHhhh-----hcCCC
Confidence            99999999999999999999987654221   22233333333333333  2457899999998876433     34678


Q ss_pred             eEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHH
Q 043110          188 RWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHL  249 (316)
Q Consensus       188 ~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~  249 (316)
                      +++|+||||.+++.+  ..+..++..+...  ..........+...|++++|||+++.+...
T Consensus       164 ~~vVvDE~d~~l~~~--~~~~~~~~~~g~~--~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~  221 (237)
T d1gkub1         164 DFIFVDDVDAILKAS--KNVDKLLHLLGFH--YDLKTKSWVGEARGCLMVSTATAKKGKKAE  221 (237)
T ss_dssp             SEEEESCHHHHHTST--HHHHHHHHHTTEE--EETTTTEEEECCSSEEEECCCCSCCCTTHH
T ss_pred             CEEEEEChhhhhhcc--cchhHHHHhcCCh--HHHHHHHhhCCCCCeEEEEeCCCCcccHHH
Confidence            999999999998864  3455555544210  001111233455789999999998766443

>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=99.96  E-value=1.9e-29  Score=210.98  Aligned_cols=189  Identities=20%  Similarity=0.214  Sum_probs=143.2

Q ss_pred             CCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           42 LDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        42 l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      +++.+...| ++.||.+|+|+|+++++.+++|+|+++++|||+|||.+++++++..+..         +.++|+++|+++
T Consensus        10 ~~~~~~~~l-~~~g~~~l~~~Q~~ai~~l~~~~~~il~apTGsGKT~~a~l~i~~~~~~---------~~~vl~l~P~~~   79 (202)
T d2p6ra3          10 ISSYAVGIL-KEEGIEELFPPQAEAVEKVFSGKNLLLAMPTAAGKTLLAEMAMVREAIK---------GGKSLYVVPLRA   79 (202)
T ss_dssp             HHHHHHHHH-HCC---CCCCCCHHHHHHHTTCSCEEEECSSHHHHHHHHHHHHHHHHHT---------TCCEEEEESSHH
T ss_pred             hhHHHHHHH-HHcCCCCCCHHHHHHHHHHHcCCCEEEEcCCCCchhHHHHHHHHHHhhc---------cCcceeecccHH
Confidence            567788888 6689999999999999999999999999999999999999999887765         335999999999


Q ss_pred             HHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcC
Q 043110          122 LCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILEL  201 (316)
Q Consensus       122 L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~  201 (316)
                      |+.|+++.++++....  .......++.....   .....++|+++||..+...+.+ ....+..++++|+||+|.+.+.
T Consensus        80 L~~q~~~~~~~~~~~~--~~v~~~~~~~~~~~---~~~~~~~ii~~~~~~~~~~~~~-~~~~~~~~~~ii~DE~h~~~~~  153 (202)
T d2p6ra3          80 LAGEKYESFKKWEKIG--LRIGISTGDYESRD---EHLGDCDIIVTTSEKADSLIRN-RASWIKAVSCLVVDEIHLLDSE  153 (202)
T ss_dssp             HHHHHHHHHTTTTTTT--CCEEEECSSCBCCS---SCSTTCSEEEEEHHHHHHHHHT-TCSGGGGCCEEEETTGGGGGCT
T ss_pred             HHHHHHHHHHHHhhcc--ccceeeccCccccc---ccccccceeeeccHHHHHHHhc-cchhhhhhhhccccHHHHhccc
Confidence            9999999998776432  22222333322211   1123578999999999988876 4455678999999999999988


Q ss_pred             CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHHhcCCCEEE
Q 043110          202 GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKISLETPVLI  260 (316)
Q Consensus       202 ~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~p~~i  260 (316)
                      ++...++.+++.+..            .++++|++++|||+++ .+++. .++..+.++
T Consensus       154 ~r~~~~~~~l~~i~~------------~~~~~~~l~lSATl~n-~~~~~-~~l~~~~~~  198 (202)
T d2p6ra3         154 KRGATLEILVTKMRR------------MNKALRVIGLSATAPN-VTEIA-EWLDADYYV  198 (202)
T ss_dssp             TTHHHHHHHHHHHHH------------HCTTCEEEEEECCCTT-HHHHH-HHTTCEEEE
T ss_pred             ccchHHHHHHHHHHh------------cCCCCcEEEEcCCCCc-HHHHH-HHcCCCeee
Confidence            887777777776653            1227899999999975 56654 666655555

>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=99.93  E-value=2.5e-24  Score=179.05  Aligned_cols=168  Identities=20%  Similarity=0.199  Sum_probs=125.4

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      +|+++|.+++..+. ++|+++++|||+|||+++++++...+.+.        +.++||++|+++|+.|+++.++++....
T Consensus         9 ~pr~~Q~~~~~~~~-~~n~lv~~pTGsGKT~i~~~~~~~~~~~~--------~~~il~i~P~~~L~~q~~~~~~~~~~~~   79 (200)
T d1wp9a1           9 QPRIYQEVIYAKCK-ETNCLIVLPTGLGKTLIAMMIAEYRLTKY--------GGKVLMLAPTKPLVLQHAESFRRLFNLP   79 (200)
T ss_dssp             CCCHHHHHHHHHGG-GSCEEEECCTTSCHHHHHHHHHHHHHHHS--------CSCEEEECSSHHHHHHHHHHHHHHBCSC
T ss_pred             CCCHHHHHHHHHHh-cCCeEEEeCCCCcHHHHHHHHHHHHHHhc--------CCcEEEEcCchHHHHHHHHHHHHhhccc
Confidence            69999999998875 66899999999999999998887776542        3359999999999999999999987543


Q ss_pred             CCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccC
Q 043110          138 RWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSR  217 (316)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~  217 (316)
                      . ..+....++...... ......++++++||+.+...+.. ....+.+++++|+||||++.+......+...+..... 
T Consensus        80 ~-~~v~~~~~~~~~~~~-~~~~~~~~i~i~t~~~~~~~~~~-~~~~~~~~~~vIiDE~H~~~~~~~~~~~~~~~~~~~~-  155 (200)
T d1wp9a1          80 P-EKIVALTGEKSPEER-SKAWARAKVIVATPQTIENDLLA-GRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAK-  155 (200)
T ss_dssp             G-GGEEEECSCSCHHHH-HHHHHHCSEEEECHHHHHHHHHT-TSCCTTSCSEEEEETGGGCSTTCHHHHHHHHHHHHCS-
T ss_pred             c-cceeeeecccchhHH-HHhhhcccccccccchhHHHHhh-hhhhccccceEEEEehhhhhcchhHHHHHHHHHhcCC-
Confidence            3 334444455454443 33334568999999999988876 4556678999999999998776544444434333333 


Q ss_pred             cccccCCCCccccccceEEEEeeecchhHHHHHHH
Q 043110          218 NIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKI  252 (316)
Q Consensus       218 ~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~  252 (316)
                                    .++++++|||++.....+.+.
T Consensus       156 --------------~~~~l~~SATp~~~~~~~~~~  176 (200)
T d1wp9a1         156 --------------NPLVIGLTASPGSTPEKIMEV  176 (200)
T ss_dssp             --------------SCCEEEEESCSCSSHHHHHHH
T ss_pred             --------------CCcEEEEEecCCCcHHHHHHH
Confidence                          678999999987666655443

>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=99.83  E-value=9.9e-19  Score=146.86  Aligned_cols=176  Identities=24%  Similarity=0.265  Sum_probs=132.6

Q ss_pred             CCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHh----CC--CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeE
Q 043110           40 LGLDSTLCDQLRERLGFEAPTKVQAQAIPVIL----SG--RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFA  113 (316)
Q Consensus        40 ~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il----~g--~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~  113 (316)
                      +..+.+..+.+.+.+.|. +|+-|..++..+.    ++  .+.+++|.||||||.+|+.++...+..         |.++
T Consensus        38 ~~~~~~~~~~~~~~lP~~-lt~~Q~~~~~~i~~~~~~~~~~~~LL~GdvGsGKT~V~~~a~~~~~~~---------g~qv  107 (233)
T d2eyqa3          38 FKHDREQYQLFCDSFPFE-TTPDQAQAINAVLSDMCQPLAMDRLVCGDVGFGKTEVAMRAAFLAVDN---------HKQV  107 (233)
T ss_dssp             CCCCHHHHHHHHHTCCSC-CCHHHHHHHHHHHHHHHSSSCCEEEEECCCCTTTHHHHHHHHHHHHTT---------TCEE
T ss_pred             CCCCHHHHHhhhhccccc-cchhHHHHHHHHHHHHhccCccCeEEEcCCCCCcHHHHHHHHHHHHHc---------CCce
Confidence            345678888887888887 8999999998875    33  378999999999999999999888865         6779


Q ss_pred             EEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH---HHHHhc-CCcEEEeCcHHHHHHHhcCCccccCceeE
Q 043110          114 LVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE---KARLRK-GISILVATPGHLLDHLKHTSSFLHTNLRW  189 (316)
Q Consensus       114 lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~~-~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~  189 (316)
                      ++++||..|+.|.++.+++++..++ ..+..++++......   +..+.. .++|+|||...+.      ..+.++++.+
T Consensus       108 ~~l~Pt~~La~Q~~~~~~~~~~~~~-~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~------~~~~f~~LgL  180 (233)
T d2eyqa3         108 AVLVPTTLLAQQHYDNFRDRFANWP-VRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ------SDVKFKDLGL  180 (233)
T ss_dssp             EEECSSHHHHHHHHHHHHHHSTTTT-CCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH------SCCCCSSEEE
T ss_pred             EEEccHHHhHHHHHHHHHHHHhhCC-CEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc------cCCccccccc
Confidence            9999999999999999999887655 455566666655433   333443 4799999976554      2344578999


Q ss_pred             EEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHHH
Q 043110          190 IIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTKI  252 (316)
Q Consensus       190 lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~~  252 (316)
                      +|+||-|+.   |+.  -+..+.....               ++.++++|||..++...++..
T Consensus       181 iIiDEeH~f---g~k--Q~~~l~~~~~---------------~~~~l~~SATPiprtl~~~~~  223 (233)
T d2eyqa3         181 LIVDEEHRF---GVR--HKERIKAMRA---------------NVDILTLTATPIPRTLNMAMS  223 (233)
T ss_dssp             EEEESGGGS---CHH--HHHHHHHHHT---------------TSEEEEEESSCCCHHHHHHHT
T ss_pred             eeeechhhh---hhH--HHHHHHhhCC---------------CCCEEEEecchhHHHHHHHHH
Confidence            999999983   232  2333333333               678999999998777666553

>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=99.81  E-value=1.4e-20  Score=165.76  Aligned_cols=140  Identities=19%  Similarity=0.173  Sum_probs=96.6

Q ss_pred             HhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCC
Q 043110           70 ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGG  149 (316)
Q Consensus        70 il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~  149 (316)
                      +.+|+++++.||||||||++|+.|++......        +.++||++||++||.|+++.++.+.......    .    
T Consensus         6 ~~~~~~~lv~~~TGsGKT~~~l~~~~~~~~~~--------~~~~lvi~Ptr~La~q~~~~l~~~~~~~~~~----~----   69 (305)
T d2bmfa2           6 FRKKRLTIMDLHPGAGKTKRYLPAIVREAIKR--------GLRTLILAPTRVVAAEMEEALRGLPIRYQTP----A----   69 (305)
T ss_dssp             SSTTCEEEECCCTTSSTTTTHHHHHHHHHHHH--------TCCEEEEESSHHHHHHHHHHTTTSCCBCCC----------
T ss_pred             hhcCCcEEEEECCCCCHHHHHHHHHHHHHHhc--------CCEEEEEccHHHHHHHHHHHHhcCCcceeee----E----
Confidence            45789999999999999999988888766552        4569999999999999988776543211100    0    


Q ss_pred             ChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccc
Q 043110          150 NRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVS  229 (316)
Q Consensus       150 ~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~  229 (316)
                          ..........|+++||+.+..+...  ...+.+++++|+||||++.++++  ....++..+..             
T Consensus        70 ----~~~~~~~~~~i~~~t~~~l~~~~~~--~~~~~~~~~vViDE~H~~~~~~~--~~~~~l~~~~~-------------  128 (305)
T d2bmfa2          70 ----IRAEHTGREIVDLMCHATFTMRLLS--PIRVPNYNLIIMDEAHFTDPASI--AARGYISTRVE-------------  128 (305)
T ss_dssp             ----------CCCSEEEEEHHHHHHHHTS--SSCCCCCSEEEEESTTCCSHHHH--HHHHHHHHHHH-------------
T ss_pred             ----EeecccCccccccCCcHHHHHHHhc--CccccceeEEEeeeeeecchhhH--HHHHHHHHhhc-------------
Confidence                0112234467999999988877654  33456899999999999876543  22223333221             


Q ss_pred             cccceEEEEeeecchhH
Q 043110          230 NVKRQNLLLSATLNEKV  246 (316)
Q Consensus       230 ~~~~q~i~~SAT~~~~v  246 (316)
                      .+..|++++|||++...
T Consensus       129 ~~~~~~v~~SAT~~~~~  145 (305)
T d2bmfa2         129 MGEAAGIFMTATPPGSR  145 (305)
T ss_dssp             HTSCEEEEECSSCTTCC
T ss_pred             cccceEEEeecCCCcce
Confidence            12679999999998643

>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=99.80  E-value=9.6e-19  Score=149.68  Aligned_cols=173  Identities=25%  Similarity=0.338  Sum_probs=125.6

Q ss_pred             CCHHHHHHHHHHcCCCCCcHHHHHHHHHHhC----C--CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEE
Q 043110           42 LDSTLCDQLRERLGFEAPTKVQAQAIPVILS----G--RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALV  115 (316)
Q Consensus        42 l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~----g--~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~li  115 (316)
                      .+.++.+.+.+.+.|+ +|+-|++|+..+..    +  .+.+++|.||||||.+|+.++...+..         |.++++
T Consensus        68 ~~~~l~~~f~~~LPFe-LT~~Q~~ai~ei~~d~~~~~~m~rLL~GdvGSGKT~Va~~a~~~~~~~---------g~q~~~  137 (264)
T d1gm5a3          68 IEGKLAEEFIKSLPFK-LTNAQKRAHQEIRNDMISEKPMNRLLQGDVGSGKTVVAQLAILDNYEA---------GFQTAF  137 (264)
T ss_dssp             CCTHHHHHHHHHSSSC-CCHHHHHHHHHHHHHHHSSSCCCCEEECCSSSSHHHHHHHHHHHHHHH---------TSCEEE
T ss_pred             CChHHHHHHHhhcccc-CCchHHHHHHHHHHHhhccCcceeeeeccccccccHHHHHHHHHHHhc---------ccceeE
Confidence            4456666666888997 99999999988862    3  368999999999999999999988876         566999


Q ss_pred             EeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHH---HHHHh-cCCcEEEeCcHHHHHHHhcCCccccCceeEEE
Q 043110          116 LVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKE---KARLR-KGISILVATPGHLLDHLKHTSSFLHTNLRWII  191 (316)
Q Consensus       116 l~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lV  191 (316)
                      ++||..|+.|.++.+++++..++ ..+..+.|+....+.   +..+. ..++|+|||..-+.+      .+.+.++.++|
T Consensus       138 m~Pt~~La~Qh~~~~~~~f~~~~-~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~~------~~~f~~Lglvi  210 (264)
T d1gm5a3         138 MVPTSILAIQHYRRTVESFSKFN-IHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE------DVHFKNLGLVI  210 (264)
T ss_dssp             ECSCHHHHHHHHHHHHHHHTCSS-CCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH------CCCCSCCCEEE
T ss_pred             EeehHhhhHHHHHHHHHhhhhcc-ccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhcC------CCCccccceee
Confidence            99999999999999999987654 455566666655432   33333 358999999866543      23346899999


Q ss_pred             EecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHH
Q 043110          192 FDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK  251 (316)
Q Consensus       192 iDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~  251 (316)
                      |||-|+..-   ..  +..+   .            .....+.++++|||.-++-..++.
T Consensus       211 iDEqH~fgv---~Q--r~~l---~------------~~~~~~~~l~~SATPiprtl~~~~  250 (264)
T d1gm5a3         211 IDEQHRFGV---KQ--REAL---M------------NKGKMVDTLVMSATPIPRSMALAF  250 (264)
T ss_dssp             EESCCCC----------CCC---C------------SSSSCCCEEEEESSCCCHHHHHHH
T ss_pred             eccccccch---hh--HHHH---H------------HhCcCCCEEEEECCCCHHHHHHHH
Confidence            999998421   11  1111   0            111257899999998766655554

>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=99.75  E-value=3.1e-18  Score=149.13  Aligned_cols=153  Identities=18%  Similarity=0.197  Sum_probs=106.1

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      .|+++|.+++..++..+..++.+|||+|||+.....+......        ...++|||+|+++|+.|+++.+.+++...
T Consensus       113 ~~rdyQ~~av~~~l~~~~~il~~pTGsGKT~i~~~i~~~~~~~--------~~~k~Liivp~~~Lv~Q~~~~f~~~~~~~  184 (282)
T d1rifa_         113 EPHWYQKDAVFEGLVNRRRILNLPTSAGRSLIQALLARYYLEN--------YEGKILIIVPTTALTTQMADDFVDYRLFS  184 (282)
T ss_dssp             CCCHHHHHHHHHHHHHSEEEECCCTTSCHHHHHHHHHHHHHHH--------CSSEEEEECSSHHHHHHHHHHHHHHTSCC
T ss_pred             ccchHHHHHHHHHHhcCCceeEEEcccCccHHHHHHHHHhhhc--------ccceEEEEEcCchhHHHHHHHHHHhhccc
Confidence            5999999999999998899999999999999865433333322        13459999999999999999998876432


Q ss_pred             CCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccC
Q 043110          138 RWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSR  217 (316)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~  217 (316)
                       ...+....+|......   .....+|+|+|+..+...    ....+++++++|+||||+..    ...+..++..+.. 
T Consensus       185 -~~~~~~~~~g~~~~~~---~~~~~~i~i~t~qs~~~~----~~~~~~~f~~VIvDEaH~~~----a~~~~~il~~~~~-  251 (282)
T d1rifa_         185 -HAMIKKIGGGASKDDK---YKNDAPVVVGTWQTVVKQ----PKEWFSQFGMMMNDECHLAT----GKSISSIISGLNN-  251 (282)
T ss_dssp             -GGGEEECSTTCSSTTC---CCTTCSEEEECHHHHTTS----CGGGGGGEEEEEEETGGGCC----HHHHHHHTTTCTT-
T ss_pred             -cccceeecceeccccc---ccccceEEEEeeehhhhh----cccccCCCCEEEEECCCCCC----chhHHHHHHhccC-
Confidence             2233334444332111   112468999998776542    22345689999999999864    3455556554432 


Q ss_pred             cccccCCCCccccccceEEEEeeecchh
Q 043110          218 NIASIGEGNEVSNVKRQNLLLSATLNEK  245 (316)
Q Consensus       218 ~~~~~~~~~~~~~~~~q~i~~SAT~~~~  245 (316)
                                    ....+++|||++..
T Consensus       252 --------------~~~rlGlTaT~~~~  265 (282)
T d1rifa_         252 --------------CMFKFGLSGSLRDG  265 (282)
T ss_dssp             --------------CCEEEEECSSCCTT
T ss_pred             --------------CCeEEEEEeecCCC
Confidence                          23458999998654

>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=99.74  E-value=1.1e-18  Score=135.38  Aligned_cols=136  Identities=18%  Similarity=0.115  Sum_probs=89.6

Q ss_pred             hCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCC
Q 043110           71 LSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGN  150 (316)
Q Consensus        71 l~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~  150 (316)
                      .+|+++++++|||+|||.+++.+++......        +.++++++|+++++.|.++.+....       .........
T Consensus         5 ~~~~~~il~~~tGsGKT~~~~~~~~~~~~~~--------~~~vli~~p~~~l~~q~~~~~~~~~-------~~~~~~~~~   69 (140)
T d1yksa1           5 KKGMTTVLDFHPGAGKTRRFLPQILAECARR--------RLRTLVLAPTRVVLSEMKEAFHGLD-------VKFHTQAFS   69 (140)
T ss_dssp             STTCEEEECCCTTSSTTTTHHHHHHHHHHHT--------TCCEEEEESSHHHHHHHHHHTTTSC-------EEEESSCCC
T ss_pred             HcCCcEEEEcCCCCChhHHHHHHHHHHhhhc--------CceeeeeecchhHHHHHHHHhhhhh-------hhhcccccc
Confidence            4688999999999999998877777766552        4459999999999999887653321       111111111


Q ss_pred             hHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCcccc
Q 043110          151 RSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSN  230 (316)
Q Consensus       151 ~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~  230 (316)
                      ..     -.....+.+.|...+......  ...+.+++++|+||||.+...++  ..+.++..+...             
T Consensus        70 ~~-----~~~~~~~~~~~~~~l~~~~~~--~~~~~~~~lvIiDEaH~~~~~~~--~~~~~~~~~~~~-------------  127 (140)
T d1yksa1          70 AH-----GSGREVIDAMCHATLTYRMLE--PTRVVNWEVIIMDEAHFLDPASI--AARGWAAHRARA-------------  127 (140)
T ss_dssp             CC-----CCSSCCEEEEEHHHHHHHHTS--SSCCCCCSEEEETTTTCCSHHHH--HHHHHHHHHHHT-------------
T ss_pred             cc-----cccccchhhhhHHHHHHHHhc--cccccceeEEEEccccccChhhH--HHHHHHHHHhhC-------------
Confidence            00     012346788888877665543  34557899999999998754322  223333333221             


Q ss_pred             ccceEEEEeeecc
Q 043110          231 VKRQNLLLSATLN  243 (316)
Q Consensus       231 ~~~q~i~~SAT~~  243 (316)
                      .+.+++++|||+|
T Consensus       128 ~~~~~l~lTATPp  140 (140)
T d1yksa1         128 NESATILMTATPP  140 (140)
T ss_dssp             TSCEEEEECSSCT
T ss_pred             CCCCEEEEEcCCC
Confidence            1789999999987

>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=99.74  E-value=5.2e-18  Score=141.15  Aligned_cols=136  Identities=25%  Similarity=0.220  Sum_probs=97.4

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhc
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRF  137 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~  137 (316)
                      .|+++|++++..+++++..++.+|||+|||++++..+ ..+           +.++||+||+++|+.|+.+.++.++.. 
T Consensus        70 ~Lr~yQ~eav~~~~~~~~~ll~~~tG~GKT~~a~~~~-~~~-----------~~~~Liv~p~~~L~~q~~~~~~~~~~~-  136 (206)
T d2fz4a1          70 SLRDYQEKALERWLVDKRGCIVLPTGSGKTHVAMAAI-NEL-----------STPTLIVVPTLALAEQWKERLGIFGEE-  136 (206)
T ss_dssp             CCCHHHHHHHHHHTTTSEEEEEESSSTTHHHHHHHHH-HHS-----------CSCEEEEESSHHHHHHHHHHHGGGCGG-
T ss_pred             CcCHHHHHHHHHHHhCCCcEEEeCCCCCceehHHhHH-HHh-----------cCceeEEEcccchHHHHHHHHHhhccc-
Confidence            5899999999999999999999999999998865433 222           223999999999999999988765432 


Q ss_pred             CCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccC
Q 043110          138 RWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSR  217 (316)
Q Consensus       138 ~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~  217 (316)
                         ......|+.         ....+|+|+|...+......    ...++++||+||||++...    .+..++..++  
T Consensus       137 ---~~~~~~~~~---------~~~~~i~i~t~~~~~~~~~~----~~~~~~lvIiDEaH~~~a~----~~~~i~~~~~--  194 (206)
T d2fz4a1         137 ---YVGEFSGRI---------KELKPLTVSTYDSAYVNAEK----LGNRFMLLIFDEVHHLPAE----SYVQIAQMSI--  194 (206)
T ss_dssp             ---GEEEESSSC---------BCCCSEEEEEHHHHHHTHHH----HTTTCSEEEEECSSCCCTT----THHHHHHTCC--
T ss_pred             ---chhhccccc---------ccccccccceehhhhhhhHh----hCCcCCEEEEECCeeCCcH----HHHHHHhccC--
Confidence               222332322         12357999999887665443    1246789999999997543    2344554443  


Q ss_pred             cccccCCCCccccccceEEEEeeec
Q 043110          218 NIASIGEGNEVSNVKRQNLLLSATL  242 (316)
Q Consensus       218 ~~~~~~~~~~~~~~~~q~i~~SAT~  242 (316)
                                    ....+++|||+
T Consensus       195 --------------~~~~lgLTATl  205 (206)
T d2fz4a1         195 --------------APFRLGLTATF  205 (206)
T ss_dssp             --------------CSEEEEEEESC
T ss_pred             --------------CCcEEEEecCC
Confidence                          34568899997

>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=99.63  E-value=4.3e-16  Score=120.60  Aligned_cols=129  Identities=24%  Similarity=0.155  Sum_probs=84.8

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRS  152 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~  152 (316)
                      .+..++.+|||+|||+.+...+    ..        .+.+++|++|+++|++|+.+.+......    ......++... 
T Consensus         8 ~~~~ll~apTGsGKT~~~~~~~----~~--------~~~~vli~~P~~~l~~q~~~~~~~~~~~----~~~~~~~~~~~-   70 (136)
T d1a1va1           8 FQVAHLHAPTGSGKSTKVPAAY----AA--------QGYKVLVLNPSVAATLGFGAYMSKAHGV----DPNIRTGVRTI-   70 (136)
T ss_dssp             CEEEEEECCTTSCTTTHHHHHH----HT--------TTCCEEEEESCHHHHHHHHHHHHHHHSC----CCEEECSSCEE-
T ss_pred             CCEEEEEeCCCCCHHHHHHHHH----HH--------cCCcEEEEcChHHHHHHHHHHHHHHhhc----ccccccccccc-
Confidence            3468999999999997643222    22        2445999999999999999988876532    22223333221 


Q ss_pred             HHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCcccccc
Q 043110          153 KEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVK  232 (316)
Q Consensus       153 ~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~  232 (316)
                            .....++++|.+.+....    ...+.+++++|+||+|++-. .....+..+++.+...             ++
T Consensus        71 ------~~~~~~~~~~~~~~~~~~----~~~~~~~~~vIiDE~H~~~~-~~~~~~~~~l~~~~~~-------------~~  126 (136)
T d1a1va1          71 ------TTGSPITYSTYGKFLADG----GCSGGAYDIIICDECHSTDA-TSILGIGTVLDQAETA-------------GA  126 (136)
T ss_dssp             ------CCCCSEEEEEHHHHHHTT----GGGGCCCSEEEEETTTCCSH-HHHHHHHHHHHHTTTT-------------TC
T ss_pred             ------ccccceEEEeeeeecccc----chhhhcCCEEEEecccccCH-HHHHHHHHHHHHHHHC-------------CC
Confidence                  123468899988765432    23457899999999998532 2223355566655431             26


Q ss_pred             ceEEEEeeec
Q 043110          233 RQNLLLSATL  242 (316)
Q Consensus       233 ~q~i~~SAT~  242 (316)
                      ..++++|||.
T Consensus       127 ~~~l~~TATP  136 (136)
T d1a1va1         127 RLVVLATATP  136 (136)
T ss_dssp             SEEEEEESSC
T ss_pred             CcEEEEeCCC
Confidence            7899999994

>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=99.19  E-value=7.9e-10  Score=96.01  Aligned_cols=159  Identities=19%  Similarity=0.255  Sum_probs=98.8

Q ss_pred             CCcHHHHHHHHHHh---------CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHH
Q 043110           58 APTKVQAQAIPVIL---------SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYE  128 (316)
Q Consensus        58 ~p~~~Q~~~i~~il---------~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~  128 (316)
                      .++|+|.+++..+.         .+..+++.-..|.|||+..+. ++..+....... ......+|||||. .|..|+.+
T Consensus        55 ~Lr~hQ~~gv~~l~~~~~~~~~~~~~g~iLaDemGlGKT~qaia-~l~~l~~~~~~~-~~~~~~~LIV~P~-sl~~qW~~  131 (298)
T d1z3ix2          55 VLRPHQREGVKFLWDCVTGRRIENSYGCIMADEMGLGKTLQCIT-LIWTLLKQSPDC-KPEIDKVIVVSPS-SLVRNWYN  131 (298)
T ss_dssp             TCCHHHHHHHHHHHHHHTTSSSTTCCEEEECCCTTSCHHHHHHH-HHHHHHHCCTTS-SCSCSCEEEEECH-HHHHHHHH
T ss_pred             cccHHHHHHHHHHHHHHHhhhhccCCceEEEeCCCCCHHHHHHH-HHHHHHHhcccc-cCCCCcEEEEccc-hhhHHHHH
Confidence            47899999997653         344689999999999987543 344443322211 1123359999997 58899999


Q ss_pred             HHHHHHhhcCCceeEEeeCCCChHHHHHHH---h------cCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhh
Q 043110          129 ILQKLLHRFRWIVPGYVMGGGNRSKEKARL---R------KGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       129 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~------~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~  199 (316)
                      .+.+++...  .......++ .........   .      ...+++|+|.+.+......   +...+.+++|+||+|++-
T Consensus       132 Ei~k~~~~~--~~~v~~~~~-~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~~---l~~~~~~~vI~DEaH~ik  205 (298)
T d1z3ix2         132 EVGKWLGGR--VQPVAIDGG-SKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAEV---LHKGKVGLVICDEGHRLK  205 (298)
T ss_dssp             HHHHHHGGG--CCEEEECSS-CHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTTT---TTTSCCCEEEETTGGGCC
T ss_pred             HHHhhcCCc--eeEEEEeCc-hHHHHHHHHHHhhhccCccccceEEEEeecccccchhc---ccccceeeeecccccccc
Confidence            999887542  222333333 333222221   1      1246999998887654432   222356799999999986


Q ss_pred             cCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecc
Q 043110          200 ELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLN  243 (316)
Q Consensus       200 ~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~  243 (316)
                      ..+  ......+..+.                ....+++|||.-
T Consensus       206 n~~--s~~~~a~~~l~----------------~~~rllLTGTPi  231 (298)
T d1z3ix2         206 NSD--NQTYLALNSMN----------------AQRRVLISGTPI  231 (298)
T ss_dssp             TTC--HHHHHHHHHHC----------------CSEEEEECSSCS
T ss_pred             ccc--chhhhhhhccc----------------cceeeeecchHH
Confidence            543  23333444443                446789999974

>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=99.11  E-value=2.5e-09  Score=89.37  Aligned_cols=139  Identities=22%  Similarity=0.299  Sum_probs=104.0

Q ss_pred             HHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHH
Q 043110           46 LCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLL  125 (316)
Q Consensus        46 l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q  125 (316)
                      +.++-.+.+|.. |+++|...--.+..|+  +++..||-|||++..+|+.-....         |..+-|++....||..
T Consensus        69 VREAakRtlG~R-hyDVQLiGgi~L~~G~--iaem~TGEGKTL~a~l~a~l~al~---------g~~vhvvTvNdyLA~R  136 (273)
T d1tf5a3          69 VREASRRVTGMF-PFKVQLMGGVALHDGN--IAEMKTGEGKTLTSTLPVYLNALT---------GKGVHVVTVNEYLASR  136 (273)
T ss_dssp             HHHHHHHHHSCC-CCHHHHHHHHHHHTTS--EEECCTTSCHHHHHHHHHHHHHTT---------SSCEEEEESSHHHHHH
T ss_pred             HHHHHHHhhceE-EehhHHHHHHHHHhhh--heeecCCCcchhHHHHHHHHHHhc---------CCCceEEecCccccch
Confidence            334444556775 8999988877777885  899999999999999998776655         3348999999999999


Q ss_pred             HHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHH-HHHHhcCC-----ccccCceeEEEEecchhhh
Q 043110          126 VYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHL-LDHLKHTS-----SFLHTNLRWIIFDEADRIL  199 (316)
Q Consensus       126 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l-~~~l~~~~-----~~~~~~l~~lViDEad~l~  199 (316)
                      =.+++..+...++ +.+++...+.+..... ..+ .+||+.+|...+ +++++..-     ......+.+.|+||+|.++
T Consensus       137 Dae~m~~iy~~lG-lsvg~~~~~~~~~~r~-~~Y-~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r~~~~aIvDEvDsil  213 (273)
T d1tf5a3         137 DAEQMGKIFEFLG-LTVGLNLNSMSKDEKR-EAY-AADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSIL  213 (273)
T ss_dssp             HHHHHHHHHHHTT-CCEEECCTTSCHHHHH-HHH-HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCCCCCEEEEETHHHHH
T ss_pred             hhhHHhHHHHHcC-CCccccccccCHHHHH-HHh-hCCceecchhhhhhhhcchhhhcChhhhccCCCCEEEEEcchhhh
Confidence            9999999998876 5566665555544433 333 479999999876 55554421     1234568899999999876

>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=99.06  E-value=6.7e-10  Score=92.74  Aligned_cols=156  Identities=20%  Similarity=0.213  Sum_probs=95.6

Q ss_pred             CCcHHHHHHHHHHh----CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVIL----SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        58 ~p~~~Q~~~i~~il----~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      .+.|+|.+++..+.    .+..+++.-++|.|||+..+. ++..+....      ...++||||| ..+..|+.+.+.++
T Consensus        12 ~L~~yQ~~~v~~~~~~~~~~~g~iLaDe~GlGKT~~~i~-~~~~~~~~~------~~~~~LIv~p-~~l~~~W~~e~~~~   83 (230)
T d1z63a1          12 NLRPYQIKGFSWMRFMNKLGFGICLADDMGLGKTLQTIA-VFSDAKKEN------ELTPSLVICP-LSVLKNWEEELSKF   83 (230)
T ss_dssp             CCCHHHHHHHHHHHHHHHTTCCEEECCCTTSCHHHHHHH-HHHHHHHTT------CCSSEEEEEC-STTHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHhhhcCCCEEEEeCCCCChHHHHHH-hhhhhhhcc------cccccceecc-hhhhhHHHHHHHhh
Confidence            57899999997653    455689999999999998754 444443321      1234899999 57788888888877


Q ss_pred             HhhcCCceeEEeeCCCChHHHHHHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhhhcCCcHHHHHHHHHH
Q 043110          134 LHRFRWIVPGYVMGGGNRSKEKARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRILELGFGKEIEEILDI  213 (316)
Q Consensus       134 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l~~~~~~~~i~~i~~~  213 (316)
                      ....   .............     ..+.+|+++|.+.+.....    ..--...++|+||+|.+-.....  .......
T Consensus        84 ~~~~---~~~~~~~~~~~~~-----~~~~~vvi~~~~~~~~~~~----l~~~~~~~vI~DEah~~k~~~s~--~~~~~~~  149 (230)
T d1z63a1          84 APHL---RFAVFHEDRSKIK-----LEDYDIILTTYAVLLRDTR----LKEVEWKYIVIDEAQNIKNPQTK--IFKAVKE  149 (230)
T ss_dssp             CTTS---CEEECSSSTTSCC-----GGGSSEEEEEHHHHTTCHH----HHTCCEEEEEEETGGGGSCTTSH--HHHHHHT
T ss_pred             cccc---cceeeccccchhh-----ccCcCEEEeeHHHHHhHHH----HhcccceEEEEEhhhcccccchh--hhhhhhh
Confidence            5432   2222221111110     1236899999887643221    11125688999999998654322  2222233


Q ss_pred             hccCcccccCCCCccccccceEEEEeeec-chhHHHHHH
Q 043110          214 LGSRNIASIGEGNEVSNVKRQNLLLSATL-NEKVNHLTK  251 (316)
Q Consensus       214 l~~~~~~~~~~~~~~~~~~~q~i~~SAT~-~~~v~~~~~  251 (316)
                      +.                ....+++|||. +.+..++..
T Consensus       150 l~----------------a~~r~~LTgTPi~n~~~dl~~  172 (230)
T d1z63a1         150 LK----------------SKYRIALTGTPIENKVDDLWS  172 (230)
T ss_dssp             SC----------------EEEEEEECSSCSTTCHHHHHH
T ss_pred             hc----------------cceEEEEecchHHhHHHHHHH
Confidence            32                34568899997 445555433

>d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {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: Exodeoxyribonuclease V alpha chain (RecD)
species: Escherichia coli [TaxId: 562]

Probab=98.40  E-value=2.5e-06  Score=75.24  Aligned_cols=89  Identities=22%  Similarity=0.258  Sum_probs=60.3

Q ss_pred             CCHHH-HHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCCh
Q 043110           42 LDSTL-CDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTS  120 (316)
Q Consensus        42 l~~~l-~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~  120 (316)
                      +++.. .+.+...+.-....+.|+.|+..++.++-+++.||.|+|||.... .++..+....    ...+.++++++||.
T Consensus       131 ~~~~~~~~~~~~~~~~~~~~~~Q~~A~~~al~~~~~vI~G~pGTGKTt~i~-~~l~~l~~~~----~~~~~~I~l~ApTg  205 (359)
T d1w36d1         131 VDEALLAQTLDKLFPVSDEINWQKVAAAVALTRRISVISGGPGTGKTTTVA-KLLAALIQMA----DGERCRIRLAAPTG  205 (359)
T ss_dssp             CCHHHHHHHHHTTCCCTTSCCHHHHHHHHHHTBSEEEEECCTTSTHHHHHH-HHHHHHHHTC----SSCCCCEEEEBSSH
T ss_pred             CChHHHHHHHHHhccCcccccHHHHHHHHHHcCCeEEEEcCCCCCceehHH-HHHHHHHHHH----hccCCeEEEecCcH
Confidence            44443 344433344455678999999999999899999999999998742 2333333211    12456799999999


Q ss_pred             HHHHHHHHHHHHHHh
Q 043110          121 ELCLLVYEILQKLLH  135 (316)
Q Consensus       121 ~L~~Q~~~~~~~~~~  135 (316)
                      .-+..+.+.+.....
T Consensus       206 kAA~~L~e~~~~~~~  220 (359)
T d1w36d1         206 KAAARLTESLGKALR  220 (359)
T ss_dssp             HHHHHHHHHHTHHHH
T ss_pred             HHHHHHHHHHHHHHh
Confidence            888777766655443

>d1uaaa1 c.37.1.19 (A:2-307) DEXX box DNA helicase {Escherichia coli, RepD [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: DEXX box DNA helicase
species: Escherichia coli, RepD [TaxId: 562]

Probab=97.87  E-value=1.9e-05  Score=67.33  Aligned_cols=70  Identities=20%  Similarity=0.139  Sum_probs=51.6

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLL  134 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~  134 (316)
                      +++|-|++++..  ....++|.|+.|||||.+.+--+...+.....     ..-+++++++|++++..+.+.+.++.
T Consensus         1 ~L~~eQ~~av~~--~~~~~lI~g~aGTGKTt~l~~rv~~ll~~~~~-----~~~~ILvlt~tn~a~~~i~~~~~~~~   70 (306)
T d1uaaa1           1 RLNPGQQQAVEF--VTGPCLVLAGAGSGKTRVITNKIAHLIRGCGY-----QARHIAAVTFTNKAAREMKERVGQTL   70 (306)
T ss_dssp             CCCHHHHHHHHC--CSSEEEECCCTTSCHHHHHHHHHHHHHHHHCC-----CGGGEEEEESSHHHHHHHHHHHHHHS
T ss_pred             CcCHHHHHHHhC--CCCCEEEEeeCCccHHHHHHHHHHHHHHhcCC-----ChhHEEEEeCcHHHHHHHHHHHHHhc
Confidence            478999999965  34569999999999998865544444433221     12249999999999999888876654

>d1pjra1 c.37.1.19 (A:1-318) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [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: DEXX box DNA helicase
species: Bacillus stearothermophilus, PcrA [TaxId: 1422]

Probab=97.56  E-value=0.00016  Score=61.87  Aligned_cols=71  Identities=23%  Similarity=0.176  Sum_probs=52.8

Q ss_pred             CCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           58 APTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        58 ~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      .+++-|++++..  .+..++|.|+.|||||.+.+--+.+.+.....     ..-+++++++|+..+..+...+.....
T Consensus        11 ~L~~eQ~~~v~~--~~g~~lV~g~aGSGKTt~l~~ri~~ll~~~~~-----~p~~il~lt~t~~aa~~~~~~~~~~~~   81 (318)
T d1pjra1          11 HLNKEQQEAVRT--TEGPLLIMAGAGSGKTRVLTHRIAYLMAEKHV-----APWNILAITFTNKAAREMRERVQSLLG   81 (318)
T ss_dssp             TSCHHHHHHHHC--CSSCEEEEECTTSCHHHHHHHHHHHHHHTTCC-----CGGGEEEEESSHHHHHHHHHHHHHHHG
T ss_pred             hCCHHHHHHHhC--CCCCEEEEecCCccHHHHHHHHHHHHHHcCCC-----CHHHeEeEeccHHHHHHHHHHHHhhcc
Confidence            478999999975  34579999999999999865545444433211     112599999999999999988876543

>d1a5ta2 c.37.1.20 (A:1-207) delta prime subunit of DNA polymerase III, N-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: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=96.90  E-value=0.0037  Score=49.82  Aligned_cols=40  Identities=20%  Similarity=0.248  Sum_probs=27.9

Q ss_pred             CcHHHHHHHHHHh----CCC--c-EEEEcCCCCchHHHHHHHHHHHhh
Q 043110           59 PTKVQAQAIPVIL----SGR--D-VLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        59 p~~~Q~~~i~~il----~g~--d-~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      .+|||..++..+.    +++  + +++.||.|+|||..... ++..+.
T Consensus         3 ~yPw~~~~~~~l~~~~~~~~l~h~lLl~Gp~G~GKtt~a~~-~a~~l~   49 (207)
T d1a5ta2           3 WYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYA-LSRYLL   49 (207)
T ss_dssp             CCGGGHHHHHHHHHHHHTTCCCSEEEEECCTTSCHHHHHHH-HHHHHT
T ss_pred             CCcccHHHHHHHHHHHHcCCcCeEEEEECCCCCcHHHHHHH-HHHhcc
Confidence            4578887776553    444  3 89999999999987644 444443

>d1njfa_ c.37.1.20 (A:) delta prime subunit of DNA polymerase III, N-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: Extended AAA-ATPase domain
domain: delta prime subunit of DNA polymerase III, N-domain
species: Escherichia coli [TaxId: 562]

Probab=96.80  E-value=0.02  Score=46.29  Aligned_cols=51  Identities=20%  Similarity=0.240  Sum_probs=34.1

Q ss_pred             cccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC---CcEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           32 FASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG---RDVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        32 ~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g---~d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      +...+|+++-.++++.+.|.+..                .++   +.+++.||+|+|||..+.+ +...+.
T Consensus         6 yrP~~~~dlig~~~~~~~L~~~i----------------~~~~~~~~~Ll~Gp~G~GKtt~a~~-~~~~l~   59 (239)
T d1njfa_           6 WRPQTFADVVGQEHVLTALANGL----------------SLGRIHHAYLFSGTRGVGKTSIARL-LAKGLN   59 (239)
T ss_dssp             TCCSSGGGSCSCHHHHHHHHHHH----------------HTTCCCSEEEEECSTTSSHHHHHHH-HHHHHH
T ss_pred             hCCCCHHHccChHHHHHHHHHHH----------------HcCCCCeeEEEECCCCCcHHHHHHH-HHHHhc
Confidence            34567888887888887773321                122   2389999999999987643 444443

>d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}

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: Chromosomal replication initiation factor DnaA
species: Aquifex aeolicus [TaxId: 63363]

Probab=96.65  E-value=0.0078  Score=48.09  Aligned_cols=62  Identities=18%  Similarity=0.218  Sum_probs=35.4

Q ss_pred             ceeEEEEecchhhhcC-CcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhH----HHHHHHhcCCCEEE
Q 043110          186 NLRWIIFDEADRILEL-GFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKV----NHLTKISLETPVLI  260 (316)
Q Consensus       186 ~l~~lViDEad~l~~~-~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v----~~~~~~~l~~p~~i  260 (316)
                      ..++|+||++|.+... .....+-.+++.+...              +.++++.|...|...    .++..+. ..-..+
T Consensus        97 ~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~--------------~~~iiits~~~p~~l~~~~~dL~SRL-~~g~~~  161 (213)
T d1l8qa2          97 SVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLL--------------EKQIILASDRHPQKLDGVSDRLVSRF-EGGILV  161 (213)
T ss_dssp             TCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHT--------------TCEEEEEESSCGGGCTTSCHHHHHHH-HTSEEE
T ss_pred             hccchhhhhhhhhcCchHHHHHHHHHHHHHhhc--------------cceEEEecCCcchhccccchHHHHHh-hCceEE
Confidence            5779999999998754 2444555666655431              556666555445433    2344443 334444


Q ss_pred             Ec
Q 043110          261 GL  262 (316)
Q Consensus       261 ~~  262 (316)
                      .+
T Consensus       162 ~i  163 (213)
T d1l8qa2         162 EI  163 (213)
T ss_dssp             EC
T ss_pred             EE
Confidence            44

>d1sxje2 c.37.1.20 (E:4-255) Replication factor C5 {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: Extended AAA-ATPase domain
domain: Replication factor C5
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.61  E-value=0.0012  Score=54.12  Aligned_cols=54  Identities=19%  Similarity=0.367  Sum_probs=35.5

Q ss_pred             ccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHHHHHHHHh
Q 043110           31 IFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYLAPIINHL   98 (316)
Q Consensus        31 ~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l   98 (316)
                      .+...+|+++-.++++.+.| ..+ +...           ....++++.||.|+|||.... .+++.+
T Consensus         4 ky~P~~~~diig~~~~~~~L-~~~-~~~~-----------~~~~~lll~Gp~G~GKTt~~~-~la~~l   57 (252)
T d1sxje2           4 KYRPKSLNALSHNEELTNFL-KSL-SDQP-----------RDLPHLLLYGPNGTGKKTRCM-ALLESI   57 (252)
T ss_dssp             TTCCCSGGGCCSCHHHHHHH-HTT-TTCT-----------TCCCCEEEECSTTSSHHHHHH-THHHHH
T ss_pred             ccCCCCHHHccCcHHHHHHH-HHH-HHcC-----------CCCCeEEEECCCCCCHHHHHH-HHHHhh
Confidence            34556789998889998888 332 1110           122358999999999998753 344443

>d1sxjb2 c.37.1.20 (B:7-230) Replication factor C4 {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: Extended AAA-ATPase domain
domain: Replication factor C4
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.58  E-value=0.01  Score=47.41  Aligned_cols=44  Identities=18%  Similarity=0.316  Sum_probs=29.0

Q ss_pred             cccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC--CcEEEEcCCCCchHHHHH
Q 043110           32 FASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        32 ~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g--~d~li~a~TGsGKT~~~~   91 (316)
                      +...+|+++=-++++++.|.+-                +.++  .++++.||.|+|||.++-
T Consensus         9 yrP~~~~d~ig~~~~~~~L~~~----------------~~~~~~~~~ll~Gp~G~GKTt~a~   54 (224)
T d1sxjb2           9 YRPQVLSDIVGNKETIDRLQQI----------------AKDGNMPHMIISGMPGIGKTTSVH   54 (224)
T ss_dssp             TCCSSGGGCCSCTHHHHHHHHH----------------HHSCCCCCEEEECSTTSSHHHHHH
T ss_pred             hCCCCHHHhcCCHHHHHHHHHH----------------HHcCCCCeEEEECCCCCCchhhHH
Confidence            4456677776666666666321                1223  258999999999998753

>d1sxjd2 c.37.1.20 (D:26-262) Replication factor C2 {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: Extended AAA-ATPase domain
domain: Replication factor C2
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.55  E-value=0.0072  Score=48.57  Aligned_cols=45  Identities=18%  Similarity=0.226  Sum_probs=28.2

Q ss_pred             cccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           32 FASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        32 ~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      +...+|+++--++++.+.|.+.+.-.              ...++++.||+|+|||...
T Consensus         6 y~P~~~~diig~~~~~~~l~~~i~~~--------------~~~~lll~Gp~G~GKTtl~   50 (237)
T d1sxjd2           6 YRPKNLDEVTAQDHAVTVLKKTLKSA--------------NLPHMLFYGPPGTGKTSTI   50 (237)
T ss_dssp             TCCSSTTTCCSCCTTHHHHHHHTTCT--------------TCCCEEEECSTTSSHHHHH
T ss_pred             hCCCCHHHccCcHHHHHHHHHHHHcC--------------CCCeEEEECCCCCChHHHH
Confidence            44567777765566566663322111              1135899999999999764

>d1ls1a2 c.37.1.10 (A:89-295) GTPase domain of the signal sequence recognition protein Ffh {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Thermus aquaticus [TaxId: 271]

Probab=96.47  E-value=0.0096  Score=47.31  Aligned_cols=16  Identities=25%  Similarity=0.333  Sum_probs=13.5

Q ss_pred             EEEEcCCCCchHHHHH
Q 043110           76 VLVNAATGTGKTVAYL   91 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~   91 (316)
                      +++.+|||+|||.+..
T Consensus        13 i~lvGp~GvGKTTTia   28 (207)
T d1ls1a2          13 WFLVGLQGSGKTTTAA   28 (207)
T ss_dssp             EEEECCTTTTHHHHHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5779999999998754

>d1sxjc2 c.37.1.20 (C:12-238) Replication factor C3 {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: Extended AAA-ATPase domain
domain: Replication factor C3
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=96.40  E-value=0.0027  Score=51.08  Aligned_cols=43  Identities=19%  Similarity=0.267  Sum_probs=29.5

Q ss_pred             cccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCC--CcEEEEcCCCCchHHHH
Q 043110           32 FASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSG--RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        32 ~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g--~d~li~a~TGsGKT~~~   90 (316)
                      +...+|+++--.+++++.|.+-.                .++  .++++.||+|+|||...
T Consensus         8 yrP~~~~divg~~~~~~~L~~~i----------------~~~~~~~lLl~Gp~G~GKttl~   52 (227)
T d1sxjc2           8 YRPETLDEVYGQNEVITTVRKFV----------------DEGKLPHLLFYGPPGTGKTSTI   52 (227)
T ss_dssp             TCCSSGGGCCSCHHHHHHHHHHH----------------HTTCCCCEEEECSSSSSHHHHH
T ss_pred             hCCCCHHHccCcHHHHHHHHHHH----------------HcCCCCeEEEECCCCCChhHHH
Confidence            34467788777777777773321                122  25899999999999764

>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=96.37  E-value=0.019  Score=45.14  Aligned_cols=51  Identities=18%  Similarity=0.266  Sum_probs=29.8

Q ss_pred             HHHHHHHHhC---CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCC
Q 043110           63 QAQAIPVILS---GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPT  119 (316)
Q Consensus        63 Q~~~i~~il~---g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt  119 (316)
                      |.+.+..+.+   +.++++.||.|+|||..+...+ ..+.....     ..+-++++.|.
T Consensus         2 ~~~~l~~~i~~~~~~~~l~~G~~g~gk~~~a~~l~-~~i~~~~~-----~h~D~~~i~~~   55 (198)
T d2gnoa2           2 QLETLKRIIEKSEGISILINGEDLSYPREVSLELP-EYVEKFPP-----KASDVLEIDPE   55 (198)
T ss_dssp             HHHHHHHHHHTCSSEEEEEECSSSSHHHHHHHHHH-HHHHTSCC-----CTTTEEEECCS
T ss_pred             HHHHHHHHHhcCCCceEEEECCCCCCHHHHHHHHH-HHHhcccc-----CCCCEEEEeCC
Confidence            4455555443   3469999999999998764322 33332211     12236777664

>d1t5la1 c.37.1.19 (A:2-414) 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=96.27  E-value=0.0036  Score=55.26  Aligned_cols=65  Identities=29%  Similarity=0.427  Sum_probs=47.0

Q ss_pred             CcHHHHHHHHHHh----CC-CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHH
Q 043110           59 PTKVQAQAIPVIL----SG-RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKL  133 (316)
Q Consensus        59 p~~~Q~~~i~~il----~g-~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~  133 (316)
                      |+--|=+||..+.    .| ++.++.|-||||||+.. ..++....   .        .+|||+|+..+|.|+++.++.+
T Consensus        12 p~gDQP~aI~~l~~~l~~g~~~q~l~GltGS~ka~~i-A~l~~~~~---r--------p~LVVt~n~~~A~qL~~dL~~~   79 (413)
T d1t5la1          12 PQGDQPQAIAKLVDGLRRGVKHQTLLGATGTGKTFTI-SNVIAQVN---K--------PTLVIAHNKTLAGQLYSELKEF   79 (413)
T ss_dssp             CCTTHHHHHHHHHHHHHHTCSEEEEEECTTSCHHHHH-HHHHHHHT---C--------CEEEECSSHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHhcCCCcEEEeCCCCcHHHHHH-HHHHHHhC---C--------CEEEEeCCHHHHHHHHHHHHHH
Confidence            6666666665554    34 56889999999999763 22333221   1        1999999999999999999988


Q ss_pred             Hh
Q 043110          134 LH  135 (316)
Q Consensus       134 ~~  135 (316)
                      ..
T Consensus        80 l~   81 (413)
T d1t5la1          80 FP   81 (413)
T ss_dssp             CT
T ss_pred             cC
Confidence            63

>d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon 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: Extended AAA-ATPase domain
domain: Replication factor C
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=95.91  E-value=0.061  Score=42.77  Aligned_cols=48  Identities=21%  Similarity=0.266  Sum_probs=33.0

Q ss_pred             cccccCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHHH
Q 043110           30 EIFASCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        30 ~~~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~~   91 (316)
                      +.+...+|+++-.++.+.+.|.+-+        +.      ..-.++++.||+|+|||.+.-
T Consensus        16 ~ky~P~~~~diig~~~~~~~l~~~i--------~~------~~~~~lll~Gp~G~GKTtla~   63 (231)
T d1iqpa2          16 EKYRPQRLDDIVGQEHIVKRLKHYV--------KT------GSMPHLLFAGPPGVGKTTAAL   63 (231)
T ss_dssp             HHTCCCSTTTCCSCHHHHHHHHHHH--------HH------TCCCEEEEESCTTSSHHHHHH
T ss_pred             HHhCCCCHHHccCcHHHHHHHHHHH--------Hc------CCCCeEEEECCCCCcHHHHHH
Confidence            3455568999888888887773321        10      122469999999999998753

>d1ixza_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {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: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Thermus thermophilus [TaxId: 274]

Probab=95.69  E-value=0.04  Score=44.82  Aligned_cols=52  Identities=19%  Similarity=0.266  Sum_probs=32.0

Q ss_pred             cCCcccCCCCHHHHHHHHHHcC-CCCCcHHHHHHHHHHh--CCCcEEEEcCCCCchHHHH
Q 043110           34 SCCFSSLGLDSTLCDQLRERLG-FEAPTKVQAQAIPVIL--SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g-~~~p~~~Q~~~i~~il--~g~d~li~a~TGsGKT~~~   90 (316)
                      ..+|++++-.+++++.|.+-.. +..|     +.+..+-  ..+.+++.||+|+|||+..
T Consensus         5 ~~~~~di~G~~~~k~~l~~~i~~l~~~-----~~~~~~g~~~~~giLl~GppGtGKT~la   59 (247)
T d1ixza_           5 KVTFKDVAGAEEAKEELKEIVEFLKNP-----SRFHEMGARIPKGVLLVGPPGVGKTHLA   59 (247)
T ss_dssp             SCCGGGCCSCHHHHHHHHHHHHHHHCH-----HHHHHTTCCCCSEEEEECCTTSSHHHHH
T ss_pred             CCcHHHHccHHHHHHHHHHHHHHHHCH-----HHHHHcCCCCCceEEEecCCCCChhHHH
Confidence            3579999877877777743211 1111     1122211  1245999999999999874

>d1d2na_ c.37.1.20 (A:) Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein {Chinese hamster (Cricetulus griseus) [TaxId: 10029]}

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: Hexamerization domain of N-ethylmalemide-sensitive fusion (NSF) protein
species: Chinese hamster (Cricetulus griseus) [TaxId: 10029]

Probab=95.64  E-value=0.044  Score=44.48  Aligned_cols=16  Identities=31%  Similarity=0.430  Sum_probs=14.4

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      .+++.||+|+|||...
T Consensus        42 ~vLL~GppGtGKT~la   57 (246)
T d1d2na_          42 SVLLEGPPHSGKTALA   57 (246)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECcCCCCHHHHH
Confidence            5999999999999874

>d2qy9a2 c.37.1.10 (A:285-495) GTPase domain of the signal recognition particle receptor FtsY {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: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Escherichia coli [TaxId: 562]

Probab=95.53  E-value=0.14  Score=40.27  Aligned_cols=51  Identities=22%  Similarity=0.203  Sum_probs=28.5

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEE-eCC-hHHHHHHHHHHHHHHhhcC
Q 043110           76 VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVL-VPT-SELCLLVYEILQKLLHRFR  138 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil-~Pt-~~L~~Q~~~~~~~~~~~~~  138 (316)
                      +++.+|||+|||.+..=-+ .++...        +.++.++ +-| |.=+   .++++.+++..+
T Consensus        12 i~lvGptGvGKTTTiAKLA-~~~~~~--------g~kV~lit~Dt~R~gA---~eQL~~~a~~l~   64 (211)
T d2qy9a2          12 ILMVGVNGVGKTTTIGKLA-RQFEQQ--------GKSVMLAAGDTFRAAA---VEQLQVWGQRNN   64 (211)
T ss_dssp             EEEECCTTSCHHHHHHHHH-HHHHTT--------TCCEEEECCCTTCHHH---HHHHHHHHHHTT
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHC--------CCcEEEEecccccccc---hhhhhhhhhhcC
Confidence            6679999999999854322 233221        2224444 444 3333   455666665544

>d1vmaa2 c.37.1.10 (A:82-294) GTPase domain of the signal recognition particle receptor FtsY {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: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermotoga maritima [TaxId: 2336]

Probab=95.48  E-value=0.16  Score=40.06  Aligned_cols=85  Identities=18%  Similarity=0.149  Sum_probs=42.7

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHH
Q 043110           76 VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK  155 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (316)
                      +++.+|||+|||.+..=-+ .++....       ...+||-+.|.-.+.  .++++.++...+.. ......+.+.....
T Consensus        14 i~lvGptGvGKTTTiAKLA-a~~~~~~-------~kV~lit~Dt~R~gA--~eQL~~~a~~l~i~-~~~~~~~~d~~~~~   82 (213)
T d1vmaa2          14 IMVVGVNGTGKTTSCGKLA-KMFVDEG-------KSVVLAAADTFRAAA--IEQLKIWGERVGAT-VISHSEGADPAAVA   82 (213)
T ss_dssp             EEEECCTTSSHHHHHHHHH-HHHHHTT-------CCEEEEEECTTCHHH--HHHHHHHHHHHTCE-EECCSTTCCHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHH-HHHHHCC-------CceEEEeecccccch--hHHHHHHhhhcCcc-ccccCCCCcHHHHH
Confidence            6789999999999854322 3333311       123555565433222  34556655554422 22222333332211


Q ss_pred             -----HHHhcCCc-EEEeCcHH
Q 043110          156 -----ARLRKGIS-ILVATPGH  171 (316)
Q Consensus       156 -----~~l~~~~~-IlV~Tp~~  171 (316)
                           ....++++ |+|=|+|+
T Consensus        83 ~~~~~~~~~~~~d~ilIDTaGr  104 (213)
T d1vmaa2          83 FDAVAHALARNKDVVIIDTAGR  104 (213)
T ss_dssp             HHHHHHHHHTTCSEEEEEECCC
T ss_pred             HHHHHHHHHcCCCEEEEecccc
Confidence                 11223444 88999984

>d1okkd2 c.37.1.10 (D:97-303) GTPase domain of the signal recognition particle receptor FtsY {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal recognition particle receptor FtsY
species: Thermus aquaticus [TaxId: 271]

Probab=95.30  E-value=0.044  Score=43.28  Aligned_cols=19  Identities=47%  Similarity=0.627  Sum_probs=15.4

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 043110           73 GRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~   91 (316)
                      ++-+++.+|||+|||.+..
T Consensus         6 ~~vi~lvGptGvGKTTTia   24 (207)
T d1okkd2           6 GRVVLVVGVNGVGKTTTIA   24 (207)
T ss_dssp             SSEEEEECSTTSSHHHHHH
T ss_pred             CEEEEEECCCCCCHHHHHH
Confidence            3457889999999999854

>d1j8yf2 c.37.1.10 (F:87-297) GTPase domain of the signal sequence recognition protein Ffh {Archaeon Acidianus ambivalens [TaxId: 2283]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nitrogenase iron protein-like
domain: GTPase domain of the signal sequence recognition protein Ffh
species: Archaeon Acidianus ambivalens [TaxId: 2283]

Probab=94.46  E-value=0.092  Score=41.45  Aligned_cols=16  Identities=25%  Similarity=0.409  Sum_probs=9.6

Q ss_pred             EEEEcCCCCchHHHHH
Q 043110           76 VLVNAATGTGKTVAYL   91 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~   91 (316)
                      +++.+|||+|||.+..
T Consensus        15 i~lvGptGvGKTTTiA   30 (211)
T d1j8yf2          15 IMLVGVQGTGKATTAG   30 (211)
T ss_dssp             EEEECSCCC----HHH
T ss_pred             EEEECCCCCCHHHHHH
Confidence            5678999999998853

>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=94.19  E-value=0.099  Score=41.12  Aligned_cols=93  Identities=16%  Similarity=0.109  Sum_probs=64.3

Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHH---HHHh-cCCcEEEeCcHHHHHHHhcCCccccC
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK---ARLR-KGISILVATPGHLLDHLKHTSSFLHT  185 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~l~-~~~~IlV~Tp~~l~~~l~~~~~~~~~  185 (316)
                      |.++.||+|..+-....++.++++.   +...+.+++|.....+..   ..+. ...+|+|||.-     +.  ..++..
T Consensus        31 GgQvy~V~p~I~~~e~~~~~l~~~~---p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Ttv-----IE--vGiDvp  100 (211)
T d2eyqa5          31 GGQVYYLYNDVENIQKAAERLAELV---PEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTTI-----IE--TGIDIP  100 (211)
T ss_dssp             TCEEEEECCCSSCHHHHHHHHHHHC---TTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESST-----TG--GGSCCT
T ss_pred             CCeEEEEEcCccchhhHHHHHHHhC---CceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEehh-----hh--hccCCC
Confidence            7779999999988888777776654   556777788776654432   2333 34899999951     22  456778


Q ss_pred             ceeEEEEecchhhhcCCcHHHHHHHHHHhcc
Q 043110          186 NLRWIIFDEADRILELGFGKEIEEILDILGS  216 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~~~~~i~~i~~~l~~  216 (316)
                      +..++||..||++    -..++..+..+...
T Consensus       101 nA~~iiI~~a~rf----GLaQLhQLRGRVGR  127 (211)
T d2eyqa5         101 TANTIIIERADHF----GLAQLHQLRGRVGR  127 (211)
T ss_dssp             TEEEEEETTTTSS----CHHHHHHHHTTCCB
T ss_pred             CCcEEEEecchhc----cccccccccceeee
Confidence            9999999999984    23455555554443

>d2b8ta1 c.37.1.24 (A:11-149) Thymidine kinase, TK1, N-terminal domain {Ureaplasma urealyticum [TaxId: 2130]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Ureaplasma urealyticum [TaxId: 2130]

Probab=93.71  E-value=0.29  Score=35.69  Aligned_cols=87  Identities=20%  Similarity=0.208  Sum_probs=50.5

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHH
Q 043110           76 VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEK  155 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  155 (316)
                      -++.||..||||.-.+ -.+++...        .+.+++++-|...-            ++...+.   ...|..     
T Consensus         5 ~~i~GpMfsGKTteLi-~~~~~~~~--------~~~kv~~ikp~~D~------------R~~~~i~---s~~g~~-----   55 (139)
T d2b8ta1           5 EFITGPMFAGKTAELI-RRLHRLEY--------ADVKYLVFKPKIDT------------RSIRNIQ---SRTGTS-----   55 (139)
T ss_dssp             EEEECSTTSCHHHHHH-HHHHHHHH--------TTCCEEEEEECCCG------------GGCSSCC---CCCCCS-----
T ss_pred             EEEEccccCHHHHHHH-HHHHHHHH--------CCCcEEEEEEcccc------------cccceEE---cccCce-----
Confidence            4788999999997643 33343333        13449999998552            0111111   111211     


Q ss_pred             HHHhcCCcEEEeCcHHHHHHHhcCCccccCceeEEEEecchhh
Q 043110          156 ARLRKGISILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADRI  198 (316)
Q Consensus       156 ~~l~~~~~IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~l  198 (316)
                           -..+.+.....+.+.+.....  ..+.+++.||||+-+
T Consensus        56 -----~~~~~~~~~~~~~~~~~~~~~--~~~~dvI~IDE~QFf   91 (139)
T d2b8ta1          56 -----LPSVEVESAPEILNYIMSNSF--NDETKVIGIDEVQFF   91 (139)
T ss_dssp             -----SCCEEESSTHHHHHHHHSTTS--CTTCCEEEECSGGGS
T ss_pred             -----eeeEEeccchhhHHHHHhhcc--ccCcCEEEechhhhc
Confidence                 124666666666666654222  247889999999975

>d1g6oa_ c.37.1.11 (A:) Hexameric traffic ATPase, HP0525 {Helicobacter pylori [TaxId: 210]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Hexameric traffic ATPase, HP0525
species: Helicobacter pylori [TaxId: 210]

Probab=93.68  E-value=0.016  Score=49.26  Aligned_cols=54  Identities=28%  Similarity=0.437  Sum_probs=35.0

Q ss_pred             cHHHHHHHHH-HhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           60 TKVQAQAIPV-ILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        60 ~~~Q~~~i~~-il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      .+-+...+.. +..+++++++|+||||||.. +-+++..+    +     ..-+++.+-.+.||.
T Consensus       152 ~~~~~~~l~~~v~~~~nili~G~tgSGKTT~-l~al~~~i----~-----~~~rivtiEd~~El~  206 (323)
T d1g6oa_         152 KEQAISAIKDGIAIGKNVIVCGGTGSGKTTY-IKSIMEFI----P-----KEERIISIEDTEEIV  206 (323)
T ss_dssp             HHHHHHHHHHHHHHTCCEEEEESTTSSHHHH-HHHHGGGS----C-----TTCCEEEEESSCCCC
T ss_pred             HHHHHHHHHHHHHhCCCEEEEeeccccchHH-HHHHhhhc----c-----cccceeeccchhhhh
Confidence            3444444433 45778999999999999975 23333322    1     234488888888873

>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=93.53  E-value=1.1  Score=33.81  Aligned_cols=116  Identities=19%  Similarity=0.214  Sum_probs=73.8

Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHH---h-cCCcEEEeCcHHHHHHHhcCCccccC
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARL---R-KGISILVATPGHLLDHLKHTSSFLHT  185 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~-~~~~IlV~Tp~~l~~~l~~~~~~~~~  185 (316)
                      +-++||.|+|+.-|+.+.+.+...     .+....++|+....+....+   . ...+|||+|.-     +  ..+++..
T Consensus        31 g~r~lvfc~t~~~~~~l~~~L~~~-----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~v-----~--~~GiDip   98 (174)
T d1c4oa2          31 GERTLVTVLTVRMAEELTSFLVEH-----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINL-----L--REGLDIP   98 (174)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCC-----C--CTTCCCT
T ss_pred             CCcEEEEEcchhHHHHHHHHHHhc-----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeeee-----e--eeeccCC
Confidence            556999999999999988888764     36677888887765544333   3 34799999941     1  2567788


Q ss_pred             ceeEEEEecchhhhcCCcHHHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHH
Q 043110          186 NLRWIIFDEADRILELGFGKEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLT  250 (316)
Q Consensus       186 ~l~~lViDEad~l~~~~~~~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~  250 (316)
                      +++++|+=.++..   ++......++......          ....+...+++.....+.+.+++
T Consensus        99 ~V~~Vi~~~~~~~---~~~~~~~~~iq~~GR~----------gR~~~g~~~~~~~~~~~~~~~~i  150 (174)
T d1c4oa2          99 EVSLVAILDADKE---GFLRSERSLIQTIGRA----------ARNARGEVWLYADRVSEAMQRAI  150 (174)
T ss_dssp             TEEEEEETTTTSC---SGGGSHHHHHHHHGGG----------TTSTTCEEEEECSSCCHHHHHHH
T ss_pred             CCcEEEEeccccc---cccchhHHHHHHhhhh----------hhcCCCeeEEeecCCCHHHHHHH
Confidence            9999998777652   2333344445554431          11123455666555555555544

>d1c4oa1 c.37.1.19 (A:2-409) 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=93.37  E-value=0.078  Score=46.35  Aligned_cols=66  Identities=36%  Similarity=0.443  Sum_probs=45.1

Q ss_pred             CCcHHHHHHHHHH----hCCCc-EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHHHHHHHHHHH
Q 043110           58 APTKVQAQAIPVI----LSGRD-VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELCLLVYEILQK  132 (316)
Q Consensus        58 ~p~~~Q~~~i~~i----l~g~d-~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~~Q~~~~~~~  132 (316)
                      .|+.-|-+||..+    ..|+. ..+.+-+||+|++.. ..+.+...+           -+|||+|+...|.++++.+..
T Consensus         8 ~p~~dqp~aI~~l~~~L~~g~~~~~L~GlsgS~ka~~~-A~l~~~~~r-----------p~LvVt~~~~~A~~l~~dL~~   75 (408)
T d1c4oa1           8 SPKGDQPKAIAGLVEALRDGERFVTLLGATGTGKTVTM-AKVIEALGR-----------PALVLAPNKILAAQLAAEFRE   75 (408)
T ss_dssp             CCCTTHHHHHHHHHHHHHTTCSEEEEEECTTSCHHHHH-HHHHHHHTC-----------CEEEEESSHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHhcCCCcEEEecCCCCHHHHHH-HHHHHHhCC-----------CEEEEeCCHHHHHHHHHHHHH
Confidence            3444555555544    35554 688999999999652 122222211           189999999999999999998


Q ss_pred             HHh
Q 043110          133 LLH  135 (316)
Q Consensus       133 ~~~  135 (316)
                      ++.
T Consensus        76 ~l~   78 (408)
T d1c4oa1          76 LFP   78 (408)
T ss_dssp             HCT
T ss_pred             hcC
Confidence            864

>d1g5ta_ c.37.1.11 (A:) ATP:corrinoid adenosyltransferase CobA {Salmonella typhimurium [TaxId: 90371]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: ATP:corrinoid adenosyltransferase CobA
species: Salmonella typhimurium [TaxId: 90371]

Probab=93.16  E-value=0.086  Score=39.51  Aligned_cols=52  Identities=12%  Similarity=0.220  Sum_probs=37.6

Q ss_pred             CceeEEEEecchhhhcCCcH--HHHHHHHHHhccCcccccCCCCccccccceEEEEeeecchhHHHHHH
Q 043110          185 TNLRWIIFDEADRILELGFG--KEIEEILDILGSRNIASIGEGNEVSNVKRQNLLLSATLNEKVNHLTK  251 (316)
Q Consensus       185 ~~l~~lViDEad~l~~~~~~--~~i~~i~~~l~~~~~~~~~~~~~~~~~~~q~i~~SAT~~~~v~~~~~  251 (316)
                      ...++||+||+-..++.++-  +++..+++..|.               ..-+|+.--..|+++.+.+.
T Consensus        93 ~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~---------------~~evVlTGr~~p~~L~e~AD  146 (157)
T d1g5ta_          93 PLLDMVVLDELTYMVAYDYLPLEEVISALNARPG---------------HQTVIITGRGCHRDILDLAD  146 (157)
T ss_dssp             TTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCT---------------TCEEEEECSSCCHHHHHHCS
T ss_pred             CccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCC---------------CCEEEEECCCCCHHHHHhcc
Confidence            45789999999999988753  556566655444               66777777778887777654

>d1w36b1 c.37.1.19 (B:1-485) Exodeoxyribonuclease V beta chain (RecB), N-terminal 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: Exodeoxyribonuclease V beta chain (RecB), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=92.89  E-value=0.18  Score=44.14  Aligned_cols=63  Identities=21%  Similarity=0.169  Sum_probs=42.0

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCC---eeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSG---TFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~---~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      ...++|.|..|||||.+.+-=++..+...........+   -.+|+|+=|+.-|.++.+++...+.
T Consensus        16 ~g~~lv~A~AGsGKT~~l~~r~~~ll~~~~~~~~~~~~~~~~~IL~lTFT~kAA~Emk~RI~~~L~   81 (485)
T d1w36b1          16 QGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPLTVEELLVVTFTEAATAELRGRIRSNIH   81 (485)
T ss_dssp             SSCEEEECCTTSCHHHHHHHHHHHHHTTCSSSSSCSSCCCGGGEEEEESCHHHHHHHHHHHHHHHH
T ss_pred             CCCeEEEEcCchHHHHHHHHHHHHHHhhCcccccccCCCCcccEeEeccHHHHHHHHHHHHHHHHH
Confidence            34689999999999988665566655442221111111   2399999999988888877655543

>d1w5sa2 c.37.1.20 (A:7-293) CDC6-like protein APE0152, N-terminal domain {Aeropyrum pernix [TaxId: 56636]}

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: CDC6-like protein APE0152, N-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=92.40  E-value=0.08  Score=42.92  Aligned_cols=15  Identities=27%  Similarity=0.124  Sum_probs=12.5

Q ss_pred             EEEEcCCCCchHHHH
Q 043110           76 VLVNAATGTGKTVAY   90 (316)
Q Consensus        76 ~li~a~TGsGKT~~~   90 (316)
                      +++.||+|+|||.+.
T Consensus        49 l~l~GppGtGKT~l~   63 (287)
T d1w5sa2          49 YGSIGRVGIGKTTLA   63 (287)
T ss_dssp             EECTTCCSSSHHHHH
T ss_pred             EEeECCCCCCHHHHH
Confidence            456799999999875

>d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}

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: ClpX
species: Helicobacter pylori [TaxId: 210]

Probab=92.39  E-value=0.076  Score=45.70  Aligned_cols=17  Identities=35%  Similarity=0.602  Sum_probs=15.3

Q ss_pred             CcEEEEcCCCCchHHHH
Q 043110           74 RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~   90 (316)
                      .++++.||||+|||..+
T Consensus        69 ~niLfiGPTGvGKTElA   85 (364)
T d1um8a_          69 SNILLIGPTGSGKTLMA   85 (364)
T ss_dssp             CCEEEECCTTSSHHHHH
T ss_pred             cceeeeCCCCccHHHHH
Confidence            57999999999999875

>d1tf7a2 c.37.1.11 (A:256-497) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=92.11  E-value=0.69  Score=36.28  Aligned_cols=38  Identities=26%  Similarity=0.245  Sum_probs=24.7

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCC
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPT  119 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt  119 (316)
                      |.-+++.+++|+|||...+--+.+.+..         +..+++++-.
T Consensus        26 gsl~li~G~pGsGKT~l~~qia~~~~~~---------~~~~~~is~e   63 (242)
T d1tf7a2          26 DSIILATGATGTGKTLLVSRFVENACAN---------KERAILFAYE   63 (242)
T ss_dssp             SCEEEEEECTTSSHHHHHHHHHHHHHTT---------TCCEEEEESS
T ss_pred             CeEEEEEeCCCCCHHHHHHHHHHHHHHh---------ccccceeecc
Confidence            4569999999999998754433333322         3337777643

>d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {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: RecA protein-like (ATPase-domain)
domain: Bacterial conjugative coupling protein TrwB
species: Escherichia coli [TaxId: 562]

Probab=91.78  E-value=0.072  Score=46.58  Aligned_cols=28  Identities=39%  Similarity=0.438  Sum_probs=20.3

Q ss_pred             hCCCcEEEEcCCCCchHHHHHHHHHHHhh
Q 043110           71 LSGRDVLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        71 l~g~d~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      ...+++++.|+||+|||.+. ..++..+.
T Consensus        48 ~~~~H~~I~G~tGsGKT~~l-~~li~~~~   75 (433)
T d1e9ra_          48 AEPRHLLVNGATGTGKSVLL-RELAYTGL   75 (433)
T ss_dssp             GGGGCEEEEECTTSSHHHHH-HHHHHHHH
T ss_pred             cccceEEEEeCCCCcHHHHH-HHHHHHHH
Confidence            45578999999999999874 33444433

>d2i3ba1 c.37.1.11 (A:1-189) Cancer-related NTPase, C1orf57 {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: RecA protein-like (ATPase-domain)
domain: Cancer-related NTPase, C1orf57
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.63  E-value=0.13  Score=38.46  Aligned_cols=26  Identities=31%  Similarity=0.428  Sum_probs=19.9

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      |++++.||+|+|||... -.++..+..
T Consensus         2 k~v~ItG~~GtGKTtl~-~~i~~~l~~   27 (189)
T d2i3ba1           2 RHVFLTGPPGVGKTTLI-HKASEVLKS   27 (189)
T ss_dssp             CCEEEESCCSSCHHHHH-HHHHHHHHH
T ss_pred             cEEEEECCCCCcHHHHH-HHHHHHHHH
Confidence            68999999999999853 445555554

>d1in4a2 c.37.1.20 (A:17-254) Holliday junction helicase RuvB {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: Holliday junction helicase RuvB
species: Thermotoga maritima [TaxId: 2336]

Probab=91.25  E-value=0.19  Score=39.88  Aligned_cols=48  Identities=21%  Similarity=0.085  Sum_probs=29.5

Q ss_pred             cCCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           34 SCCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      ..+|+++--.+.+++.|..-.        +. ....-....++++.||+|+|||..+
T Consensus         5 P~~~~divGqe~~~~~l~~~i--------~~-~~~~~~~~~~~L~~GPpGtGKT~lA   52 (238)
T d1in4a2           5 PKSLDEFIGQENVKKKLSLAL--------EA-AKMRGEVLDHVLLAGPPGLGKTTLA   52 (238)
T ss_dssp             CSSGGGCCSCHHHHHHHHHHH--------HH-HHHHTCCCCCEEEESSTTSSHHHHH
T ss_pred             CCcHHHcCChHHHHHHHHHHH--------HH-HHhcCCCCCeEEEECCCCCcHHHHH
Confidence            347888877777777663211        10 0000001247999999999999875

>d1g41a_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

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: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=91.21  E-value=0.048  Score=48.34  Aligned_cols=18  Identities=33%  Similarity=0.492  Sum_probs=15.9

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      .+|+++.+|||+|||+.+
T Consensus        49 ksNILliGPTGvGKTlLA   66 (443)
T d1g41a_          49 PKNILMIGPTGVGKTEIA   66 (443)
T ss_dssp             CCCEEEECCTTSSHHHHH
T ss_pred             cccEEEECCCCCCHHHHH
Confidence            468999999999999864

>d1ofha_ c.37.1.20 (A:) HslU {Haemophilus influenzae [TaxId: 727]}

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: HslU
species: Haemophilus influenzae [TaxId: 727]

Probab=91.18  E-value=0.12  Score=43.17  Aligned_cols=19  Identities=32%  Similarity=0.492  Sum_probs=16.6

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      ..+.+++.||||+|||+.+
T Consensus        48 ~~~~iLl~GPpG~GKT~lA   66 (309)
T d1ofha_          48 TPKNILMIGPTGVGKTEIA   66 (309)
T ss_dssp             CCCCEEEECCTTSSHHHHH
T ss_pred             CCceEEEECCCCCCHHHHH
Confidence            3578999999999999875

>d1p9ra_ c.37.1.11 (A:) Extracellular secretion NTPase EpsE {Vibrio cholerae [TaxId: 666]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Extracellular secretion NTPase EpsE
species: Vibrio cholerae [TaxId: 666]

Probab=91.13  E-value=0.12  Score=45.05  Aligned_cols=38  Identities=18%  Similarity=0.325  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHhCCCc--EEEEcCCCCchHHHHHHHHHHHhh
Q 043110           61 KVQAQAIPVILSGRD--VLVNAATGTGKTVAYLAPIINHLQ   99 (316)
Q Consensus        61 ~~Q~~~i~~il~g~d--~li~a~TGsGKT~~~~lp~l~~l~   99 (316)
                      +.|.+.+..++....  +++.||||||||.+. ..++..+.
T Consensus       144 ~~~~~~l~~l~~~~~GliLvtGpTGSGKSTTl-~~~l~~~~  183 (401)
T d1p9ra_         144 AHNHDNFRRLIKRPHGIILVTGPTGSGKSTTL-YAGLQELN  183 (401)
T ss_dssp             HHHHHHHHHHHTSSSEEEEEECSTTSCHHHHH-HHHHHHHC
T ss_pred             HHHHHHHHHHHhhhhceEEEEcCCCCCccHHH-HHHhhhhc
Confidence            455555555554443  899999999999874 44566553

>d1xbta1 c.37.1.24 (A:18-150) Thymidine kinase, TK1, N-terminal domain {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: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.03  E-value=0.49  Score=34.06  Aligned_cols=37  Identities=16%  Similarity=0.176  Sum_probs=24.4

Q ss_pred             EEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           76 VLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        76 ~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      -++.||..||||.- ++-.+.....        .+.+++++-|...
T Consensus         5 ~li~GpMfsGKTt~-Li~~~~~~~~--------~g~~v~~ikp~~D   41 (133)
T d1xbta1           5 QVILGPMFSGKSTE-LMRRVRRFQI--------AQYKCLVIKYAKD   41 (133)
T ss_dssp             EEEECCTTSCHHHH-HHHHHHHHHT--------TTCCEEEEEETTC
T ss_pred             EEEEecccCHHHHH-HHHHHHHHHH--------cCCcEEEEecccc
Confidence            57889999999975 3434443332        1344888888744

>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=90.72  E-value=0.76  Score=34.90  Aligned_cols=76  Identities=14%  Similarity=0.105  Sum_probs=55.7

Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHH---h-cCCcEEEeCcHHHHHHHhcCCccccC
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARL---R-KGISILVATPGHLLDHLKHTSSFLHT  185 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~-~~~~IlV~Tp~~l~~~l~~~~~~~~~  185 (316)
                      +.++||.+++++-++.++..++..     ...+..++|+.+.......+   . ...+|||||.-       -..+++..
T Consensus        31 ~~~~iif~~~~~~~~~~~~~l~~~-----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv-------~~rGiDip   98 (181)
T d1t5la2          31 NERTLVTTLTKKMAEDLTDYLKEA-----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINL-------LREGLDIP   98 (181)
T ss_dssp             TCEEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCC-------CSSSCCCT
T ss_pred             CCeEEEEeehhhhhHHHHHHHHhC-----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhH-------HHccCCCC
Confidence            446999999999998888777653     35667788887765544333   3 35899999941       12567788


Q ss_pred             ceeEEEEecchh
Q 043110          186 NLRWIIFDEADR  197 (316)
Q Consensus       186 ~l~~lViDEad~  197 (316)
                      +++++|.-++..
T Consensus        99 ~v~~VI~~d~p~  110 (181)
T d1t5la2          99 EVSLVAILDADK  110 (181)
T ss_dssp             TEEEEEETTTTS
T ss_pred             CCCEEEEecCCc
Confidence            999999988875

>d1xx6a1 c.37.1.24 (A:2-142) Thymidine kinase, TK1, N-terminal domain {Clostridium acetobutylicum [TaxId: 1488]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Type II thymidine kinase
domain: Thymidine kinase, TK1, N-terminal domain
species: Clostridium acetobutylicum [TaxId: 1488]

Probab=90.15  E-value=0.73  Score=33.50  Aligned_cols=40  Identities=15%  Similarity=0.133  Sum_probs=25.5

Q ss_pred             CCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChH
Q 043110           73 GRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSE  121 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~  121 (316)
                      |.=-++.||..||||.-. +-.+.+...        .+.+++++-|...
T Consensus         7 G~l~lI~GpMfSGKTteL-i~~~~~~~~--------~g~~vl~i~~~~D   46 (141)
T d1xx6a1           7 GWVEVIVGPMYSGKSEEL-IRRIRRAKI--------AKQKIQVFKPEID   46 (141)
T ss_dssp             CEEEEEECSTTSSHHHHH-HHHHHHHHH--------TTCCEEEEEEC--
T ss_pred             eeEEEEEeccccHHHHHH-HHHHHHhhh--------cCCcEEEEEeccc
Confidence            343578999999999764 334444333        2344999999854

>d1qvra2 c.37.1.20 (A:149-535) ClpB, AAA+ modules {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: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Thermus thermophilus [TaxId: 274]

Probab=89.45  E-value=0.85  Score=39.14  Aligned_cols=35  Identities=17%  Similarity=0.321  Sum_probs=21.8

Q ss_pred             HHHHHHh-CC-CcEEEEcCCCCchHHHHHHHHHHHhhh
Q 043110           65 QAIPVIL-SG-RDVLVNAATGTGKTVAYLAPIINHLQS  100 (316)
Q Consensus        65 ~~i~~il-~g-~d~li~a~TGsGKT~~~~lp~l~~l~~  100 (316)
                      +.+..+. .+ .|.++.|+.|.|||...- .+.+.+..
T Consensus        33 ~~~~~L~r~~k~n~llvG~~GvGKtaiv~-~la~~i~~   69 (387)
T d1qvra2          33 RVIQILLRRTKNNPVLIGEPGVGKTAIVE-GLAQRIVK   69 (387)
T ss_dssp             HHHHHHHCSSCCCCEEEECTTSCHHHHHH-HHHHHHHH
T ss_pred             HHHHHHhcCCCCCCeEECCCCCCHHHHHH-HHHHHHHh
Confidence            3344444 33 369999999999997643 33444444

>d1mo6a1 c.37.1.11 (A:1-269) RecA protein, ATPase-domain {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: RecA protein-like (ATPase-domain)
domain: RecA protein, ATPase-domain
species: Mycobacterium tuberculosis [TaxId: 1773]

Probab=88.89  E-value=0.22  Score=40.70  Aligned_cols=43  Identities=23%  Similarity=0.302  Sum_probs=29.4

Q ss_pred             CCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC  123 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~  123 (316)
                      .|+=+.+.++.|+|||...+..+.+....         +..++|+---..+.
T Consensus        59 ~g~i~e~~G~~~~GKT~l~l~~~~~~q~~---------g~~~vyIDtE~~~~  101 (269)
T d1mo6a1          59 RGRVIEIYGPESSGKTTVALHAVANAQAA---------GGVAAFIDAEHALD  101 (269)
T ss_dssp             SSSEEEEECSSSSSHHHHHHHHHHHHHHT---------TCEEEEEESSCCCC
T ss_pred             cceeEEEecCCCcHHHHHHHHHHHHHhcC---------CCEEEEEECCccCC
Confidence            35668999999999998876655544332         45577776544444

>d1jbka_ c.37.1.20 (A:) ClpB, AAA+ modules {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: Extended AAA-ATPase domain
domain: ClpB, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=88.69  E-value=3.1  Score=31.71  Aligned_cols=119  Identities=14%  Similarity=0.199  Sum_probs=60.3

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCChHHH------HHHHHHHHHHHhhc----CCcee-
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPTSELC------LLVYEILQKLLHRF----RWIVP-  142 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt~~L~------~Q~~~~~~~~~~~~----~~~~~-  142 (316)
                      .|+++.++.|.|||...- -+.+.+....-. ..-.+. -++-+....|.      .|+.+.++.+....    +.... 
T Consensus        44 ~n~lLvG~pGVGKTalv~-~LA~ri~~~~vp-~~L~~~-~i~~ld~~~LiAg~~~rG~~E~rl~~il~e~~~~~~~iILf  120 (195)
T d1jbka_          44 NNPVLIGEPGVGKTAIVE-GLAQRIINGEVP-EGLKGR-RVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVILF  120 (195)
T ss_dssp             CEEEEECCTTSCHHHHHH-HHHHHHHHTCSC-GGGTTC-EEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEEEE
T ss_pred             CCeEEEecCCcccHHHHH-HHHHHHHhCCCC-HHHcCc-eEEEeeHHHHhccCCccHHHHHHHHHHHHHHhcCCCcEEEE
Confidence            379999999999997653 334444432211 111123 35544444443      25555555544322    11110 


Q ss_pred             ----------EEeeCCCChHHH-HHHHhcC-Cc-EEEeCcHHHHHHHhcCCccccCceeEEEEecch
Q 043110          143 ----------GYVMGGGNRSKE-KARLRKG-IS-ILVATPGHLLDHLKHTSSFLHTNLRWIIFDEAD  196 (316)
Q Consensus       143 ----------~~~~~~~~~~~~-~~~l~~~-~~-IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad  196 (316)
                                +...|+.+..+. ...+..+ .. |.-+||+.+..++..... ....+..+-++|-+
T Consensus       121 IDeih~l~~~g~~~g~~d~~~~Lkp~L~rg~l~~IgatT~eey~~~~e~d~a-L~rrF~~I~V~Ep~  186 (195)
T d1jbka_         121 IDELHTMVGAGKADGAMDAGNMLKPALARGELHCVGATTLDEYRQYIEKDAA-LERRFQKVFVAEPS  186 (195)
T ss_dssp             EETGGGGTT------CCCCHHHHHHHHHTTSCCEEEEECHHHHHHHTTTCHH-HHTTEEEEECCCCC
T ss_pred             cchHHHHhcCCCCCCcccHHHHHHHHHhCCCceEEecCCHHHHHHHHHcCHH-HHhcCCEeecCCCC
Confidence                      001112222222 2223333 33 557888988888776333 33678889898875

>d1lv7a_ c.37.1.20 (A:) AAA domain of cell division protein FtsH {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: Extended AAA-ATPase domain
domain: AAA domain of cell division protein FtsH
species: Escherichia coli [TaxId: 562]

Probab=88.25  E-value=0.086  Score=42.97  Aligned_cols=54  Identities=20%  Similarity=0.265  Sum_probs=32.3

Q ss_pred             cCCcccCCCCHHHHHHHHHHcC-CCCCcHHHHHHHHHHhCCCcEEEEcCCCCchHHHH
Q 043110           34 SCCFSSLGLDSTLCDQLRERLG-FEAPTKVQAQAIPVILSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        34 ~~~f~~~~l~~~l~~~l~~~~g-~~~p~~~Q~~~i~~il~g~d~li~a~TGsGKT~~~   90 (316)
                      ..+|+|.+-.+.+.+.|.+... +..|..+|...   +-..+.+++.||+|+|||+..
T Consensus         8 ~~t~~Di~Gl~~~k~~l~e~v~~~~~~~~~~~~g---~~~~~~iLL~GppGtGKT~la   62 (256)
T d1lv7a_           8 KTTFADVAGCDEAKEEVAELVEYLREPSRFQKLG---GKIPKGVLMVGPPGTGKTLLA   62 (256)
T ss_dssp             CCCGGGSCSCHHHHHHTHHHHHHHHCGGGC--------CCCCEEEEECCTTSCHHHHH
T ss_pred             CCCHHHHhchHHHHHHHHHHHHHHHCHHHHHHcC---CCCCCeEEeeCCCCCCccHHH
Confidence            4579999888887777733211 12222222211   112356999999999999874

>d1bg2a_ c.37.1.9 (A:) Kinesin {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: Motor proteins
domain: Kinesin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.10  E-value=0.17  Score=42.48  Aligned_cols=25  Identities=24%  Similarity=0.432  Sum_probs=21.1

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .++.+++|.+  +++.|+||||||...
T Consensus        67 lv~~~l~G~n~~i~aYGqtgSGKTyT~   93 (323)
T d1bg2a_          67 IVKDVLEGYNGTIFAYGQTSSGKTHTM   93 (323)
T ss_dssp             HHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHcCCCcceeeecccCCCCceec
Confidence            3566779987  899999999999884

>d1kaga_ c.37.1.2 (A:) Shikimate kinase (AroK) {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: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Escherichia coli [TaxId: 562]

Probab=87.90  E-value=0.19  Score=36.68  Aligned_cols=19  Identities=21%  Similarity=0.391  Sum_probs=16.2

Q ss_pred             CCcEEEEcCCCCchHHHHH
Q 043110           73 GRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~~   91 (316)
                      .|++++.|++|+|||...-
T Consensus         2 ~k~I~l~G~~GsGKSTvak   20 (169)
T d1kaga_           2 KRNIFLVGPMGAGKSTIGR   20 (169)
T ss_dssp             CCCEEEECCTTSCHHHHHH
T ss_pred             CCeEEEECCCCCCHHHHHH
Confidence            4689999999999998753

>d1sxja2 c.37.1.20 (A:295-547) Replication factor C1 {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: Extended AAA-ATPase domain
domain: Replication factor C1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=87.80  E-value=0.036  Score=44.75  Aligned_cols=56  Identities=16%  Similarity=0.119  Sum_probs=33.3

Q ss_pred             cccCCcccCCCCHHHHHHHHHHcCCCCCcHHH-HHHHHHH-----hCCCcEEEEcCCCCchHHHH
Q 043110           32 FASCCFSSLGLDSTLCDQLRERLGFEAPTKVQ-AQAIPVI-----LSGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        32 ~~~~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q-~~~i~~i-----l~g~d~li~a~TGsGKT~~~   90 (316)
                      +...+|+++...+..++.|.+-+.-   .... ...++..     ...+.+++.||+|+|||.+.
T Consensus         8 y~P~~~~dlig~~~~~~~L~~~l~~---~~~~~~~~~~~~~~~~~~~~~~lll~GPpG~GKTt~a   69 (253)
T d1sxja2           8 YAPTNLQQVCGNKGSVMKLKNWLAN---WENSKKNSFKHAGKDGSGVFRAAMLYGPPGIGKTTAA   69 (253)
T ss_dssp             TCCSSGGGCCSCHHHHHHHHHHHHT---HHHHHHTTTCCCCTTSTTSCSEEEEECSTTSSHHHHH
T ss_pred             cCCCCHHHhcCCHHHHHHHHHHHHh---hhhcchhhhhhhcccCCCCCceEEEECCCCCCHHHHH
Confidence            4556799999999988877432100   0000 0000000     01246999999999999875

>d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

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: CDC6, N-domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=86.97  E-value=0.2  Score=40.14  Aligned_cols=24  Identities=25%  Similarity=0.266  Sum_probs=17.9

Q ss_pred             CcEEEEcCCCCchHHHHHHHHHHHh
Q 043110           74 RDVLVNAATGTGKTVAYLAPIINHL   98 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~~lp~l~~l   98 (316)
                      .++++.||+|+|||.+.- .+...+
T Consensus        44 ~~lll~GppGtGKT~l~~-~l~~~l   67 (276)
T d1fnna2          44 PRATLLGRPGTGKTVTLR-KLWELY   67 (276)
T ss_dssp             CEEEEECCTTSSHHHHHH-HHHHHH
T ss_pred             CceEEECCCCCCHHHHHH-HHHHHH
Confidence            579999999999997642 244444

>d1ixsb2 c.37.1.20 (B:4-242) Holliday junction helicase RuvB {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: Extended AAA-ATPase domain
domain: Holliday junction helicase RuvB
species: Thermus thermophilus [TaxId: 274]

Probab=86.48  E-value=0.16  Score=40.28  Aligned_cols=43  Identities=16%  Similarity=0.111  Sum_probs=27.5

Q ss_pred             CCcccCCCCHHHHHHHHHHcCCCCCcHHHHHHHHHHhC----CCcEEEEcCCCCchHHHH
Q 043110           35 CCFSSLGLDSTLCDQLRERLGFEAPTKVQAQAIPVILS----GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        35 ~~f~~~~l~~~l~~~l~~~~g~~~p~~~Q~~~i~~il~----g~d~li~a~TGsGKT~~~   90 (316)
                      .+|+++--.+++++.| +.+            +.....    -.++++.||+|+|||..+
T Consensus         6 ~~~ddivGq~~~~~~L-~~~------------i~~~~~~~~~~~~~Ll~GPpG~GKTtla   52 (239)
T d1ixsb2           6 KTLDEYIGQERLKQKL-RVY------------LEAAKARKEPLEHLLLFGPPGLGKTTLA   52 (239)
T ss_dssp             CSGGGSCSCHHHHHHH-HHH------------HHHHTTSSSCCCCEEEECCTTSCHHHHH
T ss_pred             CCHHHhCCHHHHHHHH-HHH------------HHHHHhcCCCCCeEEEECCCCCCHHHHH
Confidence            4677775566666666 221            111111    247999999999999875

>d1y63a_ c.37.1.1 (A:) Probable kinase LmjF30.1890 {Leishmania major [TaxId: 5664]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Probable kinase LmjF30.1890
species: Leishmania major [TaxId: 5664]

Probab=85.72  E-value=0.2  Score=37.23  Aligned_cols=19  Identities=37%  Similarity=0.630  Sum_probs=16.2

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .+.++++.|++|||||...
T Consensus         4 k~~~I~i~G~~GsGKTT~~   22 (174)
T d1y63a_           4 KGINILITGTPGTGKTSMA   22 (174)
T ss_dssp             SSCEEEEECSTTSSHHHHH
T ss_pred             CCCEEEEEeCCCCCHHHHH
Confidence            3567999999999999864

>d1v8ka_ c.37.1.9 (A:) Kinesin {Mouse (Mus musculus), kif2c [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif2c [TaxId: 10090]

Probab=85.72  E-value=0.28  Score=41.93  Aligned_cols=24  Identities=29%  Similarity=0.522  Sum_probs=19.9

Q ss_pred             HHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           67 IPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        67 i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      +..+++|.|  +++.|+||||||...
T Consensus       106 v~~~l~G~n~tifaYGqTGSGKTyTm  131 (362)
T d1v8ka_         106 VQTIFEGGKATCFAYGQTGSGKTHTM  131 (362)
T ss_dssp             HHHHHTTCEEEEEEEESTTSSHHHHH
T ss_pred             HHHHHhccCceEEeeccCCCCCceee
Confidence            456678987  788899999999885

>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=85.67  E-value=3.6  Score=30.30  Aligned_cols=75  Identities=11%  Similarity=0.018  Sum_probs=51.5

Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHh----cCCcEEEeCcHHHHHHHhcCCccccC
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLR----KGISILVATPGHLLDHLKHTSSFLHT  185 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~----~~~~IlV~Tp~~l~~~l~~~~~~~~~  185 (316)
                      +.++||.|.++.-+..++..+...+     ..+..++|+.........+.    ...+|+|||.-       -..++.+.
T Consensus        32 ~~k~iVF~~~~~~~~~l~~~L~~~g-----~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~-------~~~Gid~~   99 (171)
T d1s2ma2          32 INQAIIFCNSTNRVELLAKKITDLG-----YSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL-------LTRGIDIQ   99 (171)
T ss_dssp             CSEEEEECSSHHHHHHHHHHHHHHT-----CCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC-------SSSSCCCT
T ss_pred             CCceEEEEeeeehhhHhHHhhhccc-----ccccccccccchhhhhhhhhhcccCccccccchhH-------hhhccccc
Confidence            3469999999999988888877653     44456677776554433332    34789999963       12567778


Q ss_pred             ceeEEEEecch
Q 043110          186 NLRWIIFDEAD  196 (316)
Q Consensus       186 ~l~~lViDEad  196 (316)
                      +++++|.-++.
T Consensus       100 ~v~~VI~~d~p  110 (171)
T d1s2ma2         100 AVNVVINFDFP  110 (171)
T ss_dssp             TEEEEEESSCC
T ss_pred             eeEEEEecCCc
Confidence            88888865444

>d1zp6a1 c.37.1.25 (A:6-181) Hypothetical protein Atu3015 {Agrobacterium tumefaciens [TaxId: 358]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein Atu3015
species: Agrobacterium tumefaciens [TaxId: 358]

Probab=85.50  E-value=0.16  Score=37.90  Aligned_cols=19  Identities=26%  Similarity=0.496  Sum_probs=16.2

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      .|+-+++.|++|||||...
T Consensus         3 ~g~iI~l~G~~GsGKSTia   21 (176)
T d1zp6a1           3 GGNILLLSGHPGSGKSTIA   21 (176)
T ss_dssp             TTEEEEEEECTTSCHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            5667899999999999864

>d1goja_ c.37.1.9 (A:) Kinesin {Neurospora crassa [TaxId: 5141]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Neurospora crassa [TaxId: 5141]

Probab=85.47  E-value=0.29  Score=41.64  Aligned_cols=25  Identities=32%  Similarity=0.543  Sum_probs=20.6

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .++.+++|.+  +++.|+||||||...
T Consensus        71 lv~~~l~G~n~ti~aYG~tgSGKT~Tm   97 (354)
T d1goja_          71 TVDDILNGYNGTVFAYGQTGAGKSYTM   97 (354)
T ss_dssp             HHHHHTTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHhhccCceeEEecccCCCCcceee
Confidence            4556679988  789999999999874

>d1ly1a_ c.37.1.1 (A:) Polynucleotide kinase, kinase domain {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: Nucleotide and nucleoside kinases
domain: Polynucleotide kinase, kinase domain
species: Bacteriophage T4 [TaxId: 10665]

Probab=85.39  E-value=0.2  Score=36.46  Aligned_cols=15  Identities=27%  Similarity=0.423  Sum_probs=13.0

Q ss_pred             EEEEcCCCCchHHHH
Q 043110           76 VLVNAATGTGKTVAY   90 (316)
Q Consensus        76 ~li~a~TGsGKT~~~   90 (316)
                      +++.|++|||||...
T Consensus         5 Iii~G~pGsGKTTla   19 (152)
T d1ly1a_           5 ILTIGCPGSGKSTWA   19 (152)
T ss_dssp             EEEECCTTSSHHHHH
T ss_pred             EEEECCCCCCHHHHH
Confidence            688999999999853

>d1r6bx2 c.37.1.20 (X:169-436) ClpA, an Hsp100 chaperone, AAA+ modules {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: Extended AAA-ATPase domain
domain: ClpA, an Hsp100 chaperone, AAA+ modules
species: Escherichia coli [TaxId: 562]

Probab=85.32  E-value=3.7  Score=33.00  Aligned_cols=33  Identities=12%  Similarity=0.074  Sum_probs=24.3

Q ss_pred             EEEeCcHHHHHHHhcCCccccCceeEEEEecchh
Q 043110          164 ILVATPGHLLDHLKHTSSFLHTNLRWIIFDEADR  197 (316)
Q Consensus       164 IlV~Tp~~l~~~l~~~~~~~~~~l~~lViDEad~  197 (316)
                      |.-+||+.+..++.....+ ...+..+-++|-+.
T Consensus       151 IgatT~eey~~~~e~d~al-~rrF~~I~V~Eps~  183 (268)
T d1r6bx2         151 IGSTTYQEFSNIFEKDRAL-ARRFQKIDITEPSI  183 (268)
T ss_dssp             EEEECHHHHHCCCCCTTSS-GGGEEEEECCCCCH
T ss_pred             EEeCCHHHHHHHHhhcHHH-HhhhcccccCCCCH
Confidence            6678888888777654433 36789999999884

>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=85.08  E-value=4.2  Score=30.96  Aligned_cols=70  Identities=14%  Similarity=0.117  Sum_probs=46.7

Q ss_pred             eeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHH---h-cCCcEEEeCcHHHHHHHhcCCccccCc
Q 043110          111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARL---R-KGISILVATPGHLLDHLKHTSSFLHTN  186 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~  186 (316)
                      .++||.++|+.-+..++..+...     ...+...+|+.........+   . ...+|+|+|--       -..++++.+
T Consensus        31 ~~~IIF~~t~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~-------~~~GiD~p~   98 (200)
T d1oywa3          31 KSGIIYCNSRAKVEDTAARLQSK-----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVA-------FGMGINKPN   98 (200)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTT-------SCTTTCCTT
T ss_pred             CCEEEEEeeehhhHHhhhhhccC-----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecch-------hhhccCCCC
Confidence            34999999999999888777653     24556667776654433322   2 34789999941       124566678


Q ss_pred             eeEEEE
Q 043110          187 LRWIIF  192 (316)
Q Consensus       187 l~~lVi  192 (316)
                      ++++|.
T Consensus        99 v~~VI~  104 (200)
T d1oywa3          99 VRFVVH  104 (200)
T ss_dssp             CCEEEE
T ss_pred             CCEEEE
Confidence            887764

>d1sdma_ c.37.1.9 (A:) Kinesin heavy chain-like protein {Potato (Solanum tuberosum) [TaxId: 4113]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin heavy chain-like protein
species: Potato (Solanum tuberosum) [TaxId: 4113]

Probab=85.06  E-value=0.26  Score=42.14  Aligned_cols=25  Identities=24%  Similarity=0.484  Sum_probs=21.0

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .++.+++|.|  +++.|+||||||...
T Consensus        66 lv~~~l~G~n~~i~aYGqTGSGKTyTm   92 (364)
T d1sdma_          66 LVQSAVDGYNVCIFAYGQTGSGKTFTI   92 (364)
T ss_dssp             HHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHhcCCceeeeccccCCCCccccc
Confidence            4667789987  789999999999874

>d2zfia1 c.37.1.9 (A:4-352) Kinesin {Mouse (Mus musculus), kif1a [TaxId: 10090]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Mouse (Mus musculus), kif1a [TaxId: 10090]

Probab=84.87  E-value=0.32  Score=41.22  Aligned_cols=25  Identities=20%  Similarity=0.437  Sum_probs=20.6

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .++.+++|.|  +++.|+||||||...
T Consensus        78 lv~~~l~G~n~ti~aYGqTgSGKT~Tm  104 (349)
T d2zfia1          78 MLQHAFEGYNVCIFAYGQTGAGKSYTM  104 (349)
T ss_dssp             HHHHHHTTCCEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHhccCceeeeeccCCCCCceee
Confidence            3455678987  899999999999885

>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=84.65  E-value=3.5  Score=30.16  Aligned_cols=73  Identities=12%  Similarity=0.065  Sum_probs=50.6

Q ss_pred             eeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHHh----cCCcEEEeCcHHHHHHHhcCCccccCc
Q 043110          111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARLR----KGISILVATPGHLLDHLKHTSSFLHTN  186 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~----~~~~IlV~Tp~~l~~~l~~~~~~~~~~  186 (316)
                      .++||.|.++.-++++++.+...     ...+..++|+....+....+.    ...+|+|+|--     +  ..++++.+
T Consensus        28 ~k~iIF~~s~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv-----~--~rGiDi~~   95 (162)
T d1fuka_          28 TQAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDL-----L--ARGIDVQQ   95 (162)
T ss_dssp             SCEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGG-----G--TTTCCCCS
T ss_pred             CcEEEEEEEEchHHHHHHHHhhc-----CceEEEeccCCchhhHHHHHHHHhhcccceeecccc-----c--cccccCCC
Confidence            34999999999999988877653     245567777777655544332    34789999952     2  25667778


Q ss_pred             eeEEEEecc
Q 043110          187 LRWIIFDEA  195 (316)
Q Consensus       187 l~~lViDEa  195 (316)
                      ++++|.=+.
T Consensus        96 v~~VI~~d~  104 (162)
T d1fuka_          96 VSLVINYDL  104 (162)
T ss_dssp             CSEEEESSC
T ss_pred             ceEEEEecc
Confidence            888887543

>d1x88a1 c.37.1.9 (A:18-362) Kinesin {Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin
species: Human (Homo sapiens), mitotic kinesin eg5 [TaxId: 9606]

Probab=84.40  E-value=0.32  Score=41.22  Aligned_cols=25  Identities=28%  Similarity=0.526  Sum_probs=20.8

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .+..+++|.+  +++.|+||||||...
T Consensus        72 lv~~~l~G~n~~i~aYGqtgSGKTyTm   98 (345)
T d1x88a1          72 ILDEVIMGYNCTIFAYGQTGTGKTFTM   98 (345)
T ss_dssp             HHHHHHTTCEEEEEEEECTTSSHHHHH
T ss_pred             hHHHHhccCCceEEeeeeccccceEEe
Confidence            4566778987  789999999999874

>d2ncda_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=84.34  E-value=0.29  Score=41.87  Aligned_cols=26  Identities=31%  Similarity=0.493  Sum_probs=21.8

Q ss_pred             HHHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           65 QAIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        65 ~~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      ..++.+++|.|  ++..|+||||||...
T Consensus       115 plv~~vl~G~n~ti~aYGqtGSGKT~Tm  142 (368)
T d2ncda_         115 PLIQSALDGYNICIFAYGQTGSGKTYTM  142 (368)
T ss_dssp             HHHHHHHTTCEEEEEEECSTTSSHHHHH
T ss_pred             HHHHHHhcccceeEEeeccCCCccceEe
Confidence            35677789987  899999999999874

>d1lw7a2 c.37.1.1 (A:220-411) Transcriptional regulator NadR, ribosylnicotinamide kinase domain {Haemophilus influenzae [TaxId: 727]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Transcriptional regulator NadR, ribosylnicotinamide kinase domain
species: Haemophilus influenzae [TaxId: 727]

Probab=84.26  E-value=0.18  Score=37.70  Aligned_cols=18  Identities=22%  Similarity=0.385  Sum_probs=15.5

Q ss_pred             CCcEEEEcCCCCchHHHH
Q 043110           73 GRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        73 g~d~li~a~TGsGKT~~~   90 (316)
                      -|.+++.|++|+|||...
T Consensus         7 ~K~I~i~G~~GsGKTTla   24 (192)
T d1lw7a2           7 AKTVAILGGESSGKSVLV   24 (192)
T ss_dssp             CEEEEEECCTTSHHHHHH
T ss_pred             ceEEEEECCCCCCHHHHH
Confidence            357999999999999864

>d2bdta1 c.37.1.25 (A:1-176) Hypothetical protein BH3686 {Bacillus halodurans [TaxId: 86665]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Atu3015-like
domain: Hypothetical protein BH3686
species: Bacillus halodurans [TaxId: 86665]

Probab=83.84  E-value=0.24  Score=36.47  Aligned_cols=16  Identities=19%  Similarity=0.432  Sum_probs=13.8

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      -+++.|++|||||..+
T Consensus         4 lI~i~G~~GsGKTTva   19 (176)
T d2bdta1           4 LYIITGPAGVGKSTTC   19 (176)
T ss_dssp             EEEEECSTTSSHHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            3789999999999864

>d1gvnb_ c.37.1.21 (B:) Plasmid maintenance system epsilon/zeta, toxin zeta subunit {Streptococcus pyogenes [TaxId: 1314]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
domain: Plasmid maintenance system epsilon/zeta, toxin zeta subunit
species: Streptococcus pyogenes [TaxId: 1314]

Probab=83.73  E-value=0.23  Score=39.95  Aligned_cols=16  Identities=31%  Similarity=0.476  Sum_probs=14.2

Q ss_pred             cEEEEcCCCCchHHHH
Q 043110           75 DVLVNAATGTGKTVAY   90 (316)
Q Consensus        75 d~li~a~TGsGKT~~~   90 (316)
                      .+++.||+|+|||..+
T Consensus        34 ~ilL~GpPGtGKT~la   49 (273)
T d1gvnb_          34 AFLLGGQPGSGKTSLR   49 (273)
T ss_dssp             EEEEECCTTSCTHHHH
T ss_pred             EEEEECCCCCCHHHHH
Confidence            4899999999999864

>d1rkba_ c.37.1.1 (A:) Adenylate kinase {Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Nucleotide and nucleoside kinases
domain: Adenylate kinase
species: Human (Homo sapiens), isoenzyme 6 [TaxId: 9606]

Probab=83.18  E-value=0.28  Score=36.22  Aligned_cols=17  Identities=29%  Similarity=0.503  Sum_probs=14.7

Q ss_pred             CcEEEEcCCCCchHHHH
Q 043110           74 RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~   90 (316)
                      ..+++.|+.|||||...
T Consensus         5 ~~I~i~G~pGsGKTTia   21 (173)
T d1rkba_           5 PNILLTGTPGVGKTTLG   21 (173)
T ss_dssp             CCEEEECSTTSSHHHHH
T ss_pred             CEEEEECCCCCCHHHHH
Confidence            46899999999999864

>d1f9va_ c.37.1.9 (A:) Kinesin motor Ncd (non-claret disjunctional) {Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Motor proteins
domain: Kinesin motor Ncd (non-claret disjunctional)
species: Baker's yeast (Saccharomyces cerevisiae), Kar [TaxId: 4932]

Probab=82.59  E-value=0.36  Score=40.78  Aligned_cols=25  Identities=28%  Similarity=0.506  Sum_probs=21.3

Q ss_pred             HHHHHhCCCc--EEEEcCCCCchHHHH
Q 043110           66 AIPVILSGRD--VLVNAATGTGKTVAY   90 (316)
Q Consensus        66 ~i~~il~g~d--~li~a~TGsGKT~~~   90 (316)
                      .++.+++|.+  ++..++||||||...
T Consensus        74 ~v~~~l~G~n~~i~aYGqtgSGKT~T~  100 (342)
T d1f9va_          74 LVQSSLDGYNVCIFAYGQTGSGKTFTM  100 (342)
T ss_dssp             HHGGGGGTCCEEEEEECCTTSSHHHHH
T ss_pred             hhcchhcccccceeeeeccCCcccccc
Confidence            5667788987  788999999999885

>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=82.46  E-value=3.3  Score=30.58  Aligned_cols=74  Identities=14%  Similarity=0.102  Sum_probs=50.5

Q ss_pred             CeeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHH---h-cCCcEEEeCcHHHHHHHhcCCccccC
Q 043110          110 GTFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARL---R-KGISILVATPGHLLDHLKHTSSFLHT  185 (316)
Q Consensus       110 ~~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~-~~~~IlV~Tp~~l~~~l~~~~~~~~~  185 (316)
                      +.++||.|.++.-|..+++.++..+     ..+..++++....+....+   . ...+|+|+|--     +  ..++++.
T Consensus        34 ~~k~iiF~~~~~~~~~~~~~l~~~~-----~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td~-----~--~rGiDi~  101 (168)
T d2j0sa2          34 ITQAVIFCNTKRKVDWLTEKMREAN-----FTVSSMHGDMPQKERESIMKEFRSGASRVLISTDV-----W--ARGLDVP  101 (168)
T ss_dssp             SSEEEEECSSHHHHHHHHHHHHHTT-----CCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGG-----G--SSSCCCT
T ss_pred             CCceEEEeeeHHHHHHHHHHhhhcc-----cchhhhhhhhhHHHHHHHHHHHhcCCccEEeccch-----h--ccccccc
Confidence            3469999999999998887777642     4456667776665543333   2 34789999942     2  2567778


Q ss_pred             ceeEEEEecc
Q 043110          186 NLRWIIFDEA  195 (316)
Q Consensus       186 ~l~~lViDEa  195 (316)
                      +++++|.=++
T Consensus       102 ~v~~VIn~d~  111 (168)
T d2j0sa2         102 QVSLIINYDL  111 (168)
T ss_dssp             TEEEEEESSC
T ss_pred             CcceEEEecC
Confidence            8888875443

>d1cr2a_ c.37.1.11 (A:) Gene 4 protein (g4p, DNA primase), helicase domain {Bacteriophage T7 [TaxId: 10760]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Gene 4 protein (g4p, DNA primase), helicase domain
species: Bacteriophage T7 [TaxId: 10760]

Probab=82.43  E-value=0.82  Score=36.77  Aligned_cols=41  Identities=15%  Similarity=0.186  Sum_probs=26.1

Q ss_pred             hCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCCCCCCCeeEEEEeCC
Q 043110           71 LSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRIDRSSGTFALVLVPT  119 (316)
Q Consensus        71 l~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~~~~~~~~~lil~Pt  119 (316)
                      ..|.=+++.|+||+|||...+--+.+....        .+..+++++.-
T Consensus        33 ~~G~l~vi~G~~G~GKT~~~~~la~~~a~~--------~g~~v~~~s~E   73 (277)
T d1cr2a_          33 RGGEVIMVTSGSGMGKSTFVRQQALQWGTA--------MGKKVGLAMLE   73 (277)
T ss_dssp             CTTCEEEEECSTTSSHHHHHHHHHHHHHHT--------SCCCEEEEESS
T ss_pred             CCCeEEEEEeCCCCCHHHHHHHHHHhhhhh--------cccceeEeeec
Confidence            356678999999999996543333333222        24448888754

>d1nlfa_ c.37.1.11 (A:) Hexameric replicative helicase repA {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: RecA protein-like (ATPase-domain)
domain: Hexameric replicative helicase repA
species: Escherichia coli [TaxId: 562]

Probab=81.86  E-value=1.3  Score=35.44  Aligned_cols=67  Identities=13%  Similarity=0.149  Sum_probs=37.2

Q ss_pred             HHHHhCCCcEEEEcCCCCchHHHHHHHHHHHhhhcCCCC--CCCCCeeEEEEeCChHHHHHHHHHHHHHHh
Q 043110           67 IPVILSGRDVLVNAATGTGKTVAYLAPIINHLQSYSPRI--DRSSGTFALVLVPTSELCLLVYEILQKLLH  135 (316)
Q Consensus        67 i~~il~g~d~li~a~TGsGKT~~~~lp~l~~l~~~~~~~--~~~~~~~~lil~Pt~~L~~Q~~~~~~~~~~  135 (316)
                      ++-++.|.-+++.|++|+|||...+- +...+.......  ....+..++|+.-- .-..++..++..+..
T Consensus        23 i~G~~pg~~~~i~G~~G~GKS~l~l~-la~~ia~g~~~~~~~~~~~~~vl~~~~E-~~~~~~~~Rl~~~~~   91 (274)
T d1nlfa_          23 LPNMVAGTVGALVSPGGAGKSMLALQ-LAAQIAGGPDLLEVGELPTGPVIYLPAE-DPPTAIHHRLHALGA   91 (274)
T ss_dssp             ETTEETTSEEEEEESTTSSHHHHHHH-HHHHHHTCCCTTCCCCCCCCCEEEEESS-SCHHHHHHHHHHHHT
T ss_pred             hCCccCCcEEEEEeCCCCCHHHHHHH-HHHHHHcCCCcccccccCCCceEEEecc-chHHHHHHHHHHHhh
Confidence            34445677789999999999976543 333443322211  11223357776632 234455666665543

>d1tf7a1 c.37.1.11 (A:14-255) Circadian clock protein KaiC {Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RecA protein-like (ATPase-domain)
domain: Circadian clock protein KaiC
species: Synechococcus sp. strain PCC 7942 (Anacystis nidulans R2) [TaxId: 1140]

Probab=81.37  E-value=1  Score=34.71  Aligned_cols=20  Identities=45%  Similarity=0.712  Sum_probs=16.4

Q ss_pred             CCCcEEEEcCCCCchHHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAYL   91 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~~   91 (316)
                      .|.-+++.|++|+|||...+
T Consensus        25 ~G~~~~I~G~~G~GKT~la~   44 (242)
T d1tf7a1          25 IGRSTLVSGTSGTGKTLFSI   44 (242)
T ss_dssp             TTSEEEEEESTTSSHHHHHH
T ss_pred             CCeEEEEEeCCCCCHHHHHH
Confidence            45679999999999997653

>d1viaa_ c.37.1.2 (A:) Shikimate kinase (AroK) {Campylobacter jejuni [TaxId: 197]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Shikimate kinase (AroK)
domain: Shikimate kinase (AroK)
species: Campylobacter jejuni [TaxId: 197]

Probab=80.99  E-value=0.41  Score=35.44  Aligned_cols=17  Identities=18%  Similarity=0.407  Sum_probs=15.0

Q ss_pred             CcEEEEcCCCCchHHHH
Q 043110           74 RDVLVNAATGTGKTVAY   90 (316)
Q Consensus        74 ~d~li~a~TGsGKT~~~   90 (316)
                      |++++.|+.|+|||...
T Consensus         1 k~I~liG~~GsGKsTi~   17 (161)
T d1viaa_           1 KNIVFIGFMGSGKSTLA   17 (161)
T ss_dssp             CCEEEECCTTSCHHHHH
T ss_pred             CcEEEECCCCCCHHHHH
Confidence            57899999999999875

>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=80.51  E-value=4.3  Score=29.26  Aligned_cols=71  Identities=21%  Similarity=0.248  Sum_probs=46.7

Q ss_pred             eeEEEEeCChHHHHHHHHHHHHHHhhcCCceeEEeeCCCChHHHHHHH---h-cCCcEEEeCcHHHHHHHhcCCccccCc
Q 043110          111 TFALVLVPTSELCLLVYEILQKLLHRFRWIVPGYVMGGGNRSKEKARL---R-KGISILVATPGHLLDHLKHTSSFLHTN  186 (316)
Q Consensus       111 ~~~lil~Pt~~L~~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l---~-~~~~IlV~Tp~~l~~~l~~~~~~~~~~  186 (316)
                      .++||.|++++-|.++++.++..+     ..+..++++.........+   . ....|+|+|.- +.      .++++..
T Consensus        29 ~k~IIF~~s~~~~~~l~~~L~~~g-----~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~-~~------~Gid~~~   96 (155)
T d1hv8a2          29 FYGLVFCKTKRDTKELASMLRDIG-----FKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDV-MS------RGIDVND   96 (155)
T ss_dssp             CCEEEECSSHHHHHHHHHHHHHTT-----CCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTT-HH------HHCCCSC
T ss_pred             CCEEEEECchHHHHHHHhhhcccc-----cccccccccchhhhhhhhhhhhhcccceeeeehhH-Hh------hhhhhcc
Confidence            359999999999998888877642     4555666766655443333   2 34689999942 21      3445567


Q ss_pred             eeEEEEe
Q 043110          187 LRWIIFD  193 (316)
Q Consensus       187 l~~lViD  193 (316)
                      ++++|.=
T Consensus        97 v~~Vi~~  103 (155)
T d1hv8a2          97 LNCVINY  103 (155)
T ss_dssp             CSEEEES
T ss_pred             CcEEEEe
Confidence            7777743

>d1qhxa_ c.37.1.3 (A:) Chloramphenicol phosphotransferase {Streptomyces venezuelae [TaxId: 54571]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Chloramphenicol phosphotransferase
domain: Chloramphenicol phosphotransferase
species: Streptomyces venezuelae [TaxId: 54571]

Probab=80.10  E-value=0.45  Score=35.07  Aligned_cols=19  Identities=21%  Similarity=0.408  Sum_probs=15.4

Q ss_pred             CCCcEEEEcCCCCchHHHH
Q 043110           72 SGRDVLVNAATGTGKTVAY   90 (316)
Q Consensus        72 ~g~d~li~a~TGsGKT~~~   90 (316)
                      +.+=+++.|++|||||...
T Consensus         2 ~~kiI~l~G~~GsGKsTva   20 (178)
T d1qhxa_           2 TTRMIILNGGSSAGKSGIV   20 (178)
T ss_dssp             CCCEEEEECCTTSSHHHHH
T ss_pred             CCeEEEEECCCCCCHHHHH
Confidence            3456889999999999764