Citrus Sinensis ID: 030094

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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---
Protein Sequence
MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNHHNLLICL
Secondary Structure (PSIPRED)
cEEEEcccHHHHHHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHHccccEEEEcccHHHHHHccccccccccccEEEEEccccccccccHHHHHHHHHHccccccccccccccccHHHHHHHHHcccccEEEEEEccccccccccEEEEEEEEcccccHHHHHHHHHHHccccEEEEEc
Secondary Structure Prediction (SSPRO)
ccEEEccHHHHHHHHHHHHHHHHHHccccEEEEEEccccccHHHHHHHHcccEEEEEcccHHHHHHHccccEcHHHccEEEEccHHHHHccccHHHHHHHHHccccccEEEEEEccccHHHHHHHHHHccccEEEEcEcccccHHHEEEEEEEEEccccHHHHHHHHHHHHHcccccEEEEEc
Coil and Loop (DISEMBL)
mgmiisptrelssQIYHVaqpfistlpdvKSVLLVGGVEVKADVKKIEEEGAnlligtpgrlyDIMERmdvldfrnlEILVLDEADRLLDMGFQKQISYIISRLpklrrtglfsaTQTEAVEELSKaglrnpvrVEVRAeskshhvsassqqlassktplglhLEVIWNVNQMRNHHNLLICL
Flexible Loop (DISEMBL)
MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKAdvkkieeeganlligtpgrlYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVeelskaglrnpvRVEVRAESkshhvsassqqlassktPLGLHLEVIWNVNQMRNHHNLLICL
Low Complexity Region (SEG)
MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNHHNLLICL
Disordered region (IsUnstruct)
************SQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSA********************************************LGLHLEVIWNVNQMRNHHNLLIC*
Disordered Region (DISOPRED)
MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAES******ASSQQLASSKTPLGLHLEVIWNVNQMRNHHNLLICL
Disordered Region (DISEMBL)
MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEV*******************KTPLGLHLEVIWNVNQMRNHHNLLICL
Disordered Region (DISPRO)
MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNHHNLLICL
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNHHNLLICL
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	183	2.2.26 [Sep-21-2011]
Q9FLB0	593	DEAD-box ATP-dependent RN	yes	no	0.890	0.274	0.796	1e-71
Q761Z9	647	DEAD-box ATP-dependent RN	yes	no	0.978	0.276	0.662	2e-66
Q8GXD6	558	DEAD-box ATP-dependent RN	no	no	0.808	0.265	0.75	8e-59
Q9FVV4	465	DEAD-box ATP-dependent RN	no	no	0.748	0.294	0.643	3e-46
Q8JHJ2	593	ATP-dependent RNA helicas	yes	no	0.836	0.258	0.506	4e-36
Q6AZV7	594	ATP-dependent RNA helicas	N/A	no	0.841	0.259	0.491	9e-36
Q5ZLN8	591	ATP-dependent RNA helicas	yes	no	0.928	0.287	0.459	4e-35
Q8NHQ9	600	ATP-dependent RNA helicas	yes	no	0.928	0.283	0.470	5e-35
Q2NL08	601	ATP-dependent RNA helicas	yes	no	0.874	0.266	0.462	6e-35
Q6ZPL9	600	ATP-dependent RNA helicas	yes	no	0.874	0.266	0.446	6e-34

>sp|Q9FLB0|RH18_ARATH DEAD-box ATP-dependent RNA helicase 18 OS=Arabidopsis thaliana GN=RH18 PE=2 SV=1

 Score =  268 bits (686), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 133/167 (79%), Positives = 151/167 (90%), Gaps = 4/167 (2%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+IISPTRELS+QIY+VAQPF+STL +V SVLLVGG EVKAD+K IEEEG N+LIGTPG
Sbjct: 92  MGVIISPTRELSTQIYNVAQPFVSTLANVNSVLLVGGREVKADMKIIEEEGCNVLIGTPG 151

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL DIMERM++LDFRNLEIL+LDEADRLL+MGFQ+Q++YIISRLPK RRTGLFSATQTE 
Sbjct: 152 RLSDIMERMEILDFRNLEILILDEADRLLEMGFQRQVNYIISRLPKQRRTGLFSATQTEG 211

Query: 121 VEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVI 167
           VEEL+KAGLRNPVRVEVRA+SKS     SSQQL +SKTP GLHLE +
Sbjct: 212 VEELAKAGLRNPVRVEVRAKSKSE----SSQQLTNSKTPSGLHLEYM 254

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

>sp|Q761Z9|RH18_ORYSJ DEAD-box ATP-dependent RNA helicase 18 OS=Oryza sativa subsp. japonica GN=Os01g0164500 PE=1 SV=2

 Score =  251 bits (640), Expect = 2e-66,   Method: Compositional matrix adjust.
 Identities = 120/181 (66%), Positives = 153/181 (84%), Gaps = 2/181 (1%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +G+IISPTRELSSQIY+VAQPF +TL  V S+LLVGG ++KA++KK+EEEGAN+L+GTPG
Sbjct: 98  LGIIISPTRELSSQIYNVAQPFFATLKGVSSMLLVGGFDIKAELKKLEEEGANILVGTPG 157

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           +L+D+MER+D L+++NLEIL+LDEADRLLD+GFQKQI+ IIS+LPKLRRTGLFSATQTEA
Sbjct: 158 KLFDVMERLDTLNYKNLEILILDEADRLLDLGFQKQITSIISKLPKLRRTGLFSATQTEA 217

Query: 121 VEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNHHNLL 180
           V+EL+KAGLRNPVRVEV+ E K      + Q+L  SKTPLGL LE  + + +  N  + L
Sbjct: 218 VKELAKAGLRNPVRVEVKTEVKPTGKDGAQQELGPSKTPLGLRLE--YMICEASNKSSQL 275

Query: 181 I 181
           +
Sbjct: 276 V 276

Oryza sativa subsp. japonica (taxid: 39947)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q8GXD6|RH49_ARATH DEAD-box ATP-dependent RNA helicase 49 OS=Arabidopsis thaliana GN=RH49 PE=2 SV=2

 Score =  226 bits (575), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 111/148 (75%), Positives = 130/148 (87%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+IISPTRELS+QI+ VA+PF+STLP+V SVLLVGG EV+AD+  +EEEGANLLIGTPG
Sbjct: 92  MGVIISPTRELSAQIHKVAEPFVSTLPNVNSVLLVGGREVEADMNTLEEEGANLLIGTPG 151

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL D+M+RM+ LDFRNLEIL+LDEADRLLDMGFQKQ++YIISRLPK RRTGLFSATQT+A
Sbjct: 152 RLSDMMKRMEFLDFRNLEILILDEADRLLDMGFQKQVNYIISRLPKQRRTGLFSATQTQA 211

Query: 121 VEELSKAGLRNPVRVEVRAESKSHHVSA 148
           V +L+KAGLRN + V   AESKS   S 
Sbjct: 212 VADLAKAGLRNAMEVISGAESKSKTSSG 239

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q9FVV4|RH55_ARATH DEAD-box ATP-dependent RNA helicase 55 OS=Arabidopsis thaliana GN=RH55 PE=2 SV=1

 Score =  184 bits (467), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 94/146 (64%), Positives = 115/146 (78%), Gaps = 9/146 (6%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+IISPTRELS+QI+ VA+         +        EV+AD+  +EEEGANLLIGTPG
Sbjct: 93  MGVIISPTRELSAQIHKVARAVRLDFAKCR--------EVEADMNTLEEEGANLLIGTPG 144

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL D+M+RM+ LDFRNLEIL+LDEADRLLDMGFQKQ++YIISRLPK RRTGLFSATQT+A
Sbjct: 145 RLSDMMKRMEFLDFRNLEILILDEADRLLDMGFQKQVNYIISRLPKQRRTGLFSATQTQA 204

Query: 121 VEELSKAGLRNPVRVEVRAESKSHHV 146
           V +L+KAGLRNP  ++  A+ KS  +
Sbjct: 205 VADLAKAGLRNPY-LKCEADQKSSQL 229

Arabidopsis thaliana (taxid: 3702)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q8JHJ2|DDX55_DANRE ATP-dependent RNA helicase DDX55 OS=Danio rerio GN=ddx55 PE=2 SV=2

 Score =  150 bits (380), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 84/166 (50%), Positives = 111/166 (66%), Gaps = 13/166 (7%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +II+PTREL+ QI  V   F+   P    +LL+GG     DV+K++ +GAN++I TPGR
Sbjct: 85  ALIITPTRELAMQISEVMGRFLQGFPQFTQILLIGGSNPIEDVEKLKTQGANIIIATPGR 144

Query: 62  LYDIMER-MDVLDF----RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT 116
           L D+  R  D LD     ++L++LVLDEADRLLDMGF+  ++ I+  LPK RRTGLFSAT
Sbjct: 145 LEDMFRRKADGLDLATAVKSLDVLVLDEADRLLDMGFEASLNTILGYLPKQRRTGLFSAT 204

Query: 117 QTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGL 162
           QT+ +E+L +AGLRNPVR+ V    K   V+ASS Q    KTP  L
Sbjct: 205 QTQELEKLVRAGLRNPVRITV----KEKGVAASSVQ----KTPAKL 242

Probable ATP-binding RNA helicase. Plays an essential role in early embryonic development.

Danio rerio (taxid: 7955)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6AZV7|DDX55_XENLA ATP-dependent RNA helicase DDX55 OS=Xenopus laevis GN=ddx55 PE=2 SV=1

 Score =  149 bits (376), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 82/167 (49%), Positives = 107/167 (64%), Gaps = 13/167 (7%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +II+PTREL+ QI  V   F    P    +LL+GG     DV+K +E G N+++ TPGR
Sbjct: 85  ALIITPTRELAVQIDEVLSCFTKHFPQFSQILLIGGSNPVDDVRKFKEHGGNIIVATPGR 144

Query: 62  LYDIMERM-DVLDF----RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT 116
           L D+  R  D LD     + L++L+LDEADRLLDMGF+  I+ I+  LPK RRTGLFSAT
Sbjct: 145 LEDMFRRQADGLDLVICVKTLDVLILDEADRLLDMGFEASINTILGFLPKQRRTGLFSAT 204

Query: 117 QTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLH 163
           QT+ +E L +AGLRNPVR+ V    K   V+A+S Q    KTP+ L 
Sbjct: 205 QTQELENLVRAGLRNPVRIAV----KEKGVAATSTQ----KTPIRLQ 243

Probable ATP-binding RNA helicase.

Xenopus laevis (taxid: 8355)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q5ZLN8|DDX55_CHICK ATP-dependent RNA helicase DDX55 OS=Gallus gallus GN=DDX55 PE=2 SV=1

 Score =  147 bits (371), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 85/185 (45%), Positives = 115/185 (62%), Gaps = 15/185 (8%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +II+PTREL+ QI  V   F    P    +LL+GG     DV+K +E G N+++ TPGR
Sbjct: 85  AIIITPTRELAIQIDEVLTHFTKHFPKFSQILLIGGRNPMEDVEKFKEHGGNIIVATPGR 144

Query: 62  LYDIMER-MDVLDF----RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT 116
           L D+  R  D LD     ++L++LVLDEADRLLDMGF+  ++ I++ LPK RRTGLFSAT
Sbjct: 145 LEDLFRRKADGLDLASCVKSLDVLVLDEADRLLDMGFESSLNAILAFLPKQRRTGLFSAT 204

Query: 117 QTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNH 176
           QT+ VE L +AGLRNPVR+ V    K   V+A++ Q    KTP    LE  + + +    
Sbjct: 205 QTQEVENLVRAGLRNPVRISV----KEKGVAATNTQ----KTP--TRLENYYMICKADEK 254

Query: 177 HNLLI 181
            N L+
Sbjct: 255 FNQLV 259

Probable ATP-binding RNA helicase.

Gallus gallus (taxid: 9031)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q8NHQ9|DDX55_HUMAN ATP-dependent RNA helicase DDX55 OS=Homo sapiens GN=DDX55 PE=1 SV=3

 Score =  147 bits (370), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 87/185 (47%), Positives = 115/185 (62%), Gaps = 15/185 (8%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +II+PTREL+ QI  V   F    P+   +L +GG     DV++ +++G N+++ TPGR
Sbjct: 85  AIIITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGRNPGEDVERFKQQGGNIIVATPGR 144

Query: 62  LYDIMER-MDVLDF----RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT 116
           L D+  R  + LD     R+L++LVLDEADRLLDMGF+  I+ I+  LPK RRTGLFSAT
Sbjct: 145 LEDMFRRKAEGLDLASCVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSAT 204

Query: 117 QTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNH 176
           QT+ VE L +AGLRNPVRV V    K   V+ASS Q    KTP    LE  + V +    
Sbjct: 205 QTQEVENLVRAGLRNPVRVSV----KEKGVAASSAQ----KTP--SRLENYYMVCKADEK 254

Query: 177 HNLLI 181
            N L+
Sbjct: 255 FNQLV 259

Probable ATP-binding RNA helicase.

Homo sapiens (taxid: 9606)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q2NL08|DDX55_BOVIN ATP-dependent RNA helicase DDX55 OS=Bos taurus GN=DDX55 PE=2 SV=1

 Score =  147 bits (370), Expect = 6e-35,   Method: Compositional matrix adjust.
 Identities = 86/186 (46%), Positives = 113/186 (60%), Gaps = 26/186 (13%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +II+PTREL+ QI  V   F    P    +L +GG     DV + +E G N+++ TPGR
Sbjct: 85  AIIITPTRELAVQIEEVLSHFTKPFPQFSQILWIGGRNPGEDVARFKELGGNIIVATPGR 144

Query: 62  LYDIMER-MDVLDF----RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT 116
           L D+  R  + LD     R+LE+LVLDEADRLLDMGF+  I+ I+  LPK RRTGLFSAT
Sbjct: 145 LEDMFRRKAEGLDLASCVRSLEVLVLDEADRLLDMGFETSINTILEFLPKQRRTGLFSAT 204

Query: 117 QTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNH 176
           QT+ VE L +AGLRNPVR+ V    K   V+ASS Q    KTP           +++ NH
Sbjct: 205 QTQEVENLVRAGLRNPVRISV----KEKGVAASSTQ----KTP-----------SRLENH 245

Query: 177 HNLLIC 182
           +  ++C
Sbjct: 246 Y--MVC 249

Probable ATP-binding RNA helicase.

Bos taurus (taxid: 9913)

EC: 3

EC: .

EC: 6

EC: .

EC: 4

EC: .

EC: 1

EC: 3

>sp|Q6ZPL9|DDX55_MOUSE ATP-dependent RNA helicase DDX55 OS=Mus musculus GN=Ddx55 PE=2 SV=2

 Score =  143 bits (360), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 83/186 (44%), Positives = 114/186 (61%), Gaps = 26/186 (13%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++I+PTREL+ QI  V   F    P    +L +GG     DV++ ++ G N+++ TPGR
Sbjct: 85  AIVITPTRELAIQIDEVLSHFTKHFPQFSQILWIGGRNPGEDVERFKQHGGNIIVATPGR 144

Query: 62  LYDIMER-MDVLDF----RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT 116
           L D+  R  + LD     ++L++LVLDEADRLLDMGF+  I+ I+  LPK RRTGLFSAT
Sbjct: 145 LEDMFRRKAEGLDLASCVKSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSAT 204

Query: 117 QTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNH 176
           QT+ VE L +AGLRNPVR+ V    K   V+ASS Q    KTP           +++ NH
Sbjct: 205 QTQEVENLVRAGLRNPVRISV----KEKGVAASSTQ----KTP-----------SRLENH 245

Query: 177 HNLLIC 182
           +  +IC
Sbjct: 246 Y--MIC 249

Probable ATP-binding RNA helicase.

Mus musculus (taxid: 10090)

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	183
225448554	595	PREDICTED: DEAD-box ATP-dependent RNA he	0.912	0.280	0.874	3e-78
297736552	576	unnamed protein product [Vitis vinifera]	0.912	0.289	0.874	4e-78
356568033	589	PREDICTED: DEAD-box ATP-dependent RNA he	0.912	0.283	0.814	6e-73
224101199	592	predicted protein [Populus trichocarpa]	0.912	0.282	0.820	1e-72
356540003	589	PREDICTED: DEAD-box ATP-dependent RNA he	0.912	0.283	0.808	1e-71
297806553	593	hypothetical protein ARALYDRAFT_908458 [	0.890	0.274	0.808	1e-70
15239115	593	DEAD-box ATP-dependent RNA helicase 18 [	0.890	0.274	0.796	6e-70
255559531	592	dead box ATP-dependent RNA helicase, put	0.961	0.297	0.779	2e-69
357461389	659	DEAD-box ATP-dependent RNA helicase [Med	0.912	0.253	0.75	2e-69
110736442	520	ATP-dependent RNA helicase-like protein	0.890	0.313	0.790	7e-69

>gi|225448554|ref|XP_002273715.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 18-like [Vitis vinifera]

 Score =  296 bits (757), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 146/167 (87%), Positives = 161/167 (96%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +G+I+SPTRELSSQIY+VAQPFISTLP+VKSVLLVGGVEVK+D+KKIEEEGANLLIGTPG
Sbjct: 95  LGVILSPTRELSSQIYNVAQPFISTLPNVKSVLLVGGVEVKSDLKKIEEEGANLLIGTPG 154

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RLYDIMERMDVLDFRNLEIL+LDEADRLLDMGFQKQI+ II+RLPKLRRTGLFSATQTEA
Sbjct: 155 RLYDIMERMDVLDFRNLEILILDEADRLLDMGFQKQITSIIARLPKLRRTGLFSATQTEA 214

Query: 121 VEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVI 167
           VEELSKAGLRNPVRVEVRAE+KS + S SSQQLASSKTP GL++E +
Sbjct: 215 VEELSKAGLRNPVRVEVRAEAKSLNDSVSSQQLASSKTPSGLNIEYL 261

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297736552|emb|CBI25423.3| unnamed protein product [Vitis vinifera]

 Score =  295 bits (756), Expect = 4e-78,   Method: Compositional matrix adjust.
 Identities = 146/167 (87%), Positives = 161/167 (96%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +G+I+SPTRELSSQIY+VAQPFISTLP+VKSVLLVGGVEVK+D+KKIEEEGANLLIGTPG
Sbjct: 95  LGVILSPTRELSSQIYNVAQPFISTLPNVKSVLLVGGVEVKSDLKKIEEEGANLLIGTPG 154

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RLYDIMERMDVLDFRNLEIL+LDEADRLLDMGFQKQI+ II+RLPKLRRTGLFSATQTEA
Sbjct: 155 RLYDIMERMDVLDFRNLEILILDEADRLLDMGFQKQITSIIARLPKLRRTGLFSATQTEA 214

Query: 121 VEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVI 167
           VEELSKAGLRNPVRVEVRAE+KS + S SSQQLASSKTP GL++E +
Sbjct: 215 VEELSKAGLRNPVRVEVRAEAKSLNDSVSSQQLASSKTPSGLNIEYL 261

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356568033|ref|XP_003552218.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 18-like [Glycine max]

 Score =  278 bits (712), Expect = 6e-73,   Method: Compositional matrix adjust.
 Identities = 136/167 (81%), Positives = 154/167 (92%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +G+IISPTRELS+QIYHVAQPFISTL +VKS+LLVGG EVKAD+KKIEEEGAN+LIGTPG
Sbjct: 90  LGIIISPTRELSTQIYHVAQPFISTLANVKSMLLVGGAEVKADLKKIEEEGANILIGTPG 149

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RLYDIM RMDVLD +NLEIL+LDEADRLLDMGFQKQI+ II+ LPKLRRTGLFSATQTEA
Sbjct: 150 RLYDIMNRMDVLDLKNLEILILDEADRLLDMGFQKQITSIITLLPKLRRTGLFSATQTEA 209

Query: 121 VEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVI 167
           +EEL+KAGLRNPVRVEVRAE+KS +  ASS+Q  SSKTP GLH+E +
Sbjct: 210 IEELAKAGLRNPVRVEVRAETKSENGPASSKQPESSKTPSGLHIEYL 256

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224101199|ref|XP_002312182.1| predicted protein [Populus trichocarpa] gi|222852002|gb|EEE89549.1| predicted protein [Populus trichocarpa]

 Score =  277 bits (709), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 137/167 (82%), Positives = 155/167 (92%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+IISPTRELSSQIY+VAQPFI+TL + KS+LLVGG++VKADVK IEEEGANLLIGTPG
Sbjct: 92  MGIIISPTRELSSQIYNVAQPFIATLSNFKSMLLVGGMDVKADVKMIEEEGANLLIGTPG 151

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL+DIM+R+DVLDFRNLE+L+LDEADRLLDMGFQKQ++ IISRLPKLRRTGLFSATQTEA
Sbjct: 152 RLFDIMDRVDVLDFRNLEVLILDEADRLLDMGFQKQLNSIISRLPKLRRTGLFSATQTEA 211

Query: 121 VEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVI 167
           VEELSKAGLRNPV+VEVRAE+KS + S S QQLA SKTP GL LE +
Sbjct: 212 VEELSKAGLRNPVKVEVRAETKSLNNSVSGQQLAPSKTPSGLLLEYL 258

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356540003|ref|XP_003538481.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 18-like isoform 1 [Glycine max]

 Score =  274 bits (701), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 135/167 (80%), Positives = 151/167 (90%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +G+IISPTRELS+QIYHVAQ FISTL +VKS+LLVGG EVK D+KKIEEEGAN+LIGTPG
Sbjct: 90  LGIIISPTRELSTQIYHVAQSFISTLMNVKSMLLVGGAEVKTDIKKIEEEGANILIGTPG 149

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RLYDIM RMDVLD +NLEIL+LDEADRLLDMGFQKQI+ IIS LPKLRRTGLFSATQTEA
Sbjct: 150 RLYDIMNRMDVLDLKNLEILILDEADRLLDMGFQKQITSIISLLPKLRRTGLFSATQTEA 209

Query: 121 VEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVI 167
           +EEL+KAGLRNPVRVEVRAE+KS    ASS+Q  SSKTP GLH+E +
Sbjct: 210 IEELAKAGLRNPVRVEVRAETKSEKGPASSKQPESSKTPSGLHIEYL 256

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297806553|ref|XP_002871160.1| hypothetical protein ARALYDRAFT_908458 [Arabidopsis lyrata subsp. lyrata] gi|297316997|gb|EFH47419.1| hypothetical protein ARALYDRAFT_908458 [Arabidopsis lyrata subsp. lyrata]

 Score =  271 bits (692), Expect = 1e-70,   Method: Compositional matrix adjust.
 Identities = 135/167 (80%), Positives = 150/167 (89%), Gaps = 4/167 (2%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+IISPTRELSSQIY+VAQPF+STL +V SVLLVGG EVKAD+K IEEEG NLLIGTPG
Sbjct: 92  MGVIISPTRELSSQIYNVAQPFVSTLANVNSVLLVGGREVKADMKIIEEEGCNLLIGTPG 151

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL DIMERM++LDFRNLEIL+LDEADRLL+MGFQ+Q++YIISRLPK RRTGLFSATQTE 
Sbjct: 152 RLSDIMERMEILDFRNLEILILDEADRLLEMGFQRQVNYIISRLPKQRRTGLFSATQTEG 211

Query: 121 VEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVI 167
           VEEL+KAGLRNPVRVEVRA+SKS     SSQQ  +SKTP GLHLE I
Sbjct: 212 VEELAKAGLRNPVRVEVRAKSKSE----SSQQFTNSKTPSGLHLEYI 254

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15239115|ref|NP_196164.1| DEAD-box ATP-dependent RNA helicase 18 [Arabidopsis thaliana] gi|75334017|sp|Q9FLB0.1|RH18_ARATH RecName: Full=DEAD-box ATP-dependent RNA helicase 18 gi|10176757|dbj|BAB09988.1| ATP-dependent RNA helicase-like protein [Arabidopsis thaliana] gi|332003492|gb|AED90875.1| DEAD-box ATP-dependent RNA helicase 18 [Arabidopsis thaliana]

 Score =  268 bits (686), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 133/167 (79%), Positives = 151/167 (90%), Gaps = 4/167 (2%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+IISPTRELS+QIY+VAQPF+STL +V SVLLVGG EVKAD+K IEEEG N+LIGTPG
Sbjct: 92  MGVIISPTRELSTQIYNVAQPFVSTLANVNSVLLVGGREVKADMKIIEEEGCNVLIGTPG 151

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL DIMERM++LDFRNLEIL+LDEADRLL+MGFQ+Q++YIISRLPK RRTGLFSATQTE 
Sbjct: 152 RLSDIMERMEILDFRNLEILILDEADRLLEMGFQRQVNYIISRLPKQRRTGLFSATQTEG 211

Query: 121 VEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVI 167
           VEEL+KAGLRNPVRVEVRA+SKS     SSQQL +SKTP GLHLE +
Sbjct: 212 VEELAKAGLRNPVRVEVRAKSKSE----SSQQLTNSKTPSGLHLEYM 254

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255559531|ref|XP_002520785.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis] gi|223539916|gb|EEF41494.1| dead box ATP-dependent RNA helicase, putative [Ricinus communis]

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 138/177 (77%), Positives = 160/177 (90%), Gaps = 1/177 (0%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+I+SPTRELSSQIY+VAQPFI TL +VKS+LLVGGV+VKADVKKIEEEGAN+LIGTPG
Sbjct: 93  MGIILSPTRELSSQIYNVAQPFIETLSNVKSMLLVGGVDVKADVKKIEEEGANILIGTPG 152

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL+DIMER+D+LDFRNLE+L+LDEADRLLDMGFQKQI+ IISRLPKLRRTGLFSATQTEA
Sbjct: 153 RLFDIMERVDILDFRNLEVLILDEADRLLDMGFQKQITSIISRLPKLRRTGLFSATQTEA 212

Query: 121 VEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNHH 177
           VEEL+KAGLRNPVRVEVRA++KS +  ++S QL+SSKTP GL LE +     M+  H
Sbjct: 213 VEELAKAGLRNPVRVEVRAQTKSLN-ESASSQLSSSKTPSGLQLEYLECEADMKPSH 268

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357461389|ref|XP_003600976.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula] gi|355490024|gb|AES71227.1| DEAD-box ATP-dependent RNA helicase [Medicago truncatula]

 Score =  267 bits (682), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 132/176 (75%), Positives = 156/176 (88%), Gaps = 9/176 (5%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +G+IISPTREL+SQIYHVAQPFISTL +VKS+LLVGGVEVKAD+KKIEEEGAN+LIGTPG
Sbjct: 104 LGVIISPTRELASQIYHVAQPFISTLANVKSMLLVGGVEVKADIKKIEEEGANVLIGTPG 163

Query: 61  RLYDIMERMDVLDFRNLE---------ILVLDEADRLLDMGFQKQISYIISRLPKLRRTG 111
           RL+DIM RMD+LDF++ E         IL+LDEADRLLDMGFQKQI+ II+ LPKLRRTG
Sbjct: 164 RLHDIMNRMDILDFKSFEVYLLEKIGHILILDEADRLLDMGFQKQINAIITELPKLRRTG 223

Query: 112 LFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVI 167
           LFSATQT+AVEEL+KAGLRNPVRVEVRAE+K+ + SASS+++ SSKTP GL +E +
Sbjct: 224 LFSATQTQAVEELAKAGLRNPVRVEVRAETKTANDSASSKKIESSKTPSGLQIEYL 279

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|110736442|dbj|BAF00189.1| ATP-dependent RNA helicase-like protein [Arabidopsis thaliana]

 Score =  265 bits (676), Expect = 7e-69,   Method: Compositional matrix adjust.
 Identities = 132/167 (79%), Positives = 150/167 (89%), Gaps = 4/167 (2%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+IISPTRELS+QIY+VAQPF+STL +V SVLLVGG EVKAD+K IEEEG N+LIGTPG
Sbjct: 92  MGVIISPTRELSTQIYNVAQPFVSTLANVNSVLLVGGREVKADMKIIEEEGCNVLIGTPG 151

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL DIMERM++LDFRNLEIL+LDEADRLL+M FQ+Q++YIISRLPK RRTGLFSATQTE 
Sbjct: 152 RLSDIMERMEILDFRNLEILILDEADRLLEMRFQRQVNYIISRLPKQRRTGLFSATQTEG 211

Query: 121 VEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVI 167
           VEEL+KAGLRNPVRVEVRA+SKS     SSQQL +SKTP GLHLE +
Sbjct: 212 VEELAKAGLRNPVRVEVRAKSKSE----SSQQLTNSKTPSGLHLEYM 254

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	183
TAIR|locus:2153564	593	AT5G05450 [Arabidopsis thalian	0.879	0.271	0.806	6e-64
TAIR|locus:2825324	558	AT1G71370 [Arabidopsis thalian	0.781	0.256	0.769	4.9e-53
TAIR|locus:2032338	465	AT1G71280 [Arabidopsis thalian	0.732	0.288	0.657	1.7e-41
ZFIN|ZDB-GENE-021212-1	593	ddx55 "DEAD (Asp-Glu-Ala-Asp)	0.825	0.254	0.5	4.5e-33
UNIPROTKB|E2R316	483	DDX55 "Uncharacterized protein	0.825	0.312	0.487	8.5e-33
UNIPROTKB|F1NJA0	591	DDX55 "ATP-dependent RNA helic	0.830	0.257	0.490	2.7e-32
UNIPROTKB|Q5ZLN8	591	DDX55 "ATP-dependent RNA helic	0.830	0.257	0.490	2.7e-32
UNIPROTKB|F1P8J6	599	DDX55 "Uncharacterized protein	0.825	0.252	0.487	2.9e-32
UNIPROTKB|F5H5U2	569	DDX55 "ATP-dependent RNA helic	0.825	0.265	0.493	3.6e-32
UNIPROTKB|Q8NHQ9	600	DDX55 "ATP-dependent RNA helic	0.825	0.251	0.493	4.9e-32

TAIR|locus:2153564 AT5G05450 [Arabidopsis thaliana (taxid:3702)]

 Score = 652 (234.6 bits), Expect = 6.0e-64, P = 6.0e-64
 Identities = 133/165 (80%), Positives = 150/165 (90%)

Query:     1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             MG+IISPTRELS+QIY+VAQPF+STL +V SVLLVGG EVKAD+K IEEEG N+LIGTPG
Sbjct:    92 MGVIISPTRELSTQIYNVAQPFVSTLANVNSVLLVGGREVKADMKIIEEEGCNVLIGTPG 151

Query:    61 RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
             RL DIMERM++LDFRNLEIL+LDEADRLL+MGFQ+Q++YIISRLPK RRTGLFSATQTE 
Sbjct:   152 RLSDIMERMEILDFRNLEILILDEADRLLEMGFQRQVNYIISRLPKQRRTGLFSATQTEG 211

Query:   121 VEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLE 165
             VEEL+KAGLRNPVRVEVRA+SKS     SSQQL +SKTP GLHLE
Sbjct:   212 VEELAKAGLRNPVRVEVRAKSKSE----SSQQLTNSKTPSGLHLE 252

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

TAIR|locus:2825324 AT1G71370 [Arabidopsis thaliana (taxid:3702)]

 Score = 549 (198.3 bits), Expect = 4.9e-53, P = 4.9e-53
 Identities = 110/143 (76%), Positives = 129/143 (90%)

Query:     1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             MG+IISPTRELS+QI+ VA+PF+STLP+V SVLLVGG EV+AD+  +EEEGANLLIGTPG
Sbjct:    92 MGVIISPTRELSAQIHKVAEPFVSTLPNVNSVLLVGGREVEADMNTLEEEGANLLIGTPG 151

Query:    61 RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
             RL D+M+RM+ LDFRNLEIL+LDEADRLLDMGFQKQ++YIISRLPK RRTGLFSATQT+A
Sbjct:   152 RLSDMMKRMEFLDFRNLEILILDEADRLLDMGFQKQVNYIISRLPKQRRTGLFSATQTQA 211

Query:   121 VEELSKAGLRNPVRVEVRAESKS 143
             V +L+KAGLRN + V   AESKS
Sbjct:   212 VADLAKAGLRNAMEVISGAESKS 234

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

TAIR|locus:2032338 AT1G71280 [Arabidopsis thaliana (taxid:3702)]

 Score = 440 (159.9 bits), Expect = 1.7e-41, P = 1.7e-41
 Identities = 94/143 (65%), Positives = 114/143 (79%)

Query:     1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             MG+IISPTRELS+QI+ VA+         +        EV+AD+  +EEEGANLLIGTPG
Sbjct:    93 MGVIISPTRELSAQIHKVARAVRLDFAKCR--------EVEADMNTLEEEGANLLIGTPG 144

Query:    61 RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
             RL D+M+RM+ LDFRNLEIL+LDEADRLLDMGFQKQ++YIISRLPK RRTGLFSATQT+A
Sbjct:   145 RLSDMMKRMEFLDFRNLEILILDEADRLLDMGFQKQVNYIISRLPKQRRTGLFSATQTQA 204

Query:   121 VEELSKAGLRNPVRVEVRAESKS 143
             V +L+KAGLRNP  ++  A+ KS
Sbjct:   205 VADLAKAGLRNPY-LKCEADQKS 226

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;ISS

GO:0009507 "chloroplast" evidence=ISM

GO:0008266 "poly(U) RNA binding" evidence=IDA

ZFIN|ZDB-GENE-021212-1 ddx55 "DEAD (Asp-Glu-Ala-Asp) box polypeptide 55" [Danio rerio (taxid:7955)]

 Score = 365 (133.5 bits), Expect = 4.5e-33, P = 4.5e-33
 Identities = 80/160 (50%), Positives = 110/160 (68%)

Query:     3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
             +II+PTREL+ QI  V   F+   P    +LL+GG     DV+K++ +GAN++I TPGRL
Sbjct:    86 LIITPTRELAMQISEVMGRFLQGFPQFTQILLIGGSNPIEDVEKLKTQGANIIIATPGRL 145

Query:    63 YDIMERM-DVLDF----RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ 117
              D+  R  D LD     ++L++LVLDEADRLLDMGF+  ++ I+  LPK RRTGLFSATQ
Sbjct:   146 EDMFRRKADGLDLATAVKSLDVLVLDEADRLLDMGFEASLNTILGYLPKQRRTGLFSATQ 205

Query:   118 TEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSK 157
             T+ +E+L +AGLRNPVR+ V+ +     V+ASS Q   +K
Sbjct:   206 TQELEKLVRAGLRNPVRITVKEKG----VAASSVQKTPAK 241

GO:0003676 "nucleic acid binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

GO:0004386 "helicase activity" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0016787 "hydrolase activity" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

UNIPROTKB|E2R316 DDX55 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 358 (131.1 bits), Expect = 8.5e-33, P = 8.5e-33
 Identities = 78/160 (48%), Positives = 107/160 (66%)

Query:     3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
             +II+PTREL+ Q+  V   F  + P    +L +GG     DV + +E+G N+++ TPGRL
Sbjct:    86 IIITPTRELAIQVDEVLAHFTKSFPQFSQILWIGGRNPADDVSRFKEQGGNIIVATPGRL 145

Query:    63 YDIMER-MDVLDF----RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ 117
              D+  R ++ LD     ++LE+LVLDEADRLLDMGF+  I+ I+  LPK RRTGLFSATQ
Sbjct:   146 EDMFRRKVEGLDLASCVKSLEVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSATQ 205

Query:   118 TEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSK 157
             T+ VE L +AGLRNPVR+ V+ +     V+ASS Q   S+
Sbjct:   206 TQEVESLVRAGLRNPVRISVKEKG----VAASSTQKTPSR 241

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

UNIPROTKB|F1NJA0 DDX55 "ATP-dependent RNA helicase DDX55" [Gallus gallus (taxid:9031)]

 Score = 358 (131.1 bits), Expect = 2.7e-32, P = 2.7e-32
 Identities = 81/165 (49%), Positives = 109/165 (66%)

Query:     3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
             +II+PTREL+ QI  V   F    P    +LL+GG     DV+K +E G N+++ TPGRL
Sbjct:    86 IIITPTRELAIQIDEVLTHFTKHFPKFSQILLIGGRNPMEDVEKFKEHGGNIIVATPGRL 145

Query:    63 YDIMERM-DVLDF----RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ 117
              D+  R  D LD     ++L++LVLDEADRLLDMGF+  ++ I++ LPK RRTGLFSATQ
Sbjct:   146 EDLFRRKADGLDLASCVKSLDVLVLDEADRLLDMGFESSLNAILAFLPKQRRTGLFSATQ 205

Query:   118 TEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGL 162
             T+ VE L +AGLRNPVR+ V+ +     V+A++ Q    KTP  L
Sbjct:   206 TQEVENLVRAGLRNPVRISVKEKG----VAATNTQ----KTPTRL 242

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q5ZLN8 DDX55 "ATP-dependent RNA helicase DDX55" [Gallus gallus (taxid:9031)]

 Score = 358 (131.1 bits), Expect = 2.7e-32, P = 2.7e-32
 Identities = 81/165 (49%), Positives = 109/165 (66%)

Query:     3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
             +II+PTREL+ QI  V   F    P    +LL+GG     DV+K +E G N+++ TPGRL
Sbjct:    86 IIITPTRELAIQIDEVLTHFTKHFPKFSQILLIGGRNPMEDVEKFKEHGGNIIVATPGRL 145

Query:    63 YDIMERM-DVLDF----RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ 117
              D+  R  D LD     ++L++LVLDEADRLLDMGF+  ++ I++ LPK RRTGLFSATQ
Sbjct:   146 EDLFRRKADGLDLASCVKSLDVLVLDEADRLLDMGFESSLNAILAFLPKQRRTGLFSATQ 205

Query:   118 TEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGL 162
             T+ VE L +AGLRNPVR+ V+ +     V+A++ Q    KTP  L
Sbjct:   206 TQEVENLVRAGLRNPVRISVKEKG----VAATNTQ----KTPTRL 242

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1P8J6 DDX55 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 358 (131.1 bits), Expect = 2.9e-32, P = 2.9e-32
 Identities = 78/160 (48%), Positives = 107/160 (66%)

Query:     3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
             +II+PTREL+ Q+  V   F  + P    +L +GG     DV + +E+G N+++ TPGRL
Sbjct:    86 IIITPTRELAIQVDEVLAHFTKSFPQFSQILWIGGRNPADDVSRFKEQGGNIIVATPGRL 145

Query:    63 YDIMER-MDVLDF----RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ 117
              D+  R ++ LD     ++LE+LVLDEADRLLDMGF+  I+ I+  LPK RRTGLFSATQ
Sbjct:   146 EDMFRRKVEGLDLASCVKSLEVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSATQ 205

Query:   118 TEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSK 157
             T+ VE L +AGLRNPVR+ V+ +     V+ASS Q   S+
Sbjct:   206 TQEVESLVRAGLRNPVRISVKEKG----VAASSTQKTPSR 241

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|F5H5U2 DDX55 "ATP-dependent RNA helicase DDX55" [Homo sapiens (taxid:9606)]

 Score = 356 (130.4 bits), Expect = 3.6e-32, P = 3.6e-32
 Identities = 79/160 (49%), Positives = 107/160 (66%)

Query:     3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
             +II+PTREL+ QI  V   F    P+   +L +GG     DV++ +++G N+++ TPGRL
Sbjct:    86 IIITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGRNPGEDVERFKQQGGNIIVATPGRL 145

Query:    63 YDIMERM-DVLDF----RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ 117
              D+  R  + LD     R+L++LVLDEADRLLDMGF+  I+ I+  LPK RRTGLFSATQ
Sbjct:   146 EDMFRRKAEGLDLASCVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSATQ 205

Query:   118 TEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSK 157
             T+ VE L +AGLRNPVRV V+ +     V+ASS Q   S+
Sbjct:   206 TQEVENLVRAGLRNPVRVSVKEKG----VAASSAQKTPSR 241

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|Q8NHQ9 DDX55 "ATP-dependent RNA helicase DDX55" [Homo sapiens (taxid:9606)]

 Score = 356 (130.4 bits), Expect = 4.9e-32, P = 4.9e-32
 Identities = 79/160 (49%), Positives = 107/160 (66%)

Query:     3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
             +II+PTREL+ QI  V   F    P+   +L +GG     DV++ +++G N+++ TPGRL
Sbjct:    86 IIITPTRELAIQIDEVLSHFTKHFPEFSQILWIGGRNPGEDVERFKQQGGNIIVATPGRL 145

Query:    63 YDIMERM-DVLDF----RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ 117
              D+  R  + LD     R+L++LVLDEADRLLDMGF+  I+ I+  LPK RRTGLFSATQ
Sbjct:   146 EDMFRRKAEGLDLASCVRSLDVLVLDEADRLLDMGFEASINTILEFLPKQRRTGLFSATQ 205

Query:   118 TEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSK 157
             T+ VE L +AGLRNPVRV V+ +     V+ASS Q   S+
Sbjct:   206 TQEVENLVRAGLRNPVRVSVKEKG----VAASSAQKTPSR 241

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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9FLB0	RH18_ARATH	3, ., 6, ., 4, ., 1, 3	0.7964	0.8907	0.2748	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

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

---

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	183
cd00268	203	cd00268, DEADc, DEAD-box helicases	2e-54
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	1e-44
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	5e-35
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	8e-35
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	7e-29
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	6e-28
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	2e-27
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	2e-27
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	6e-25
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	2e-24
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	3e-22
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	3e-22
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	6e-22
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	1e-20
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-19

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

 Score =  171 bits (435), Expect = 2e-54
 Identities = 60/136 (44%), Positives = 91/136 (66%), Gaps = 3/136 (2%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             +I++PTREL+ QI  VA+       ++K V++ GG  +   ++K++  G ++++ TPG
Sbjct: 71  QALILAPTRELALQIAEVARKLGK-HTNLKVVVIYGGTSIDKQIRKLKR-GPHIVVATPG 128

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL D++ER   LD   ++ LVLDEADR+LDMGF+ QI  I+  LPK R+T LFSAT  + 
Sbjct: 129 RLLDLLERG-KLDLSKVKYLVLDEADRMLDMGFEDQIREILKLLPKDRQTLLFSATMPKE 187

Query: 121 VEELSKAGLRNPVRVE 136
           V +L++  LRNPVR+ 
Sbjct: 188 VRDLARKFLRNPVRIL 203

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 =  153 bits (389), Expect = 1e-44
 Identities = 56/151 (37%), Positives = 89/151 (58%), Gaps = 2/151 (1%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTREL+ QI    +     L  ++  ++ GGV ++  ++ ++  G ++++ TPGRL
Sbjct: 103 LILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKR-GVDIVVATPGRL 161

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D+++R   LD   +E LVLDEADR+LDMGF   I  I+  LP  R+T LFSAT  + + 
Sbjct: 162 LDLIKR-GKLDLSGVETLVLDEADRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIR 220

Query: 123 ELSKAGLRNPVRVEVRAESKSHHVSASSQQL 153
           EL++  L +PV +EV  E     +    Q  
Sbjct: 221 ELARRYLNDPVEIEVSVEKLERTLKKIKQFY 251

Length = 513

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

 Score =  120 bits (303), Expect = 5e-35
 Identities = 52/124 (41%), Positives = 79/124 (63%), Gaps = 1/124 (0%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             ++++PTREL+ QIY   +     L  ++  LL GG  +K   +K+++  A++L+GTPG
Sbjct: 47  QALVLAPTRELAEQIYEELKKLFKILG-LRVALLTGGTSLKEQARKLKKGKADILVGTPG 105

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL D++ R  +   +NL++LVLDEA RLLDMGF   +  I+SRLP  R+  L SAT    
Sbjct: 106 RLLDLLRRGKLKLLKNLKLLVLDEAHRLLDMGFGDDLEEILSRLPPDRQILLLSATLPRN 165

Query: 121 VEEL 124
           +E+L
Sbjct: 166 LEDL 169

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

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

 Score =  126 bits (319), Expect = 8e-35
 Identities = 60/139 (43%), Positives = 86/139 (61%), Gaps = 10/139 (7%)

Query: 3   MIISPTRELSSQIYHVAQPFISTL----PDVKSVLLVGGVEVKADVKKIEEEGANLLIGT 58
           +++ PTREL+ Q   VA+  I  L    P++K + L GGV +   +  +E  GA++++GT
Sbjct: 76  LVLCPTRELADQ---VAKE-IRRLARFIPNIKVLTLCGGVPMGPQIDSLEH-GAHIIVGT 130

Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR+ D + +   LD   L  LVLDEADR+LDMGFQ  I  II + P  R+T LFSAT  
Sbjct: 131 PGRILDHLRK-GTLDLDALNTLVLDEADRMLDMGFQDAIDAIIRQAPARRQTLLFSATYP 189

Query: 119 EAVEELSKAGLRNPVRVEV 137
           E +  +S+   R+PV V+V
Sbjct: 190 EGIAAISQRFQRDPVEVKV 208

Length = 460

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

 Score =  105 bits (264), Expect = 7e-29
 Identities = 50/135 (37%), Positives = 79/135 (58%), Gaps = 2/135 (1%)

Query: 4   IISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLY 63
           ++ PTREL+ Q     +    +L  +K V L GG   +  ++K+E    ++L+ TPGRL 
Sbjct: 59  VLVPTRELAEQWAEELKKLGPSLG-LKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLL 117

Query: 64  DIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEE 123
           D++E  D L   N+++++LDEA RLLD GF  Q+  ++  LPK  +  L SAT  E +E 
Sbjct: 118 DLLEN-DKLSLSNVDLVILDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIEN 176

Query: 124 LSKAGLRNPVRVEVR 138
           L +  L +PV ++V 
Sbjct: 177 LLELFLNDPVFIDVG 191

Length = 201

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

 Score =  107 bits (270), Expect = 6e-28
 Identities = 56/146 (38%), Positives = 95/146 (65%), Gaps = 4/146 (2%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTREL++QI    + +   L +++S+++ GGV +   + K+   G ++L+ TPGRL
Sbjct: 79  LILTPTRELAAQIGENVRDYSKYL-NIRSLVVFGGVSINPQMMKLRG-GVDVLVATPGRL 136

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D +E  + +    +EILVLDEADR+LDMGF   I  ++++LP  R+  LFSAT ++ ++
Sbjct: 137 LD-LEHQNAVKLDQVEILVLDEADRMLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIK 195

Query: 123 ELSKAGLRNPVRVEV-RAESKSHHVS 147
            L++  L NP+ +EV R  + S  V+
Sbjct: 196 ALAEKLLHNPLEIEVARRNTASEQVT 221

Length = 456

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

 Score =  106 bits (267), Expect = 2e-27
 Identities = 56/145 (38%), Positives = 84/145 (57%), Gaps = 5/145 (3%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTREL+ QI+  A+P       +K  L  GG      +K +E  G ++LIGT GRL
Sbjct: 87  LIMAPTRELAVQIHADAEPLAQA-TGLKLGLAYGGDGYDKQLKVLES-GVDILIGTTGRL 144

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLP--KLRRTGLFSATQTEA 120
            D   + + ++   ++++VLDEADR+ D+GF K I ++  R+P    R   LFSAT +  
Sbjct: 145 IDYA-KQNHINLGAIQVVVLDEADRMFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYR 203

Query: 121 VEELSKAGLRNPVRVEVRAESKSHH 145
           V EL+   + NP  VEV  E K+ H
Sbjct: 204 VRELAFEHMNNPEYVEVEPEQKTGH 228

Length = 423

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

 Score =  106 bits (266), Expect = 2e-27
 Identities = 58/144 (40%), Positives = 88/144 (61%), Gaps = 6/144 (4%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +II+PTREL  QI   A   ++    +  +  VGG++    +K++E    ++L+ TPGRL
Sbjct: 166 LIIAPTRELVVQIAKDAAA-LTKYTGLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRL 224

Query: 63  YDIMERMDV-LDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKL--RRTGLFSATQTE 119
            D  +R +V LD   +E++VLDEADR+LDMGF  Q+  II + P+   R+T LFSAT T+
Sbjct: 225 LDFNQRGEVHLDM--VEVMVLDEADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTD 282

Query: 120 AVEELSKAGLRNPVRVEVRAESKS 143
            V  L+K    +P  VE+  E+ +
Sbjct: 283 DVMNLAKQWTTDPAIVEIEPENVA 306

Length = 475

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

 Score =  100 bits (250), Expect = 6e-25
 Identities = 53/141 (37%), Positives = 89/141 (63%), Gaps = 4/141 (2%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTREL+ QI+  A  F + L  ++  L+ GGV+     +++ ++G +++I TPGRL
Sbjct: 88  LILAPTRELAIQIHKDAVKFGADL-GLRFALVYGGVDYDKQ-RELLQQGVDVIIATPGRL 145

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPK--LRRTGLFSATQTEA 120
            D +++  V+     EI VLDEADR+ D+GF K I +++ R+P+   R+T LFSAT +  
Sbjct: 146 IDYVKQHKVVSLHACEICVLDEADRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHR 205

Query: 121 VEELSKAGLRNPVRVEVRAES 141
           V EL+   +  P ++ V  E+
Sbjct: 206 VLELAYEHMNEPEKLVVETET 226

Length = 572

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

 Score = 97.6 bits (243), Expect = 2e-24
 Identities = 50/138 (36%), Positives = 84/138 (60%), Gaps = 3/138 (2%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTREL+ QI  V       L  V+    VGG  V+ D+ K++  G ++++GTPGR+
Sbjct: 100 LILAPTRELAQQIQKVVLALGDYL-KVRCHACVGGTVVRDDINKLKA-GVHMVVGTPGRV 157

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
           YD++++   L   +L++ +LDEAD +L  GF+ QI  +  +LP   +  LFSAT    + 
Sbjct: 158 YDMIDK-RHLRVDDLKLFILDEADEMLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEIL 216

Query: 123 ELSKAGLRNPVRVEVRAE 140
           EL+   +R+P R+ V+ +
Sbjct: 217 ELTTKFMRDPKRILVKKD 234

Length = 401

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

 Score = 92.5 bits (230), Expect = 3e-22
 Identities = 50/136 (36%), Positives = 80/136 (58%), Gaps = 4/136 (2%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           ++++PTREL+ QI      F      +++ +  GGV  +  +  +   G  +LI  PGRL
Sbjct: 207 LVLAPTRELAEQIREQCNKF-GASSKIRNTVAYGGVPKRGQIYALRR-GVEILIACPGRL 264

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D +E  +V + R +  LVLDEADR+LDMGF+ QI  I+S++   R+T ++SAT  + V+
Sbjct: 265 IDFLES-NVTNLRRVTYLVLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQ 323

Query: 123 ELSKAGLRN-PVRVEV 137
            L++   +  PV V V
Sbjct: 324 SLARDLCKEEPVHVNV 339

Length = 545

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

 Score = 86.6 bits (215), Expect = 3e-22
 Identities = 42/113 (37%), Positives = 66/113 (58%), Gaps = 4/113 (3%)

Query: 4   IISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLY 63
           +++PTREL++Q+    +        +K   L+GG  +K   K +     ++++GTPGRL 
Sbjct: 35  VLAPTRELANQVAERLKELFG--EGIKVGYLIGGTSIKQQEKLLSG-KTDIVVGTPGRLL 91

Query: 64  DIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT 116
           D +ER   L  + L++L+LDEA RLL+ GF      I+ +LPK R+  L SAT
Sbjct: 92  DELER-LKLSLKKLDLLILDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSAT 143

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

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

 Score = 91.8 bits (228), Expect = 6e-22
 Identities = 50/139 (35%), Positives = 82/139 (58%), Gaps = 4/139 (2%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           ++++PTREL+ Q+      F   +  V  V L GG      ++ + + G  +++GTPGRL
Sbjct: 78  LVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRALRQ-GPQIVVGTPGRL 136

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D ++R   LD   L  LVLDEAD +L MGF + +  I++++P+  +T LFSAT  EA+ 
Sbjct: 137 LDHLKR-GTLDLSKLSGLVLDEADEMLRMGFIEDVETIMAQIPEGHQTALFSATMPEAIR 195

Query: 123 ELSKAGLRNPVRVEVRAES 141
            +++  ++ P   EVR +S
Sbjct: 196 RITRRFMKEP--QEVRIQS 212

Length = 629

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

 Score = 87.9 bits (218), Expect = 1e-20
 Identities = 46/137 (33%), Positives = 83/137 (60%), Gaps = 4/137 (2%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           + M+++PTREL  Q+   A+     LP  K+ L+VGG  +   + +I++ G  L++GTPG
Sbjct: 198 LAMVLTPTRELCVQVEDQAKVLGKGLP-FKTALVVGGDAMPQQLYRIQQ-GVELIVGTPG 255

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL D++ + D+ +  N+ +LVLDE D +L+ GF+ Q+  I   L +  +  LFSAT +  
Sbjct: 256 RLIDLLSKHDI-ELDNVSVLVLDEVDCMLERGFRDQVMQIFQALSQ-PQVLLFSATVSPE 313

Query: 121 VEELSKAGLRNPVRVEV 137
           VE+ + +  ++ + + +
Sbjct: 314 VEKFASSLAKDIILISI 330

Length = 518

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

 Score = 84.2 bits (209), Expect = 2e-19
 Identities = 51/149 (34%), Positives = 85/149 (57%), Gaps = 11/149 (7%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTREL+ Q+   A+   +    +    + GGV    +  ++  E  ++++ TPGRL
Sbjct: 77  LILTPTRELAMQVADQAREL-AKHTHLDIATITGGVAY-MNHAEVFSENQDIVVATPGRL 134

Query: 63  YDIMERMDVLDF--RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT-QTE 119
              ++ +   +F  R +E L+LDEADR+LDMGF + I  I +     ++T LFSAT + +
Sbjct: 135 ---LQYIKEENFDCRAVETLILDEADRMLDMGFAQDIETIAAETRWRKQTLLFSATLEGD 191

Query: 120 AVEELSKAGLRNPVRVEV---RAESKSHH 145
           AV++ ++  L +PV VE    R E K  H
Sbjct: 192 AVQDFAERLLNDPVEVEAEPSRRERKKIH 220

Length = 434

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	183
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	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
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	99.97
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	99.97
KOG4284	980	consensus DEAD box protein [Transcription]	99.97
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	99.97
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	99.96
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	99.96
PTZ00110	545	helicase; Provisional	99.96
KOG0327	397	consensus Translation initiation factor 4F, helica	99.96
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	99.96
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.96
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	99.96
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	99.96
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	99.95
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	99.95
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	99.95
KOG0334	997	consensus RNA helicase [RNA processing and modific	99.95
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.95
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.94
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.94
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.93
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.92
PTZ00424	401	helicase 45; Provisional	99.91
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.88
PRK09401	1176	reverse gyrase; Reviewed	99.86
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.86
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.82
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.79
PRK14701	1638	reverse gyrase; Provisional	99.79
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.78
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.77
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.76
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.75
PRK10689	1147	transcription-repair coupling factor; Provisional	99.73
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.71
PRK00254	720	ski2-like helicase; Provisional	99.68
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.67
PRK02362	737	ski2-like helicase; Provisional	99.66
PRK13767	876	ATP-dependent helicase; Provisional	99.65
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.63
PHA02653	675	RNA helicase NPH-II; Provisional	99.63
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.63
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.6
PRK01172	674	ski2-like helicase; Provisional	99.59
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.57
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.56
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.49
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.48
COG1204	766	Superfamily II helicase [General function predicti	99.47
COG1205	851	Distinct helicase family with a unique C-terminal	99.47
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.46
PHA02558	501	uvsW UvsW helicase; Provisional	99.45
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.42
COG1202	830	Superfamily II helicase, archaea-specific [General	99.41
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.41
PRK13766	773	Hef nuclease; Provisional	99.36
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.34
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.34
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.33
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.33
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.32
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.32
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.26
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	99.26
PRK05580	679	primosome assembly protein PriA; Validated	99.23
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.2
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.19
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.14
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	99.11
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.08
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.06
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.03
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	98.97
KOG0354	746	consensus DEAD-box like helicase [General function	98.91
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.9
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	98.89
KOG2340	698	consensus Uncharacterized conserved protein [Funct	98.89
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	98.76
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	98.75
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	98.69
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	98.51
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.5
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	98.45
PRK09694	878	helicase Cas3; Provisional	98.43
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	98.42
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.42
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	98.36
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	98.34
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.22
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	98.19
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.02
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	97.96
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	97.93
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	97.9
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	97.8
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	97.69
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.65
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	97.6
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	97.46
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	97.41
PRK12326	764	preprotein translocase subunit SecA; Reviewed	97.3
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	97.26
PRK04914	956	ATP-dependent helicase HepA; Validated	97.21
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	97.19
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.17
PRK14873	665	primosome assembly protein PriA; Provisional	97.15
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	97.12
KOG0387	923	consensus Transcription-coupled repair protein CSB	97.11
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	97.04
CHL00122	870	secA preprotein translocase subunit SecA; Validate	96.95
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	96.94
COG1198	730	PriA Primosomal protein N' (replication factor Y)	96.94
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	96.92
KOG0353	695	consensus ATP-dependent DNA helicase [General func	96.9
COG4096	875	HsdR Type I site-specific restriction-modification	96.84
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	96.84
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	96.84
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	96.6
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	96.5
PRK10689	1147	transcription-repair coupling factor; Provisional	96.41
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	96.37
KOG4439	901	consensus RNA polymerase II transcription terminat	96.27
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	96.23
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	96.1
COG0610	962	Type I site-specific restriction-modification syst	96.05
KOG3089	271	consensus Predicted DEAD-box-containing helicase [	96.0
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	95.73
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	95.55
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	95.5
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	95.37
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	95.33
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	95.26
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	95.21
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	95.05
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	94.84
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	94.78
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	94.76
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	94.6
PRK05580	679	primosome assembly protein PriA; Validated	94.57
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	94.5
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	94.29
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	94.12
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	94.03
PTZ00110	545	helicase; Provisional	94.02
PRK05298	652	excinuclease ABC subunit B; Provisional	93.97
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	93.84
PTZ00424	401	helicase 45; Provisional	93.74
KOG1001	674	consensus Helicase-like transcription factor HLTF/	93.68
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	93.62
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	93.57
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	93.47
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	93.45
PRK15483	986	type III restriction-modification system StyLTI en	93.31
TIGR00595	505	priA primosomal protein N'. All proteins in this f	93.25
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	93.13
KOG1123	776	consensus RNA polymerase II transcription initiati	93.1
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	93.07
PRK13767	876	ATP-dependent helicase; Provisional	93.02
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	92.99
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	92.88
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	92.58
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	92.26
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	92.23
PF02463	220	SMC_N: RecF/RecN/SMC N terminal domain; InterPro:	92.01
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	91.92
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	91.88
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	91.84
PHA02653	675	RNA helicase NPH-II; Provisional	91.74
KOG1002	791	consensus Nucleotide excision repair protein RAD16	91.69
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	91.58
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	91.56
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	91.56
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	91.54
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	91.37
COG1198	730	PriA Primosomal protein N' (replication factor Y)	91.32
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	91.23
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	91.02
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	90.98
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	90.71
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	90.69
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	90.54
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	90.52
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	90.43
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	90.29
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	89.47
PRK09694	878	helicase Cas3; Provisional	89.47
COG4889	1518	Predicted helicase [General function prediction on	89.18
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	89.05
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	89.05
PRK09401	1176	reverse gyrase; Reviewed	89.04
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	88.45
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	88.36
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	88.33
PRK12422	445	chromosomal replication initiation protein; Provis	88.24
KOG0354	746	consensus DEAD-box like helicase [General function	88.05
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	87.82
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	87.36
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	87.05
KOG0964	1200	consensus Structural maintenance of chromosome pro	86.83
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	86.58
PRK05642	234	DNA replication initiation factor; Validated	86.12
PRK01172	674	ski2-like helicase; Provisional	86.02
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	85.97
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	85.94
KOG0991	333	consensus Replication factor C, subunit RFC2 [Repl	85.68
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	85.44
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	85.39
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	85.14
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	85.06
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	84.86
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	84.84
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	84.75
PF13604	196	AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL	84.71
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	84.41
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	84.29
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	84.15
PRK13766	773	Hef nuclease; Provisional	83.81
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	83.77
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	83.77
TIGR01447	586	recD exodeoxyribonuclease V, alpha subunit. This f	83.62
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	83.56
PRK10875	615	recD exonuclease V subunit alpha; Provisional	83.23
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	82.84
PRK04914	956	ATP-dependent helicase HepA; Validated	82.63
KOG0327	397	consensus Translation initiation factor 4F, helica	81.71
COG1196	1163	Smc Chromosome segregation ATPases [Cell division	81.62
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	80.8
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	80.72
PRK06893	229	DNA replication initiation factor; Validated	80.67
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	80.65
PHA02544	316	44 clamp loader, small subunit; Provisional	80.01

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

Probab=100.00  E-value=7.9e-38  Score=251.88  Aligned_cols=165  Identities=34%  Similarity=0.588  Sum_probs=159.1

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +|+||+||||||.||.++++.++..+ +++++.++||.+...+...+. ..|||+|||||+|++++++++.++++.++++
T Consensus       131 ~~lVLtPtRELA~QI~e~fe~Lg~~i-glr~~~lvGG~~m~~q~~~L~-kkPhilVaTPGrL~dhl~~Tkgf~le~lk~L  208 (476)
T KOG0330|consen  131 FALVLTPTRELAQQIAEQFEALGSGI-GLRVAVLVGGMDMMLQANQLS-KKPHILVATPGRLWDHLENTKGFSLEQLKFL  208 (476)
T ss_pred             eEEEecCcHHHHHHHHHHHHHhcccc-CeEEEEEecCchHHHHHHHhh-cCCCEEEeCcHHHHHHHHhccCccHHHhHHH
Confidence            58999999999999999999999888 999999999999999999985 5899999999999999998899999999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||++++++|.+.+..|++.+|.++|+++||||++..+..+.+.-+.+|+.|.+...               +.+.+
T Consensus       209 VlDEADrlLd~dF~~~ld~ILk~ip~erqt~LfsATMt~kv~kL~rasl~~p~~v~~s~k---------------y~tv~  273 (476)
T KOG0330|consen  209 VLDEADRLLDMDFEEELDYILKVIPRERQTFLFSATMTKKVRKLQRASLDNPVKVAVSSK---------------YQTVD  273 (476)
T ss_pred             hhchHHhhhhhhhHHHHHHHHHhcCccceEEEEEeecchhhHHHHhhccCCCeEEeccch---------------hcchH
Confidence            999999999999999999999999999999999999999999999999999999999888               99999


Q ss_pred             CceEEEEEecCcchhhhhhccc
Q 030094          161 GLHLEVIWNVNQMRNHHNLLIC  182 (183)
Q Consensus       161 ~l~q~~i~~~~~~k~~~ll~ll  182 (183)
                      +++|+|++++..+|..+|+.+|
T Consensus       274 ~lkQ~ylfv~~k~K~~yLV~ll  295 (476)
T KOG0330|consen  274 HLKQTYLFVPGKDKDTYLVYLL  295 (476)
T ss_pred             HhhhheEeccccccchhHHHHH
Confidence            9999999999999999999875

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

Probab=100.00  E-value=8.5e-36  Score=244.81  Aligned_cols=168  Identities=57%  Similarity=0.879  Sum_probs=158.9

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHh-cCCcCCCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMER-MDVLDFRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~-~~~~~l~~l~~l   80 (183)
                      |||+.||||||.||++++..+..+++++.+.+++||.+.+++...+...+|+|+|||||||.+++.+ ...+++++++++
T Consensus        82 alIIsPTRELa~QI~~V~~~F~~~l~~l~~~l~vGG~~v~~Di~~fkee~~nIlVgTPGRL~di~~~~~~~l~~rsLe~L  161 (567)
T KOG0345|consen   82 ALIISPTRELARQIREVAQPFLEHLPNLNCELLVGGRSVEEDIKTFKEEGPNILVGTPGRLLDILQREAEKLSFRSLEIL  161 (567)
T ss_pred             EEEecCcHHHHHHHHHHHHHHHHhhhccceEEEecCccHHHHHHHHHHhCCcEEEeCchhHHHHHhchhhhccccccceE
Confidence            8999999999999999999999998999999999999999999999999999999999999999987 445778899999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||+++++||...++.|++.+|++|++=+||||.+.++..+++..++||+.|.+..+++             ..+|+
T Consensus       162 VLDEADrLldmgFe~~~n~ILs~LPKQRRTGLFSATq~~~v~dL~raGLRNpv~V~V~~k~~-------------~~tPS  228 (567)
T KOG0345|consen  162 VLDEADRLLDMGFEASVNTILSFLPKQRRTGLFSATQTQEVEDLARAGLRNPVRVSVKEKSK-------------SATPS  228 (567)
T ss_pred             EecchHhHhcccHHHHHHHHHHhcccccccccccchhhHHHHHHHHhhccCceeeeeccccc-------------ccCch
Confidence            99999999999999999999999999999999999999999999999999999999988843             34999


Q ss_pred             CceEEEEEecCcchhhhhhccc
Q 030094          161 GLHLEVIWNVNQMRNHHNLLIC  182 (183)
Q Consensus       161 ~l~q~~i~~~~~~k~~~ll~ll  182 (183)
                      .++.+|+.|++.+|.+.|+.+|
T Consensus       229 ~L~~~Y~v~~a~eK~~~lv~~L  250 (567)
T KOG0345|consen  229 SLALEYLVCEADEKLSQLVHLL  250 (567)
T ss_pred             hhcceeeEecHHHHHHHHHHHH
Confidence            9999999999999999998775

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=1.4e-35  Score=247.57  Aligned_cols=164  Identities=40%  Similarity=0.586  Sum_probs=154.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      |||+.||||||.|+++++.+.+++. ++++.++.||...+.+...+  ++++|+|||||||+.+|..+..++.++++++|
T Consensus       144 alIISPTRELA~QtFevL~kvgk~h-~fSaGLiiGG~~~k~E~eRi--~~mNILVCTPGRLLQHmde~~~f~t~~lQmLv  220 (758)
T KOG0343|consen  144 ALIISPTRELALQTFEVLNKVGKHH-DFSAGLIIGGKDVKFELERI--SQMNILVCTPGRLLQHMDENPNFSTSNLQMLV  220 (758)
T ss_pred             eEEecchHHHHHHHHHHHHHHhhcc-ccccceeecCchhHHHHHhh--hcCCeEEechHHHHHHhhhcCCCCCCcceEEE
Confidence            8999999999999999999998876 99999999999998888887  57999999999999999997889999999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCccC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLG  161 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (183)
                      +||||+++++||...+..|++.+|+.+|+++||||-+..+..+++..++||.+|.+.....             ..+|++
T Consensus       221 LDEADR~LDMGFk~tL~~Ii~~lP~~RQTLLFSATqt~svkdLaRLsL~dP~~vsvhe~a~-------------~atP~~  287 (758)
T KOG0343|consen  221 LDEADRMLDMGFKKTLNAIIENLPKKRQTLLFSATQTKSVKDLARLSLKDPVYVSVHENAV-------------AATPSN  287 (758)
T ss_pred             eccHHHHHHHhHHHHHHHHHHhCChhheeeeeecccchhHHHHHHhhcCCCcEEEEecccc-------------ccChhh
Confidence            9999999999999999999999999999999999999999999999999999999875432             789999


Q ss_pred             ceEEEEEecCcchhhhhhcc
Q 030094          162 LHLEVIWNVNQMRNHHNLLI  181 (183)
Q Consensus       162 l~q~~i~~~~~~k~~~ll~l  181 (183)
                      ++|+|+.|+-++|++.|..+
T Consensus       288 L~Q~y~~v~l~~Ki~~L~sF  307 (758)
T KOG0343|consen  288 LQQSYVIVPLEDKIDMLWSF  307 (758)
T ss_pred             hhheEEEEehhhHHHHHHHH
Confidence            99999999999999988765

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

Probab=100.00  E-value=3.8e-35  Score=252.29  Aligned_cols=166  Identities=34%  Similarity=0.556  Sum_probs=153.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      |||++||||||.|+++.+.+++.+.+++++..++||.+...+...+.. ++||+|||||||++++.+ +.+++++++++|
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~~-~~~ivVaTPGRllD~i~~-~~l~l~~v~~lV  179 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALKR-GVDIVVATPGRLLDLIKR-GKLDLSGVETLV  179 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHhc-CCCEEEECccHHHHHHHc-CCcchhhcCEEE
Confidence            899999999999999999999987657999999999999999988854 799999999999999999 789999999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCccC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLG  161 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (183)
                      +||||+|+++||.+++..|++.+|.++|+++||||+++.+..+++.++++|..|.+..+..             ..+..+
T Consensus       180 lDEADrmLd~Gf~~~i~~I~~~~p~~~qtllfSAT~~~~i~~l~~~~l~~p~~i~v~~~~~-------------~~~~~~  246 (513)
T COG0513         180 LDEADRMLDMGFIDDIEKILKALPPDRQTLLFSATMPDDIRELARRYLNDPVEIEVSVEKL-------------ERTLKK  246 (513)
T ss_pred             eccHhhhhcCCCHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHccCCcEEEEccccc-------------cccccC
Confidence            9999999999999999999999999999999999999999999999999999999885521             448999


Q ss_pred             ceEEEEEecCcc-hhhhhhccc
Q 030094          162 LHLEVIWNVNQM-RNHHNLLIC  182 (183)
Q Consensus       162 l~q~~i~~~~~~-k~~~ll~ll  182 (183)
                      |.|+|+.|++.+ |...|..+|
T Consensus       247 i~q~~~~v~~~~~k~~~L~~ll  268 (513)
T COG0513         247 IKQFYLEVESEEEKLELLLKLL  268 (513)
T ss_pred             ceEEEEEeCCHHHHHHHHHHHH
Confidence            999999999887 888776654

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

Probab=100.00  E-value=8.9e-36  Score=246.82  Aligned_cols=152  Identities=38%  Similarity=0.565  Sum_probs=145.3

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||||||||||.|++++.++++.+. ++.+++++||-+.+.|...|. .+|||+|+||||+.+|+++..+|+++++..+|
T Consensus       255 VLVL~PTRELaiQv~sV~~qlaqFt-~I~~~L~vGGL~lk~QE~~LR-s~PDIVIATPGRlIDHlrNs~sf~ldsiEVLv  332 (691)
T KOG0338|consen  255 VLVLVPTRELAIQVHSVTKQLAQFT-DITVGLAVGGLDLKAQEAVLR-SRPDIVIATPGRLIDHLRNSPSFNLDSIEVLV  332 (691)
T ss_pred             EEEEeccHHHHHHHHHHHHHHHhhc-cceeeeeecCccHHHHHHHHh-hCCCEEEecchhHHHHhccCCCccccceeEEE
Confidence            6999999999999999999999988 899999999999999988884 68999999999999999998899999999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCccC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLG  161 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (183)
                      +||||+||+.+|.++|+.|++.+|++||+++||||+++++..+++..+++|+.|.++..               ..++..
T Consensus       333 lDEADRMLeegFademnEii~lcpk~RQTmLFSATMteeVkdL~slSL~kPvrifvd~~---------------~~~a~~  397 (691)
T KOG0338|consen  333 LDEADRMLEEGFADEMNEIIRLCPKNRQTMLFSATMTEEVKDLASLSLNKPVRIFVDPN---------------KDTAPK  397 (691)
T ss_pred             echHHHHHHHHHHHHHHHHHHhccccccceeehhhhHHHHHHHHHhhcCCCeEEEeCCc---------------cccchh
Confidence            99999999999999999999999999999999999999999999999999999999998               778899


Q ss_pred             ceEEEEEec
Q 030094          162 LHLEVIWNV  170 (183)
Q Consensus       162 l~q~~i~~~  170 (183)
                      +.|.|+.+-
T Consensus       398 LtQEFiRIR  406 (691)
T KOG0338|consen  398 LTQEFIRIR  406 (691)
T ss_pred             hhHHHheec
Confidence            999998764

>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=4e-35  Score=228.43  Aligned_cols=162  Identities=32%  Similarity=0.472  Sum_probs=153.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      ||+||.||||||.|+.+++..++.++ ++.+..+.||.+..++.+.+ +.|+|++.|||||+.+++++ +.+..+.++++
T Consensus        97 Q~lilsPTRELa~Qi~~vi~alg~~m-nvq~hacigg~n~gedikkl-d~G~hvVsGtPGrv~dmikr-~~L~tr~vkml  173 (400)
T KOG0328|consen   97 QALILSPTRELAVQIQKVILALGDYM-NVQCHACIGGKNLGEDIKKL-DYGQHVVSGTPGRVLDMIKR-RSLRTRAVKML  173 (400)
T ss_pred             eEEEecChHHHHHHHHHHHHHhcccc-cceEEEEecCCccchhhhhh-cccceEeeCCCchHHHHHHh-ccccccceeEE
Confidence            69999999999999999999999888 99999999999999999988 58999999999999999999 99999999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||.|++.+|.+++-.+.+.+|+.+|++++|||+|.++.+..++|+.+|+.|.+...               ..+.+
T Consensus       174 VLDEaDemL~kgfk~Qiydiyr~lp~~~Qvv~~SATlp~eilemt~kfmtdpvrilvkrd---------------eltlE  238 (400)
T KOG0328|consen  174 VLDEADEMLNKGFKEQIYDIYRYLPPGAQVVLVSATLPHEILEMTEKFMTDPVRILVKRD---------------ELTLE  238 (400)
T ss_pred             EeccHHHHHHhhHHHHHHHHHHhCCCCceEEEEeccCcHHHHHHHHHhcCCceeEEEecC---------------CCchh
Confidence            999999999999999999999999999999999999999999999999999999999888               67888


Q ss_pred             CceEEEEEecCcc-hhhhhhc
Q 030094          161 GLHLEVIWNVNQM-RNHHNLL  180 (183)
Q Consensus       161 ~l~q~~i~~~~~~-k~~~ll~  180 (183)
                      +|+|||+.++.++ |+..|-.
T Consensus       239 gIKqf~v~ve~EewKfdtLcd  259 (400)
T KOG0328|consen  239 GIKQFFVAVEKEEWKFDTLCD  259 (400)
T ss_pred             hhhhheeeechhhhhHhHHHH
Confidence            9999999998776 8877643

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

Probab=100.00  E-value=5.4e-35  Score=246.24  Aligned_cols=166  Identities=33%  Similarity=0.505  Sum_probs=152.8

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+|||+||||||.||.+.+.+++... .+++.+++||.+...|.+.+ +.++||+||||+||.++++. +.+++++|.++
T Consensus       167 ~vLVL~PTRELA~QV~~~~~~~~~~~-~~~~~cvyGG~~~~~Q~~~l-~~gvdiviaTPGRl~d~le~-g~~~l~~v~yl  243 (519)
T KOG0331|consen  167 IVLVLAPTRELAVQVQAEAREFGKSL-RLRSTCVYGGAPKGPQLRDL-ERGVDVVIATPGRLIDLLEE-GSLNLSRVTYL  243 (519)
T ss_pred             eEEEEcCcHHHHHHHHHHHHHHcCCC-CccEEEEeCCCCccHHHHHH-hcCCcEEEeCChHHHHHHHc-CCccccceeEE
Confidence            48999999999999999999999887 79999999999999999999 56899999999999999999 99999999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhC-CCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRL-PKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTP  159 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l-~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (183)
                      |+||||+|+++||+++++.|++.+ ++.+|+++||||||..++.++..|+.+|..+.+....+             ....
T Consensus       244 VLDEADrMldmGFe~qI~~Il~~i~~~~rQtlm~saTwp~~v~~lA~~fl~~~~~i~ig~~~~-------------~~a~  310 (519)
T KOG0331|consen  244 VLDEADRMLDMGFEPQIRKILSQIPRPDRQTLMFSATWPKEVRQLAEDFLNNPIQINVGNKKE-------------LKAN  310 (519)
T ss_pred             EeccHHhhhccccHHHHHHHHHhcCCCcccEEEEeeeccHHHHHHHHHHhcCceEEEecchhh-------------hhhh
Confidence            999999999999999999999999 56679999999999999999999999999999875521             5667


Q ss_pred             cCceEEEEEecCcchhhhhhccc
Q 030094          160 LGLHLEVIWNVNQMRNHHNLLIC  182 (183)
Q Consensus       160 ~~l~q~~i~~~~~~k~~~ll~ll  182 (183)
                      .++.|....|+...|...|..+|
T Consensus       311 ~~i~qive~~~~~~K~~~l~~lL  333 (519)
T KOG0331|consen  311 HNIRQIVEVCDETAKLRKLGKLL  333 (519)
T ss_pred             cchhhhhhhcCHHHHHHHHHHHH
Confidence            88999999999988988887654

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

Probab=100.00  E-value=7.7e-34  Score=234.25  Aligned_cols=168  Identities=38%  Similarity=0.555  Sum_probs=155.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .|+|+|||||||.|++.+++.+.++.++..+..+.||.+...+.+.+.+ +|+|+|+|||||.+++++.+.+-.++++++
T Consensus       156 ~vlIi~PTRELA~Q~~~eak~Ll~~h~~~~v~~viGG~~~~~e~~kl~k-~~niliATPGRLlDHlqNt~~f~~r~~k~l  234 (543)
T KOG0342|consen  156 GVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLVK-GCNILIATPGRLLDHLQNTSGFLFRNLKCL  234 (543)
T ss_pred             eEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhhc-cccEEEeCCchHHhHhhcCCcchhhcccee
Confidence            3799999999999999999999998889999999999999999888865 999999999999999999788889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCC-CCeEEEEccCCcccccccchhhcccCCCc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLR-NPVRVEVRAESKSHHVSASSQQLASSKTP  159 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (183)
                      |+||||++++.||.++++.|++.+|+.+|+.+||||.+++|+++++.-++ +|.+|...++++             ..+.
T Consensus       235 vlDEADrlLd~GF~~di~~Ii~~lpk~rqt~LFSAT~~~kV~~l~~~~L~~d~~~v~~~d~~~-------------~~Th  301 (543)
T KOG0342|consen  235 VLDEADRLLDIGFEEDVEQIIKILPKQRQTLLFSATQPSKVKDLARGALKRDPVFVNVDDGGE-------------RETH  301 (543)
T ss_pred             EeecchhhhhcccHHHHHHHHHhccccceeeEeeCCCcHHHHHHHHHhhcCCceEeecCCCCC-------------cchh
Confidence            99999999999999999999999999999999999999999999998877 599999988754             7788


Q ss_pred             cCceEEEEEecCcchhhhhhccc
Q 030094          160 LGLHLEVIWNVNQMRNHHNLLIC  182 (183)
Q Consensus       160 ~~l~q~~i~~~~~~k~~~ll~ll  182 (183)
                      +.+.|.|++++...++..+..+|
T Consensus       302 e~l~Qgyvv~~~~~~f~ll~~~L  324 (543)
T KOG0342|consen  302 ERLEQGYVVAPSDSRFSLLYTFL  324 (543)
T ss_pred             hcccceEEeccccchHHHHHHHH
Confidence            99999999999999877666554

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

Probab=100.00  E-value=1.3e-33  Score=233.98  Aligned_cols=162  Identities=34%  Similarity=0.507  Sum_probs=149.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      ++||+|||||||.||+.+|++|++.+ ++++.+++||.+..+|.+.|. .+|.||||||+||.++++- +..++.++.+|
T Consensus       298 i~vilvPTrela~Qi~~eaKkf~K~y-gl~~v~~ygGgsk~eQ~k~Lk-~g~EivVaTPgRlid~Vkm-Katn~~rvS~L  374 (731)
T KOG0339|consen  298 IGVILVPTRELASQIFSEAKKFGKAY-GLRVVAVYGGGSKWEQSKELK-EGAEIVVATPGRLIDMVKM-KATNLSRVSYL  374 (731)
T ss_pred             eEEEEeccHHHHHHHHHHHHHhhhhc-cceEEEeecCCcHHHHHHhhh-cCCeEEEechHHHHHHHHh-hcccceeeeEE
Confidence            58999999999999999999999988 999999999999999999996 7999999999999999988 89999999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||+|+++||..+++.|..++.+++|+++||||++..++.+++.++.+|+.+...+-               .....
T Consensus       375 V~DEadrmfdmGfe~qVrSI~~hirpdrQtllFsaTf~~kIe~lard~L~dpVrvVqg~v---------------gean~  439 (731)
T KOG0339|consen  375 VLDEADRMFDMGFEPQVRSIKQHIRPDRQTLLFSATFKKKIEKLARDILSDPVRVVQGEV---------------GEANE  439 (731)
T ss_pred             EEechhhhhccccHHHHHHHHhhcCCcceEEEeeccchHHHHHHHHHHhcCCeeEEEeeh---------------hcccc
Confidence            999999999999999999999999999999999999999999999999999999887755               44577


Q ss_pred             CceEEEEEecCcc-hhhhhhc
Q 030094          161 GLHLEVIWNVNQM-RNHHNLL  180 (183)
Q Consensus       161 ~l~q~~i~~~~~~-k~~~ll~  180 (183)
                      .|.|.+.+|++++ |.++|+.
T Consensus       440 dITQ~V~V~~s~~~Kl~wl~~  460 (731)
T KOG0339|consen  440 DITQTVSVCPSEEKKLNWLLR  460 (731)
T ss_pred             chhheeeeccCcHHHHHHHHH
Confidence            8899998887666 6666654

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

Probab=100.00  E-value=2e-33  Score=222.10  Aligned_cols=160  Identities=31%  Similarity=0.504  Sum_probs=149.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      ||+|+|||||||.|+.++|.++++++ +++++..+||.+..++.-.+ ...+|++||||||+++++++ +.-+++++.++
T Consensus       155 Q~~ilVPtrelALQtSqvc~~lskh~-~i~vmvttGGT~lrDDI~Rl-~~~VH~~vgTPGRIlDL~~K-gVa~ls~c~~l  231 (459)
T KOG0326|consen  155 QAIILVPTRELALQTSQVCKELSKHL-GIKVMVTTGGTSLRDDIMRL-NQTVHLVVGTPGRILDLAKK-GVADLSDCVIL  231 (459)
T ss_pred             eEEEEeecchhhHHHHHHHHHHhccc-CeEEEEecCCcccccceeee-cCceEEEEcCChhHHHHHhc-ccccchhceEE
Confidence            68999999999999999999999998 89999999999999888887 56899999999999999988 88899999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||.|++..|.+.++.++..+|+++|+++||||+|-.+..|+++||++|..|++-++                .++.
T Consensus       232 V~DEADKlLs~~F~~~~e~li~~lP~~rQillySATFP~tVk~Fm~~~l~kPy~INLM~e----------------Ltl~  295 (459)
T KOG0326|consen  232 VMDEADKLLSVDFQPIVEKLISFLPKERQILLYSATFPLTVKGFMDRHLKKPYEINLMEE----------------LTLK  295 (459)
T ss_pred             EechhhhhhchhhhhHHHHHHHhCCccceeeEEecccchhHHHHHHHhccCcceeehhhh----------------hhhc
Confidence            999999999999999999999999999999999999999999999999999999987665                6788


Q ss_pred             CceEEEEEecCcchhhhhh
Q 030094          161 GLHLEVIWNVNQMRNHHNL  179 (183)
Q Consensus       161 ~l~q~~i~~~~~~k~~~ll  179 (183)
                      ++.|||-+|++.+|..-|-
T Consensus       296 GvtQyYafV~e~qKvhCLn  314 (459)
T KOG0326|consen  296 GVTQYYAFVEERQKVHCLN  314 (459)
T ss_pred             chhhheeeechhhhhhhHH
Confidence            9999999999998876543

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

Probab=100.00  E-value=1.3e-33  Score=217.60  Aligned_cols=165  Identities=24%  Similarity=0.424  Sum_probs=154.3

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +|++|.|||||.||.....++++++|+++++.++||.+++.+...++ +.|||+||||||++.+.++ +.+++++++.+|
T Consensus       113 vlvmchtrelafqi~~ey~rfskymP~vkvaVFfGG~~Ikkdee~lk-~~PhivVgTPGrilALvr~-k~l~lk~vkhFv  190 (387)
T KOG0329|consen  113 VLVMCHTRELAFQISKEYERFSKYMPSVKVSVFFGGLFIKKDEELLK-NCPHIVVGTPGRILALVRN-RSLNLKNVKHFV  190 (387)
T ss_pred             EEEEeccHHHHHHHHHHHHHHHhhCCCceEEEEEcceeccccHHHHh-CCCeEEEcCcHHHHHHHHh-ccCchhhcceee
Confidence            68999999999999999999999999999999999999998888885 4899999999999999998 999999999999


Q ss_pred             Ecccchhhcc-chHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           82 LDEADRLLDM-GFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        82 vDEad~ll~~-~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      +||+|.|+++ ..+.+++.|++..|+..|..+||||++.+++..+++||.||..|.++++.              ..+..
T Consensus       191 lDEcdkmle~lDMrRDvQEifr~tp~~KQvmmfsatlskeiRpvC~kFmQdPmEi~vDdE~--------------KLtLH  256 (387)
T KOG0329|consen  191 LDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCHKFMQDPMEIFVDDEA--------------KLTLH  256 (387)
T ss_pred             hhhHHHHHHHHHHHHHHHHHhhcCcccceeeeeeeecchhhHHHHHhhhcCchhhhccchh--------------hhhhh
Confidence            9999999864 57899999999999999999999999999999999999999999999995              56889


Q ss_pred             CceEEEEEecCcchhhhhhccc
Q 030094          161 GLHLEVIWNVNQMRNHHNLLIC  182 (183)
Q Consensus       161 ~l~q~~i~~~~~~k~~~ll~ll  182 (183)
                      +++|||+..++.+|..++.-||
T Consensus       257 GLqQ~YvkLke~eKNrkl~dLL  278 (387)
T KOG0329|consen  257 GLQQYYVKLKENEKNRKLNDLL  278 (387)
T ss_pred             hHHHHHHhhhhhhhhhhhhhhh
Confidence            9999999999999888876654

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

Probab=100.00  E-value=4.1e-33  Score=232.07  Aligned_cols=181  Identities=32%  Similarity=0.503  Sum_probs=155.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +|||+|||||||.|+|+.+.+|.+.+.=+..+.+.||...+.+...+. .|++|+|||||||.++++++..+.++.++++
T Consensus       213 ~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARLR-KGiNILIgTPGRLvDHLknT~~i~~s~LRwl  291 (708)
T KOG0348|consen  213 YALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARLR-KGINILIGTPGRLVDHLKNTKSIKFSRLRWL  291 (708)
T ss_pred             eEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHHh-cCceEEEcCchHHHHHHhccchheeeeeeEE
Confidence            699999999999999999999998776678889999999999999984 6999999999999999999889999999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhC-------------CCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCc-----
Q 030094           81 VLDEADRLLDMGFQKQISYIISRL-------------PKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESK-----  142 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l-------------~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~-----  142 (183)
                      |+||||++++.||+.++..|++.+             |+..|.+++|||+++.|.++++.-++||+.|..+....     
T Consensus       292 VlDEaDrlleLGfekdit~Il~~v~~~~~~e~~~~~lp~q~q~mLlSATLtd~V~rLa~~sLkDpv~I~ld~s~~~~~p~  371 (708)
T KOG0348|consen  292 VLDEADRLLELGFEKDITQILKAVHSIQNAECKDPKLPHQLQNMLLSATLTDGVNRLADLSLKDPVYISLDKSHSQLNPK  371 (708)
T ss_pred             EecchhHHHhccchhhHHHHHHHHhhccchhcccccccHHHHhHhhhhhhHHHHHHHhhccccCceeeeccchhhhcCcc
Confidence            999999999999999999998877             23479999999999999999999999999999443211     


Q ss_pred             -----ccccccchhhcccCCCccCceEEEEEecCcchhhhhhccc
Q 030094          143 -----SHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNHHNLLIC  182 (183)
Q Consensus       143 -----~~~~~~~~~~~~~~~~~~~l~q~~i~~~~~~k~~~ll~ll  182 (183)
                           +..+.+.........+|+++.|.|.+|++.-+...|.++|
T Consensus       372 ~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L  416 (708)
T KOG0348|consen  372 DKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALL  416 (708)
T ss_pred             hhhhhhcCCcccccccccccCcHHhhhceEecCCchhHHHHHHHH
Confidence                 1111111112344789999999999999999999888776

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=99.97  E-value=3.6e-31  Score=216.32  Aligned_cols=166  Identities=24%  Similarity=0.377  Sum_probs=145.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCC-CceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCC-cCCCCce
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLP-DVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDV-LDFRNLE   78 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~-~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~-~~l~~l~   78 (183)
                      .|+|||||||||+|+|.++.++..+++ .+++.-+....+-......+ ...|||+||||+++..++.. +. ..+++++
T Consensus        95 sa~iLvPTkEL~qQvy~viekL~~~c~k~lr~~nl~s~~sdsv~~~~L-~d~pdIvV~TP~~ll~~~~~-~~~~~~~~l~  172 (569)
T KOG0346|consen   95 SAVILVPTKELAQQVYKVIEKLVEYCSKDLRAINLASSMSDSVNSVAL-MDLPDIVVATPAKLLRHLAA-GVLEYLDSLS  172 (569)
T ss_pred             eeEEEechHHHHHHHHHHHHHHHHHHHHhhhhhhhhcccchHHHHHHH-ccCCCeEEeChHHHHHHHhh-ccchhhhhee
Confidence            389999999999999999999988875 57777666555544444444 56899999999999999988 65 6789999


Q ss_pred             EEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCC
Q 030094           79 ILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKT  158 (183)
Q Consensus        79 ~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (183)
                      ++|+||||.+++.||++++..+.+.+|+..|.+++|||+++++..+.+.+++||+.+.+.+.+              -..
T Consensus       173 ~LVvDEADLllsfGYeedlk~l~~~LPr~~Q~~LmSATl~dDv~~LKkL~l~nPviLkl~e~e--------------l~~  238 (569)
T KOG0346|consen  173 FLVVDEADLLLSFGYEEDLKKLRSHLPRIYQCFLMSATLSDDVQALKKLFLHNPVILKLTEGE--------------LPN  238 (569)
T ss_pred             eEEechhhhhhhcccHHHHHHHHHhCCchhhheeehhhhhhHHHHHHHHhccCCeEEEecccc--------------CCC
Confidence            999999999999999999999999999999999999999999999999999999999987773              447


Q ss_pred             ccCceEEEEEecCcchhhhhhccc
Q 030094          159 PLGLHLEVIWNVNQMRNHHNLLIC  182 (183)
Q Consensus       159 ~~~l~q~~i~~~~~~k~~~ll~ll  182 (183)
                      +++++||++.|++++|+..+..++
T Consensus       239 ~dqL~Qy~v~cse~DKflllyall  262 (569)
T KOG0346|consen  239 PDQLTQYQVKCSEEDKFLLLYALL  262 (569)
T ss_pred             cccceEEEEEeccchhHHHHHHHH
Confidence            889999999999999998776654

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

Probab=99.97  E-value=8e-31  Score=218.24  Aligned_cols=164  Identities=35%  Similarity=0.552  Sum_probs=151.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++||||||.|+|+.++++.... .+++...+||.+...+.+.+ ..+|||+|||||||.++++. +.+.+.+++++
T Consensus       154 ~~lIlapTReL~~Qi~nea~k~~~~s-~~~~~~~ygg~~~~~q~~~~-~~gcdIlvaTpGrL~d~~e~-g~i~l~~~k~~  230 (482)
T KOG0335|consen  154 RALILAPTRELVDQIYNEARKFSYLS-GMKSVVVYGGTDLGAQLRFI-KRGCDILVATPGRLKDLIER-GKISLDNCKFL  230 (482)
T ss_pred             ceEEEeCcHHHhhHHHHHHHhhcccc-cceeeeeeCCcchhhhhhhh-ccCccEEEecCchhhhhhhc-ceeehhhCcEE
Confidence            37999999999999999999996544 89999999999999998888 56999999999999999999 99999999999


Q ss_pred             EEcccchhhc-cchHHHHHHHHHhCCC----CCeEEEEeecCChHHHHHHHhhCCC-CeEEEEccCCcccccccchhhcc
Q 030094           81 VLDEADRLLD-MGFQKQISYIISRLPK----LRRTGLFSATQTEAVEELSKAGLRN-PVRVEVRAESKSHHVSASSQQLA  154 (183)
Q Consensus        81 VvDEad~ll~-~~~~~~l~~i~~~l~~----~~Q~v~~SAT~~~~v~~~~~~~~~~-~~~i~~~~~~~~~~~~~~~~~~~  154 (183)
                      |+||||+|+| ++|.+++++|+...+.    ++|+++||||++.++..++..|+.+ .+++.+..-              
T Consensus       231 vLDEADrMlD~mgF~p~Ir~iv~~~~~~~~~~~qt~mFSAtfp~~iq~l~~~fl~~~yi~laV~rv--------------  296 (482)
T KOG0335|consen  231 VLDEADRMLDEMGFEPQIRKIVEQLGMPPKNNRQTLLFSATFPKEIQRLAADFLKDNYIFLAVGRV--------------  296 (482)
T ss_pred             EecchHHhhhhccccccHHHHhcccCCCCccceeEEEEeccCChhhhhhHHHHhhccceEEEEeee--------------
Confidence            9999999999 9999999999998854    7999999999999999999999996 888888887              


Q ss_pred             cCCCccCceEEEEEecCcchhhhhhccc
Q 030094          155 SSKTPLGLHLEVIWNVNQMRNHHNLLIC  182 (183)
Q Consensus       155 ~~~~~~~l~q~~i~~~~~~k~~~ll~ll  182 (183)
                       .....++.|.+++|.+.+|..+|+-+|
T Consensus       297 -g~~~~ni~q~i~~V~~~~kr~~Lldll  323 (482)
T KOG0335|consen  297 -GSTSENITQKILFVNEMEKRSKLLDLL  323 (482)
T ss_pred             -ccccccceeEeeeecchhhHHHHHHHh
Confidence             677999999999999999999998776

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

Probab=99.97  E-value=9e-32  Score=217.44  Aligned_cols=162  Identities=33%  Similarity=0.597  Sum_probs=143.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhh-----hCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFIS-----TLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFR   75 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~-----~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~   75 (183)
                      ++||+||+||||.|+++.+..+.+     .+|.++..+|.||.+..++.... +.|.||+|+|||||.+++.. +.+++.
T Consensus       248 ~gLiicPSRELArQt~~iie~~~~~L~e~g~P~lRs~LciGG~~v~eql~~v-~~GvHivVATPGRL~DmL~K-K~~sLd  325 (610)
T KOG0341|consen  248 YGLIICPSRELARQTHDIIEQYVAALQEAGYPELRSLLCIGGVPVREQLDVV-RRGVHIVVATPGRLMDMLAK-KIMSLD  325 (610)
T ss_pred             eeEEEcCcHHHHHHHHHHHHHHHHHHHhcCChhhhhhhhhcCccHHHHHHHH-hcCeeEEEcCcchHHHHHHH-hhccHH
Confidence            589999999999999999999976     56889999999999999999988 46999999999999999998 889999


Q ss_pred             CceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhccc
Q 030094           76 NLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLAS  155 (183)
Q Consensus        76 ~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~  155 (183)
                      -|+++++||||+|+++||.++++.|+..+...||+++||||+|..+..|++.-+-.|+.|++...+.             
T Consensus       326 ~CRyL~lDEADRmiDmGFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVGRAGA-------------  392 (610)
T KOG0341|consen  326 ACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVGRAGA-------------  392 (610)
T ss_pred             HHHHhhhhhHHHHhhccchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhcccceEEecccccc-------------
Confidence            9999999999999999999999999999999999999999999999999999999999999998743             


Q ss_pred             CCCccCceEEEEEecCcchhhhhh
Q 030094          156 SKTPLGLHLEVIWNVNQMRNHHNL  179 (183)
Q Consensus       156 ~~~~~~l~q~~i~~~~~~k~~~ll  179 (183)
                        ..-++-|.+-+|..+.|..+|+
T Consensus       393 --AsldViQevEyVkqEaKiVylL  414 (610)
T KOG0341|consen  393 --ASLDVIQEVEYVKQEAKIVYLL  414 (610)
T ss_pred             --cchhHHHHHHHHHhhhhhhhHH
Confidence              2334444455555555555554

>KOG4284 consensus DEAD box protein [Transcription]

Probab=99.97  E-value=9.7e-30  Score=215.87  Aligned_cols=154  Identities=29%  Similarity=0.561  Sum_probs=144.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +++|++||||+|.||.+.+.+++..+.+++|..+.||.....+...+  +.++|+||||||+..+++. +.+++++++++
T Consensus        95 q~~Iv~PTREiaVQI~~tv~~v~~sf~g~~csvfIGGT~~~~d~~rl--k~~rIvIGtPGRi~qL~el-~~~n~s~vrlf  171 (980)
T KOG4284|consen   95 QKVIVTPTREIAVQIKETVRKVAPSFTGARCSVFIGGTAHKLDLIRL--KQTRIVIGTPGRIAQLVEL-GAMNMSHVRLF  171 (980)
T ss_pred             eeEEEecchhhhhHHHHHHHHhcccccCcceEEEecCchhhhhhhhh--hhceEEecCchHHHHHHHh-cCCCccceeEE
Confidence            57999999999999999999999988899999999999999888887  3689999999999999999 99999999999


Q ss_pred             EEcccchhhc-cchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCc
Q 030094           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTP  159 (183)
Q Consensus        81 VvDEad~ll~-~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (183)
                      |+||||.|++ ..|.+++..|+..+|+.+|++.||||.+..+.++..+||++|.+|+.+..               ....
T Consensus       172 VLDEADkL~~t~sfq~~In~ii~slP~~rQv~a~SATYp~nLdn~Lsk~mrdp~lVr~n~~---------------d~~L  236 (980)
T KOG4284|consen  172 VLDEADKLMDTESFQDDINIIINSLPQIRQVAAFSATYPRNLDNLLSKFMRDPALVRFNAD---------------DVQL  236 (980)
T ss_pred             EeccHHhhhchhhHHHHHHHHHHhcchhheeeEEeccCchhHHHHHHHHhcccceeecccC---------------Ccee
Confidence            9999999998 56999999999999999999999999999999999999999999999888               6778


Q ss_pred             cCceEEEEEecCc
Q 030094          160 LGLHLEVIWNVNQ  172 (183)
Q Consensus       160 ~~l~q~~i~~~~~  172 (183)
                      -+|+|||+.+...
T Consensus       237 ~GikQyv~~~~s~  249 (980)
T KOG4284|consen  237 FGIKQYVVAKCSP  249 (980)
T ss_pred             echhheeeeccCC
Confidence            8999999987654

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

Probab=99.97  E-value=8.8e-30  Score=211.84  Aligned_cols=164  Identities=32%  Similarity=0.534  Sum_probs=152.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +|+||+||||||+||.+...+++... ++++..++||.+.+++--.+ ..||+|+||||++|.+-+.+ ..+-++.|.++
T Consensus       324 yaiilaptReLaqqIeeEt~kf~~~l-g~r~vsvigg~s~EEq~fql-s~gceiviatPgrLid~Len-r~lvl~qctyv  400 (673)
T KOG0333|consen  324 YAIILAPTRELAQQIEEETNKFGKPL-GIRTVSVIGGLSFEEQGFQL-SMGCEIVIATPGRLIDSLEN-RYLVLNQCTYV  400 (673)
T ss_pred             eeeeechHHHHHHHHHHHHHHhcccc-cceEEEEecccchhhhhhhh-hccceeeecCchHHHHHHHH-HHHHhccCceE
Confidence            48999999999999999999999887 89999999999999997777 56999999999999999998 88889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCC-------------------------CeEEEEeecCChHHHHHHHhhCCCCeEE
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKL-------------------------RRTGLFSATQTEAVEELSKAGLRNPVRV  135 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~-------------------------~Q~v~~SAT~~~~v~~~~~~~~~~~~~i  135 (183)
                      |+||||+|+++||++++..++..+|..                         +|+++||||+++.++.+++.||++|+.+
T Consensus       401 vldeadrmiDmgfE~dv~~iL~~mPssn~k~~tde~~~~~~~~~~~~~~k~yrqT~mftatm~p~verlar~ylr~pv~v  480 (673)
T KOG0333|consen  401 VLDEADRMIDMGFEPDVQKILEQMPSSNAKPDTDEKEGEERVRKNFSSSKKYRQTVMFTATMPPAVERLARSYLRRPVVV  480 (673)
T ss_pred             eccchhhhhcccccHHHHHHHHhCCccccCCCccchhhHHHHHhhcccccceeEEEEEecCCChHHHHHHHHHhhCCeEE
Confidence            999999999999999999999999621                         6999999999999999999999999999


Q ss_pred             EEccCCcccccccchhhcccCCCccCceEEEEEecCcchhhhhhccc
Q 030094          136 EVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNHHNLLIC  182 (183)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~q~~i~~~~~~k~~~ll~ll  182 (183)
                      .++..               ....+.++|.++.++..+|..+|+-+|
T Consensus       481 tig~~---------------gk~~~rveQ~v~m~~ed~k~kkL~eil  512 (673)
T KOG0333|consen  481 TIGSA---------------GKPTPRVEQKVEMVSEDEKRKKLIEIL  512 (673)
T ss_pred             EeccC---------------CCCccchheEEEEecchHHHHHHHHHH
Confidence            99999               777899999999999999998887654

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=99.96  E-value=1.5e-28  Score=215.48  Aligned_cols=164  Identities=30%  Similarity=0.512  Sum_probs=148.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      ++|||+||||||.|+++.+.++.++.+++++..++||.+.+.+.+.+ ..+++|+||||+++.+++.+ +.+++++++++
T Consensus        76 ~~LIL~PTreLa~Qv~~~l~~~~~~~~~i~v~~~~gG~~~~~q~~~l-~~~~~IVVgTPgrl~d~l~r-~~l~l~~l~~l  153 (629)
T PRK11634         76 QILVLAPTRELAVQVAEAMTDFSKHMRGVNVVALYGGQRYDVQLRAL-RQGPQIVVGTPGRLLDHLKR-GTLDLSKLSGL  153 (629)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEECCcCHHHHHHHh-cCCCCEEEECHHHHHHHHHc-CCcchhhceEE
Confidence            47999999999999999999998888889999999999988888877 46899999999999999988 88999999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||.|++++|..++..|++.+|..+|+++||||+++.+..+++.|+++|..|.+...               .....
T Consensus       154 VlDEAd~ml~~gf~~di~~Il~~lp~~~q~llfSAT~p~~i~~i~~~~l~~~~~i~i~~~---------------~~~~~  218 (629)
T PRK11634        154 VLDEADEMLRMGFIEDVETIMAQIPEGHQTALFSATMPEAIRRITRRFMKEPQEVRIQSS---------------VTTRP  218 (629)
T ss_pred             EeccHHHHhhcccHHHHHHHHHhCCCCCeEEEEEccCChhHHHHHHHHcCCCeEEEccCc---------------cccCC
Confidence            999999999999999999999999999999999999999999999999999999988766               55667


Q ss_pred             CceEEEEEecCcchhhhhhcc
Q 030094          161 GLHLEVIWNVNQMRNHHNLLI  181 (183)
Q Consensus       161 ~l~q~~i~~~~~~k~~~ll~l  181 (183)
                      ++.|.|+.+...+|...|..+
T Consensus       219 ~i~q~~~~v~~~~k~~~L~~~  239 (629)
T PRK11634        219 DISQSYWTVWGMRKNEALVRF  239 (629)
T ss_pred             ceEEEEEEechhhHHHHHHHH
Confidence            788888888887777666543

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=99.96  E-value=1.8e-28  Score=208.94  Aligned_cols=163  Identities=35%  Similarity=0.561  Sum_probs=147.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      ++||++||||||.|+.+.++.+.++.+++++..++||.+...+...+. .+++|+||||+++.+++.+ +.+++++++++
T Consensus        74 ~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l~-~~~~IvV~Tp~rl~~~l~~-~~~~l~~l~~l  151 (460)
T PRK11776         74 QALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSLE-HGAHIIVGTPGRILDHLRK-GTLDLDALNTL  151 (460)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHhc-CCCCEEEEChHHHHHHHHc-CCccHHHCCEE
Confidence            489999999999999999999988777899999999999988888774 6899999999999999988 78899999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||.|++.+|...+..+++.+|+.+|+++||||+++.+..++..++.+|..+.+...               . ...
T Consensus       152 ViDEad~~l~~g~~~~l~~i~~~~~~~~q~ll~SAT~~~~~~~l~~~~~~~~~~i~~~~~---------------~-~~~  215 (460)
T PRK11776        152 VLDEADRMLDMGFQDAIDAIIRQAPARRQTLLFSATYPEGIAAISQRFQRDPVEVKVEST---------------H-DLP  215 (460)
T ss_pred             EEECHHHHhCcCcHHHHHHHHHhCCcccEEEEEEecCcHHHHHHHHHhcCCCEEEEECcC---------------C-CCC
Confidence            999999999999999999999999999999999999999999999999999999987665               2 345


Q ss_pred             CceEEEEEecCcchhhhhhcc
Q 030094          161 GLHLEVIWNVNQMRNHHNLLI  181 (183)
Q Consensus       161 ~l~q~~i~~~~~~k~~~ll~l  181 (183)
                      .+.|+|+.++..+|...+..+
T Consensus       216 ~i~~~~~~~~~~~k~~~l~~l  236 (460)
T PRK11776        216 AIEQRFYEVSPDERLPALQRL  236 (460)
T ss_pred             CeeEEEEEeCcHHHHHHHHHH
Confidence            689999999988887766554

>PTZ00110 helicase; Provisional

Probab=99.96  E-value=2.8e-28  Score=211.32  Aligned_cols=164  Identities=32%  Similarity=0.519  Sum_probs=145.1

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +||||+||||||.|+++.+.+++... ++++..++||.....+...+ ..+++|+|+||++|.+++.. +..++++++++
T Consensus       205 ~~LIL~PTreLa~Qi~~~~~~~~~~~-~i~~~~~~gg~~~~~q~~~l-~~~~~IlVaTPgrL~d~l~~-~~~~l~~v~~l  281 (545)
T PTZ00110        205 IVLVLAPTRELAEQIREQCNKFGASS-KIRNTVAYGGVPKRGQIYAL-RRGVEILIACPGRLIDFLES-NVTNLRRVTYL  281 (545)
T ss_pred             EEEEECChHHHHHHHHHHHHHHhccc-CccEEEEeCCCCHHHHHHHH-HcCCCEEEECHHHHHHHHHc-CCCChhhCcEE
Confidence            37999999999999999999998776 79999999999988887777 46899999999999999988 77889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCC-CCeEEEEccCCcccccccchhhcccCCCc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLR-NPVRVEVRAESKSHHVSASSQQLASSKTP  159 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (183)
                      |+||||+|++++|...+..|+..+++++|+++||||++.++..+++.++. +|+.+.+....              ....
T Consensus       282 ViDEAd~mld~gf~~~i~~il~~~~~~~q~l~~SAT~p~~v~~l~~~l~~~~~v~i~vg~~~--------------l~~~  347 (545)
T PTZ00110        282 VLDEADRMLDMGFEPQIRKIVSQIRPDRQTLMWSATWPKEVQSLARDLCKEEPVHVNVGSLD--------------LTAC  347 (545)
T ss_pred             EeehHHhhhhcchHHHHHHHHHhCCCCCeEEEEEeCCCHHHHHHHHHHhccCCEEEEECCCc--------------cccC
Confidence            99999999999999999999999999999999999999999999999886 68888876541              2345


Q ss_pred             cCceEEEEEecCcchhhhhhcc
Q 030094          160 LGLHLEVIWNVNQMRNHHNLLI  181 (183)
Q Consensus       160 ~~l~q~~i~~~~~~k~~~ll~l  181 (183)
                      .+++|.++.++..+|...|..+
T Consensus       348 ~~i~q~~~~~~~~~k~~~L~~l  369 (545)
T PTZ00110        348 HNIKQEVFVVEEHEKRGKLKML  369 (545)
T ss_pred             CCeeEEEEEEechhHHHHHHHH
Confidence            6788999888888887766554

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

Probab=99.96  E-value=3.3e-29  Score=201.77  Aligned_cols=163  Identities=31%  Similarity=0.485  Sum_probs=151.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      ||++++||||||.|+..+...++.+. ++++..+.||.....+...+...+++|+||||+++.++++. +.+..+.++++
T Consensus        96 qalilaPtreLa~qi~~v~~~lg~~~-~~~v~~~igg~~~~~~~~~i~~~~~hivvGTpgrV~dml~~-~~l~~~~iKmf  173 (397)
T KOG0327|consen   96 QALILAPTRELAQQIQKVVRALGDHM-DVSVHACIGGTNVRREDQALLKDKPHIVVGTPGRVFDMLNR-GSLSTDGIKMF  173 (397)
T ss_pred             HHHHhcchHHHHHHHHHHHHhhhccc-ceeeeeecCcccchhhhhhhhccCceeecCCchhHHHhhcc-ccccccceeEE
Confidence            57899999999999999999998887 89999999999988776667677899999999999999998 78889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||.|++.||.+++..|++++|++.|++++|||.+.++..+.++|+++|+.|.+...               ..+.+
T Consensus       174 vlDEaDEmLs~gfkdqI~~if~~lp~~vQv~l~SAT~p~~vl~vt~~f~~~pv~i~vkk~---------------~ltl~  238 (397)
T KOG0327|consen  174 VLDEADEMLSRGFKDQIYDIFQELPSDVQVVLLSATMPSDVLEVTKKFMREPVRILVKKD---------------ELTLE  238 (397)
T ss_pred             eecchHhhhccchHHHHHHHHHHcCcchhheeecccCcHHHHHHHHHhccCceEEEecch---------------hhhhh
Confidence            999999999999999999999999999999999999999999999999999999999888               57799


Q ss_pred             CceEEEEEecCcchhhhhhc
Q 030094          161 GLHLEVIWNVNQMRNHHNLL  180 (183)
Q Consensus       161 ~l~q~~i~~~~~~k~~~ll~  180 (183)
                      .++|+|+.+..++|...|-.
T Consensus       239 gikq~~i~v~k~~k~~~l~d  258 (397)
T KOG0327|consen  239 GIKQFYINVEKEEKLDTLCD  258 (397)
T ss_pred             heeeeeeeccccccccHHHH
Confidence            99999999999998776643

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

Probab=99.96  E-value=1.8e-28  Score=199.48  Aligned_cols=159  Identities=31%  Similarity=0.466  Sum_probs=144.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      .|++.||||||.|+.-++.++. +. +.+..+++||.+..++...+ +.+.+|+|+||++|.++.-. +.++++++.++|
T Consensus       297 ~lvl~ptreLalqie~e~~kys-yn-g~ksvc~ygggnR~eqie~l-krgveiiiatPgrlndL~~~-n~i~l~siTYlV  372 (629)
T KOG0336|consen  297 VLVLTPTRELALQIEGEVKKYS-YN-GLKSVCVYGGGNRNEQIEDL-KRGVEIIIATPGRLNDLQMD-NVINLASITYLV  372 (629)
T ss_pred             eEEEeccHHHHHHHHhHHhHhh-hc-CcceEEEecCCCchhHHHHH-hcCceEEeeCCchHhhhhhc-CeeeeeeeEEEE
Confidence            6899999999999999999984 43 89999999999999999999 56999999999999999877 889999999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCccC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLG  161 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (183)
                      +||||+||+++|+++++.|+--+.+++|+++.|||||+.+..++..|+++|+.+.+..-.              -....+
T Consensus       373 lDEADrMLDMgFEpqIrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLd--------------L~a~~s  438 (629)
T KOG0336|consen  373 LDEADRMLDMGFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLD--------------LVAVKS  438 (629)
T ss_pred             ecchhhhhcccccHHHHHHhhhcCCcceeeeecccCchHHHHHHHHhhhCceEEEecccc--------------eeeeee
Confidence            999999999999999999999999999999999999999999999999999999988762              445667


Q ss_pred             ceEEEEEecCcchhhhh
Q 030094          162 LHLEVIWNVNQMRNHHN  178 (183)
Q Consensus       162 l~q~~i~~~~~~k~~~l  178 (183)
                      ++|.+++..+.+|....
T Consensus       439 VkQ~i~v~~d~~k~~~~  455 (629)
T KOG0336|consen  439 VKQNIIVTTDSEKLEIV  455 (629)
T ss_pred             eeeeEEecccHHHHHHH
Confidence            99999887777777543

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

Probab=99.96  E-value=3.4e-29  Score=203.82  Aligned_cols=163  Identities=36%  Similarity=0.531  Sum_probs=154.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      |+|+.||||||.|+.++.+.++++. ++++.+++||.+.+++...+ ..|||||++||+++..+.-. -.+.+++++++|
T Consensus        93 alilsptreLa~qtlkvvkdlgrgt-~lr~s~~~ggD~~eeqf~~l-~~npDii~ATpgr~~h~~ve-m~l~l~sveyVV  169 (529)
T KOG0337|consen   93 ALILSPTRELALQTLKVVKDLGRGT-KLRQSLLVGGDSIEEQFILL-NENPDIIIATPGRLLHLGVE-MTLTLSSVEYVV  169 (529)
T ss_pred             eeeccCcHHHHHHHHHHHHHhcccc-chhhhhhcccchHHHHHHHh-ccCCCEEEecCceeeeeehh-eeccccceeeee
Confidence            7999999999999999999999887 99999999999999999888 56899999999999998777 458899999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCccC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLG  161 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (183)
                      +||||.++++||.+++..++.++|..+|+++||||+|..+-.+++.-+.+|+.|.++-+               ..+.+.
T Consensus       170 fdEadrlfemgfqeql~e~l~rl~~~~QTllfSatlp~~lv~fakaGl~~p~lVRldve---------------tkise~  234 (529)
T KOG0337|consen  170 FDEADRLFEMGFQEQLHEILSRLPESRQTLLFSATLPRDLVDFAKAGLVPPVLVRLDVE---------------TKISEL  234 (529)
T ss_pred             ehhhhHHHhhhhHHHHHHHHHhCCCcceEEEEeccCchhhHHHHHccCCCCceEEeehh---------------hhcchh
Confidence            99999999999999999999999999999999999999999999999999999999988               778999


Q ss_pred             ceEEEEEecCcchhhhhhccc
Q 030094          162 LHLEVIWNVNQMRNHHNLLIC  182 (183)
Q Consensus       162 l~q~~i~~~~~~k~~~ll~ll  182 (183)
                      ++..|..+.+.+|..+|+.+|
T Consensus       235 lk~~f~~~~~a~K~aaLl~il  255 (529)
T KOG0337|consen  235 LKVRFFRVRKAEKEAALLSIL  255 (529)
T ss_pred             hhhheeeeccHHHHHHHHHHH
Confidence            999999999999999998875

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.96  E-value=8.8e-28  Score=202.76  Aligned_cols=163  Identities=36%  Similarity=0.549  Sum_probs=143.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +||||+||||||.|+++.+..+.+.. ++++..++||.....+...+ ..++||+||||++|.+++.. +.+++++++++
T Consensus        85 ~~lil~PtreLa~Qi~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l-~~~~~IlV~TP~~l~~~l~~-~~~~l~~v~~l  161 (423)
T PRK04837         85 RALIMAPTRELAVQIHADAEPLAQAT-GLKLGLAYGGDGYDKQLKVL-ESGVDILIGTTGRLIDYAKQ-NHINLGAIQVV  161 (423)
T ss_pred             eEEEECCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHh-cCCCCEEEECHHHHHHHHHc-CCcccccccEE
Confidence            48999999999999999999998877 89999999999888887777 46899999999999999987 78899999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCC--CCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCC
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPK--LRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKT  158 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~--~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (183)
                      |+||||.+++.+|..++..+++.++.  .+|.++||||++..+..++..++.+|..+.+...               ...
T Consensus       162 ViDEad~l~~~~f~~~i~~i~~~~~~~~~~~~~l~SAT~~~~~~~~~~~~~~~p~~i~v~~~---------------~~~  226 (423)
T PRK04837        162 VLDEADRMFDLGFIKDIRWLFRRMPPANQRLNMLFSATLSYRVRELAFEHMNNPEYVEVEPE---------------QKT  226 (423)
T ss_pred             EEecHHHHhhcccHHHHHHHHHhCCCccceeEEEEeccCCHHHHHHHHHHCCCCEEEEEcCC---------------CcC
Confidence            99999999999999999999999984  6789999999999999999999999999988766               445


Q ss_pred             ccCceEEEEEecCcchhhhhhcc
Q 030094          159 PLGLHLEVIWNVNQMRNHHNLLI  181 (183)
Q Consensus       159 ~~~l~q~~i~~~~~~k~~~ll~l  181 (183)
                      ..++++.++.+...+|...+..+
T Consensus       227 ~~~i~~~~~~~~~~~k~~~l~~l  249 (423)
T PRK04837        227 GHRIKEELFYPSNEEKMRLLQTL  249 (423)
T ss_pred             CCceeEEEEeCCHHHHHHHHHHH
Confidence            66788888777777776655443

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

Probab=99.96  E-value=1.9e-27  Score=205.23  Aligned_cols=162  Identities=29%  Similarity=0.525  Sum_probs=144.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .||||+||||||.|+++.++.+.+.. ++++..++||.....+...+ ..+++|+||||++|.+++.+ +.+.+++++++
T Consensus       198 ~aLIL~PTreLa~Qi~~~~~~l~~~~-~~~~~~~~gG~~~~~q~~~l-~~~~~IiV~TPgrL~~~l~~-~~~~l~~v~~l  274 (518)
T PLN00206        198 LAMVLTPTRELCVQVEDQAKVLGKGL-PFKTALVVGGDAMPQQLYRI-QQGVELIVGTPGRLIDLLSK-HDIELDNVSVL  274 (518)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhCCC-CceEEEEECCcchHHHHHHh-cCCCCEEEECHHHHHHHHHc-CCccchheeEE
Confidence            48999999999999999999998877 78999999999988888777 46899999999999999988 78899999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||.|++.+|...+..++..++ .+|+++||||++++++.+++.++.++..+.+...               .....
T Consensus       275 ViDEad~ml~~gf~~~i~~i~~~l~-~~q~l~~SATl~~~v~~l~~~~~~~~~~i~~~~~---------------~~~~~  338 (518)
T PLN00206        275 VLDEVDCMLERGFRDQVMQIFQALS-QPQVLLFSATVSPEVEKFASSLAKDIILISIGNP---------------NRPNK  338 (518)
T ss_pred             EeecHHHHhhcchHHHHHHHHHhCC-CCcEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCC---------------CCCCc
Confidence            9999999999999999999999885 6899999999999999999999999999988766               45566


Q ss_pred             CceEEEEEecCcchhhhhhcc
Q 030094          161 GLHLEVIWNVNQMRNHHNLLI  181 (183)
Q Consensus       161 ~l~q~~i~~~~~~k~~~ll~l  181 (183)
                      .++|.+++++..+|...++.+
T Consensus       339 ~v~q~~~~~~~~~k~~~l~~~  359 (518)
T PLN00206        339 AVKQLAIWVETKQKKQKLFDI  359 (518)
T ss_pred             ceeEEEEeccchhHHHHHHHH
Confidence            788888888887777665543

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=99.95  E-value=2.8e-27  Score=201.43  Aligned_cols=159  Identities=33%  Similarity=0.607  Sum_probs=141.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .||||+||||||.|+++.+..+.++. ++++..++||.+...+...+ ..++||+|+||++|.+++.. ..+++++++++
T Consensus        77 ~aLil~PtreLa~Qi~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l-~~~~~IiV~TP~rL~~~~~~-~~~~l~~v~~l  153 (456)
T PRK10590         77 RALILTPTRELAAQIGENVRDYSKYL-NIRSLVVFGGVSINPQMMKL-RGGVDVLVATPGRLLDLEHQ-NAVKLDQVEIL  153 (456)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHHhccC-CCEEEEEECCcCHHHHHHHH-cCCCcEEEEChHHHHHHHHc-CCcccccceEE
Confidence            38999999999999999999998876 79999999999988887776 46899999999999999987 77899999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||.+++.+|...+..++..++..+|+++||||+++++..++.+++.+|..+.+...               .....
T Consensus       154 ViDEah~ll~~~~~~~i~~il~~l~~~~q~l~~SAT~~~~~~~l~~~~~~~~~~i~~~~~---------------~~~~~  218 (456)
T PRK10590        154 VLDEADRMLDMGFIHDIRRVLAKLPAKRQNLLFSATFSDDIKALAEKLLHNPLEIEVARR---------------NTASE  218 (456)
T ss_pred             EeecHHHHhccccHHHHHHHHHhCCccCeEEEEeCCCcHHHHHHHHHHcCCCeEEEEecc---------------ccccc
Confidence            999999999999999999999999999999999999999999999999999999887665               44566


Q ss_pred             CceEEEEEecCcchhhh
Q 030094          161 GLHLEVIWNVNQMRNHH  177 (183)
Q Consensus       161 ~l~q~~i~~~~~~k~~~  177 (183)
                      ++.|++..++...|...
T Consensus       219 ~i~~~~~~~~~~~k~~~  235 (456)
T PRK10590        219 QVTQHVHFVDKKRKREL  235 (456)
T ss_pred             ceeEEEEEcCHHHHHHH
Confidence            78888887776655443

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

Probab=99.95  E-value=2.3e-28  Score=195.47  Aligned_cols=165  Identities=29%  Similarity=0.387  Sum_probs=145.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcC---CcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMD---VLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~---~~~l~~l   77 (183)
                      ||+|+.||||||.|+.+.+..+++.. ++++..++||.+.-.+...+ ..+||++|+||||+..++..+.   .+.++++
T Consensus        77 FalvlTPTrELA~QiaEQF~alGk~l-~lK~~vivGG~d~i~qa~~L-~~rPHvVvatPGRlad~l~sn~~~~~~~~~rl  154 (442)
T KOG0340|consen   77 FALVLTPTRELALQIAEQFIALGKLL-NLKVSVIVGGTDMIMQAAIL-SDRPHVVVATPGRLADHLSSNLGVCSWIFQRL  154 (442)
T ss_pred             eEEEecchHHHHHHHHHHHHHhcccc-cceEEEEEccHHHhhhhhhc-ccCCCeEecCccccccccccCCccchhhhhce
Confidence            68999999999999999999998777 99999999999988887777 5689999999999999998742   3458999


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCe--EEEEccCCcccccccchhhccc
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPV--RVEVRAESKSHHVSASSQQLAS  155 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~--~i~~~~~~~~~~~~~~~~~~~~  155 (183)
                      +++|+||||++++..|.+.++.+++.+|+.||+++||||+++.+.++..-....+.  .....+.               
T Consensus       155 kflVlDEADrvL~~~f~d~L~~i~e~lP~~RQtLlfSATitd~i~ql~~~~i~k~~a~~~e~~~~---------------  219 (442)
T KOG0340|consen  155 KFLVLDEADRVLAGCFPDILEGIEECLPKPRQTLLFSATITDTIKQLFGCPITKSIAFELEVIDG---------------  219 (442)
T ss_pred             eeEEecchhhhhccchhhHHhhhhccCCCccceEEEEeehhhHHHHhhcCCcccccceEEeccCC---------------
Confidence            99999999999999999999999999999999999999999999988887777643  3333333               


Q ss_pred             CCCccCceEEEEEecCcchhhhhhccc
Q 030094          156 SKTPLGLHLEVIWNVNQMRNHHNLLIC  182 (183)
Q Consensus       156 ~~~~~~l~q~~i~~~~~~k~~~ll~ll  182 (183)
                      ..+++++.|.|++|+...|..+|..+|
T Consensus       220 vstvetL~q~yI~~~~~vkdaYLv~~L  246 (442)
T KOG0340|consen  220 VSTVETLYQGYILVSIDVKDAYLVHLL  246 (442)
T ss_pred             CCchhhhhhheeecchhhhHHHHHHHH
Confidence            789999999999999999998887764

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.95  E-value=4.4e-27  Score=204.77  Aligned_cols=164  Identities=34%  Similarity=0.560  Sum_probs=145.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+|||+||||||.|+++.+.++.... ++++..++|+.....+...+ ..++||+||||++|.+++.+.+.++++.++++
T Consensus        86 raLIl~PTreLa~Qi~~~~~~l~~~~-~i~v~~l~Gg~~~~~q~~~l-~~~~dIiV~TP~rL~~~l~~~~~~~l~~v~~l  163 (572)
T PRK04537         86 RALILAPTRELAIQIHKDAVKFGADL-GLRFALVYGGVDYDKQRELL-QQGVDVIIATPGRLIDYVKQHKVVSLHACEIC  163 (572)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHH-hCCCCEEEECHHHHHHHHHhccccchhheeee
Confidence            38999999999999999999998876 89999999999988887776 46899999999999999987345789999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCC--CCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCC
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPK--LRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKT  158 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~--~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (183)
                      |+||||.|++.+|..++..+++.++.  .+|+++||||++..+..+...++.+|..+.+...               ...
T Consensus       164 ViDEAh~lld~gf~~~i~~il~~lp~~~~~q~ll~SATl~~~v~~l~~~~l~~p~~i~v~~~---------------~~~  228 (572)
T PRK04537        164 VLDEADRMFDLGFIKDIRFLLRRMPERGTRQTLLFSATLSHRVLELAYEHMNEPEKLVVETE---------------TIT  228 (572)
T ss_pred             EecCHHHHhhcchHHHHHHHHHhcccccCceEEEEeCCccHHHHHHHHHHhcCCcEEEeccc---------------ccc
Confidence            99999999999999999999999986  7899999999999999999999999988877666               456


Q ss_pred             ccCceEEEEEecCcchhhhhhcc
Q 030094          159 PLGLHLEVIWNVNQMRNHHNLLI  181 (183)
Q Consensus       159 ~~~l~q~~i~~~~~~k~~~ll~l  181 (183)
                      ..++.|+++.+...+|...++.+
T Consensus       229 ~~~i~q~~~~~~~~~k~~~L~~l  251 (572)
T PRK04537        229 AARVRQRIYFPADEEKQTLLLGL  251 (572)
T ss_pred             ccceeEEEEecCHHHHHHHHHHH
Confidence            67889999888888887766654

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=99.95  E-value=1.2e-27  Score=211.62  Aligned_cols=165  Identities=33%  Similarity=0.513  Sum_probs=151.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhc--CCcCCCCce
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM--DVLDFRNLE   78 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~--~~~~l~~l~   78 (183)
                      +|||++||||||.||++.++.|+... ++++.+++||....+++..++. ++.|+||||||..+++..+  +-.++.++.
T Consensus       440 i~li~aPtrela~QI~r~~~kf~k~l-~ir~v~vygg~~~~~qiaelkR-g~eIvV~tpGRmiD~l~~n~grvtnlrR~t  517 (997)
T KOG0334|consen  440 IALILAPTRELAMQIHREVRKFLKLL-GIRVVCVYGGSGISQQIAELKR-GAEIVVCTPGRMIDILCANSGRVTNLRRVT  517 (997)
T ss_pred             eEEEEcCCHHHHHHHHHHHHHHHhhc-CceEEEecCCccHHHHHHHHhc-CCceEEeccchhhhhHhhcCCccccccccc
Confidence            58999999999999999999999886 9999999999999999999964 6999999999999998752  223567777


Q ss_pred             EEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCC
Q 030094           79 ILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKT  158 (183)
Q Consensus        79 ~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (183)
                      ++|+||||+|++++|.+++..|++.++..+|+++||||++..++.++...++.|+.|.+..+               ...
T Consensus       518 ~lv~deaDrmfdmgfePq~~~Ii~nlrpdrQtvlfSatfpr~m~~la~~vl~~Pveiiv~~~---------------svV  582 (997)
T KOG0334|consen  518 YLVLDEADRMFDMGFEPQITRILQNLRPDRQTVLFSATFPRSMEALARKVLKKPVEIIVGGR---------------SVV  582 (997)
T ss_pred             eeeechhhhhheeccCcccchHHhhcchhhhhhhhhhhhhHHHHHHHHHhhcCCeeEEEccc---------------eeE
Confidence            99999999999999999999999999999999999999999999999999999999998877               778


Q ss_pred             ccCceEEEEEec-Ccchhhhhhccc
Q 030094          159 PLGLHLEVIWNV-NQMRNHHNLLIC  182 (183)
Q Consensus       159 ~~~l~q~~i~~~-~~~k~~~ll~ll  182 (183)
                      ...+.|.+.+|. ..+|+..|+.||
T Consensus       583 ~k~V~q~v~V~~~e~eKf~kL~eLl  607 (997)
T KOG0334|consen  583 CKEVTQVVRVCAIENEKFLKLLELL  607 (997)
T ss_pred             eccceEEEEEecCchHHHHHHHHHH
Confidence            889999999999 888999888765

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.95  E-value=3.3e-27  Score=197.49  Aligned_cols=165  Identities=25%  Similarity=0.444  Sum_probs=140.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCc--CCCCce
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL--DFRNLE   78 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~--~l~~l~   78 (183)
                      +|||++||||||.||.+.+..++.+. +++++.++||.....|.+.+. ..|||+|||||||++++..++.+  +++.++
T Consensus       265 ~~LV~tPTRELa~QV~~Hl~ai~~~t-~i~v~si~GGLavqKQqRlL~-~~p~IVVATPGRlweli~e~n~~l~~~k~vk  342 (731)
T KOG0347|consen  265 IALVVTPTRELAHQVKQHLKAIAEKT-QIRVASITGGLAVQKQQRLLN-QRPDIVVATPGRLWELIEEDNTHLGNFKKVK  342 (731)
T ss_pred             eeEEecChHHHHHHHHHHHHHhcccc-CeEEEEeechhHHHHHHHHHh-cCCCEEEecchHHHHHHHhhhhhhhhhhhce
Confidence            48999999999999999999998865 999999999999999988885 58999999999999999983332  589999


Q ss_pred             EEEEcccchhhccchHHHHHHHHHhCC-----CCCeEEEEeecCChH---------------------HHHHHHh--hCC
Q 030094           79 ILVLDEADRLLDMGFQKQISYIISRLP-----KLRRTGLFSATQTEA---------------------VEELSKA--GLR  130 (183)
Q Consensus        79 ~lVvDEad~ll~~~~~~~l~~i~~~l~-----~~~Q~v~~SAT~~~~---------------------v~~~~~~--~~~  130 (183)
                      ++|+||||+|+..|+-..+..|++.+.     +.+|++.||||++-.                     ++.+++.  +..
T Consensus       343 cLVlDEaDRmvekghF~Els~lL~~L~e~~~~~qrQTlVFSATlt~~~~~~~~~~~k~~~k~~~~~~kiq~Lmk~ig~~~  422 (731)
T KOG0347|consen  343 CLVLDEADRMVEKGHFEELSKLLKHLNEEQKNRQRQTLVFSATLTLVLQQPLSSSRKKKDKEDELNAKIQHLMKKIGFRG  422 (731)
T ss_pred             EEEEccHHHHhhhccHHHHHHHHHHhhhhhcccccceEEEEEEeehhhcChhHHhhhccchhhhhhHHHHHHHHHhCccC
Confidence            999999999999999999999998885     568999999999732                     3334443  344


Q ss_pred             CCeEEEEccCCcccccccchhhcccCCCccCceEEEEEecCcchhhhhhccc
Q 030094          131 NPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNHHNLLIC  182 (183)
Q Consensus       131 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~l~q~~i~~~~~~k~~~ll~ll  182 (183)
                      +|.+|.+..+               ..+..++....|.|+..+|.-+|.++|
T Consensus       423 kpkiiD~t~q---------------~~ta~~l~Es~I~C~~~eKD~ylyYfl  459 (731)
T KOG0347|consen  423 KPKIIDLTPQ---------------SATASTLTESLIECPPLEKDLYLYYFL  459 (731)
T ss_pred             CCeeEecCcc---------------hhHHHHHHHHhhcCCccccceeEEEEE
Confidence            7788888887               777888888889998888888887765

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.94  E-value=9.3e-26  Score=193.00  Aligned_cols=162  Identities=35%  Similarity=0.496  Sum_probs=142.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +||||+||||||.|+++.++.+.++. ++++..++||.+...+.+.+...+++|+|+||++|..++.. ....+++++++
T Consensus       164 ~aLil~PtreLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~~~~~~~~Iiv~TP~~Ll~~~~~-~~~~l~~l~~l  241 (475)
T PRK01297        164 RALIIAPTRELVVQIAKDAAALTKYT-GLNVMTFVGGMDFDKQLKQLEARFCDILVATPGRLLDFNQR-GEVHLDMVEVM  241 (475)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHhhccC-CCEEEEEEccCChHHHHHHHhCCCCCEEEECHHHHHHHHHc-CCcccccCceE
Confidence            37999999999999999999998876 89999999999888888877667899999999999999887 77889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCC--CCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCC
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPK--LRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKT  158 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~--~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (183)
                      |+||||.+++.+|...+..+++.++.  .+|++++|||++.++..+++.++.+|..+.+..+               ...
T Consensus       242 ViDEah~l~~~~~~~~l~~i~~~~~~~~~~q~i~~SAT~~~~~~~~~~~~~~~~~~v~~~~~---------------~~~  306 (475)
T PRK01297        242 VLDEADRMLDMGFIPQVRQIIRQTPRKEERQTLLFSATFTDDVMNLAKQWTTDPAIVEIEPE---------------NVA  306 (475)
T ss_pred             EechHHHHHhcccHHHHHHHHHhCCCCCCceEEEEEeecCHHHHHHHHHhccCCEEEEeccC---------------cCC
Confidence            99999999999999999999999864  6799999999999999999999999999887766               445


Q ss_pred             ccCceEEEEEecCcchhhhhh
Q 030094          159 PLGLHLEVIWNVNQMRNHHNL  179 (183)
Q Consensus       159 ~~~l~q~~i~~~~~~k~~~ll  179 (183)
                      ..++.|+++.+...+|...+.
T Consensus       307 ~~~~~~~~~~~~~~~k~~~l~  327 (475)
T PRK01297        307 SDTVEQHVYAVAGSDKYKLLY  327 (475)
T ss_pred             CCcccEEEEEecchhHHHHHH
Confidence            566777777777777665544

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.94  E-value=1.6e-25  Score=189.54  Aligned_cols=153  Identities=31%  Similarity=0.484  Sum_probs=136.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||++||+|||.|+++.+..+..+. ++++..++||.....+...+ ..+++|+||||++|.+++.. +.+++++++++|
T Consensus        76 ~lil~Pt~eLa~Q~~~~~~~l~~~~-~~~v~~~~gg~~~~~~~~~l-~~~~~IlV~Tp~rl~~~~~~-~~~~~~~v~~lV  152 (434)
T PRK11192         76 ILILTPTRELAMQVADQARELAKHT-HLDIATITGGVAYMNHAEVF-SENQDIVVATPGRLLQYIKE-ENFDCRAVETLI  152 (434)
T ss_pred             EEEECCcHHHHHHHHHHHHHHHccC-CcEEEEEECCCCHHHHHHHh-cCCCCEEEEChHHHHHHHHc-CCcCcccCCEEE
Confidence            7999999999999999999998877 89999999999888877666 46899999999999999988 889999999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCCh-HHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE-AVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~-~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      +||||.|++++|...+..+...++..+|+++||||++. .+..+...++.+|..+.+...               .....
T Consensus       153 iDEah~~l~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~~~~~~~~i~~~~~---------------~~~~~  217 (434)
T PRK11192        153 LDEADRMLDMGFAQDIETIAAETRWRKQTLLFSATLEGDAVQDFAERLLNDPVEVEAEPS---------------RRERK  217 (434)
T ss_pred             EECHHHHhCCCcHHHHHHHHHhCccccEEEEEEeecCHHHHHHHHHHHccCCEEEEecCC---------------ccccc
Confidence            99999999999999999999999999999999999985 588999999999999987766               44566


Q ss_pred             CceEEEEEecCc
Q 030094          161 GLHLEVIWNVNQ  172 (183)
Q Consensus       161 ~l~q~~i~~~~~  172 (183)
                      ++.|+++.++..
T Consensus       218 ~i~~~~~~~~~~  229 (434)
T PRK11192        218 KIHQWYYRADDL  229 (434)
T ss_pred             CceEEEEEeCCH
Confidence            778888777653

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

Probab=99.93  E-value=8.7e-26  Score=187.18  Aligned_cols=169  Identities=25%  Similarity=0.394  Sum_probs=146.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCC----cEEEeCcHHHHHHHHhcCCcCCCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGA----NLLIGTPGRLYDIMERMDVLDFRN   76 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~----~IiV~TP~~l~~~l~~~~~~~l~~   76 (183)
                      .|+|++|||+|+.|+++.+.+++... ++.|+.+.|..+.+.+.+.+.+..+    ||+|+|||||.+++.+++++++++
T Consensus       217 RavVivPtr~L~~QV~~~f~~~~~~t-gL~V~~~sgq~sl~~E~~qL~~~~~~~~~DIlVaTPGRLVDHl~~~k~f~Lk~  295 (620)
T KOG0350|consen  217 RAVVIVPTRELALQVYDTFKRLNSGT-GLAVCSLSGQNSLEDEARQLASDPPECRIDILVATPGRLVDHLNNTKSFDLKH  295 (620)
T ss_pred             EEEEEeeHHHHHHHHHHHHHHhccCC-ceEEEecccccchHHHHHHHhcCCCccccceEEcCchHHHHhccCCCCcchhh
Confidence            48999999999999999999999887 8999999999999999999977677    999999999999999889999999


Q ss_pred             ceEEEEcccchhhccchHHHHHHHHHhCCC----------------------------------CCeEEEEeecCChHHH
Q 030094           77 LEILVLDEADRLLDMGFQKQISYIISRLPK----------------------------------LRRTGLFSATQTEAVE  122 (183)
Q Consensus        77 l~~lVvDEad~ll~~~~~~~l~~i~~~l~~----------------------------------~~Q~v~~SAT~~~~v~  122 (183)
                      ++++|+||||+|++..|.+++-.++..+..                                  .-+.++||||++..-.
T Consensus       296 LrfLVIDEADRll~qsfQ~Wl~~v~~~~~~~k~~~~~~nii~~~~~~~pt~~~e~~t~~~~~~~~l~kL~~satLsqdP~  375 (620)
T KOG0350|consen  296 LRFLVIDEADRLLDQSFQEWLDTVMSLCKTMKRVACLDNIIRQRQAPQPTVLSELLTKLGKLYPPLWKLVFSATLSQDPS  375 (620)
T ss_pred             ceEEEechHHHHHHHHHHHHHHHHHHHhCCchhhcChhhhhhhcccCCchhhHHHHhhcCCcCchhHhhhcchhhhcChH
Confidence            999999999999999999888887766521                                  1268899999999999


Q ss_pred             HHHHhhCCCCeEEEEccCCcccccccchhhcccCCCccCceEEEEEecCcchhhhhhcc
Q 030094          123 ELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNHHNLLI  181 (183)
Q Consensus       123 ~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~l~q~~i~~~~~~k~~~ll~l  181 (183)
                      .+...-+..|..+.+...           .++.+.+|+.++|+++.++...|...+..+
T Consensus       376 Kl~~l~l~~Prl~~v~~~-----------~~~ryslp~~l~~~~vv~~~~~kpl~~~~l  423 (620)
T KOG0350|consen  376 KLKDLTLHIPRLFHVSKP-----------LIGRYSLPSSLSHRLVVTEPKFKPLAVYAL  423 (620)
T ss_pred             HHhhhhcCCCceEEeecc-----------cceeeecChhhhhceeecccccchHhHHHH
Confidence            999999999987776532           123489999999999999988877666543

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

Probab=99.92  E-value=1.6e-25  Score=180.21  Aligned_cols=159  Identities=26%  Similarity=0.376  Sum_probs=139.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      ||+.|+||||||.|+.+++.+++++. ++++.+...|...+ +-+.   -..+|+|||||.+.+++..-+-++++.++.+
T Consensus       162 Q~iCLaPtrELA~Q~~eVv~eMGKf~-~ita~yair~sk~~-rG~~---i~eqIviGTPGtv~Dlm~klk~id~~kikvf  236 (477)
T KOG0332|consen  162 QCICLAPTRELAPQTGEVVEEMGKFT-ELTASYAIRGSKAK-RGNK---LTEQIVIGTPGTVLDLMLKLKCIDLEKIKVF  236 (477)
T ss_pred             CceeeCchHHHHHHHHHHHHHhcCce-eeeEEEEecCcccc-cCCc---chhheeeCCCccHHHHHHHHHhhChhhceEE
Confidence            68889999999999999999999887 89888887766221 1111   2358999999999999987677899999999


Q ss_pred             EEcccchhhc-cchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCc
Q 030094           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTP  159 (183)
Q Consensus        81 VvDEad~ll~-~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (183)
                      |+||||.|++ .||.++-..|.+.+|+++|.++||||+.+.++.|+.+..+||..+.+..+               ....
T Consensus       237 VlDEAD~Mi~tqG~~D~S~rI~~~lP~~~QllLFSATf~e~V~~Fa~kivpn~n~i~Lk~e---------------el~L  301 (477)
T KOG0332|consen  237 VLDEADVMIDTQGFQDQSIRIMRSLPRNQQLLLFSATFVEKVAAFALKIVPNANVIILKRE---------------ELAL  301 (477)
T ss_pred             EecchhhhhhcccccccchhhhhhcCCcceEEeeechhHHHHHHHHHHhcCCCceeeeehh---------------hccc
Confidence            9999999997 47999999999999999999999999999999999999999999999999               7889


Q ss_pred             cCceEEEEEecCcc-hhhhhh
Q 030094          160 LGLHLEVIWNVNQM-RNHHNL  179 (183)
Q Consensus       160 ~~l~q~~i~~~~~~-k~~~ll  179 (183)
                      .+|+|+|+.|..++ |+..|.
T Consensus       302 ~~IkQlyv~C~~~~~K~~~l~  322 (477)
T KOG0332|consen  302 DNIKQLYVLCACRDDKYQALV  322 (477)
T ss_pred             cchhhheeeccchhhHHHHHH
Confidence            99999999997554 777654

>PTZ00424 helicase 45; Provisional

Probab=99.91  E-value=3.7e-23  Score=173.10  Aligned_cols=153  Identities=34%  Similarity=0.581  Sum_probs=133.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++||+|||.|+++.+..++... ++++..+.|+.....+...+ ..+++|+||||+++.+++.+ +.+.+++++++
T Consensus        98 ~~lil~Pt~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~-~~~~~Ivv~Tp~~l~~~l~~-~~~~l~~i~lv  174 (401)
T PTZ00424         98 QALILAPTRELAQQIQKVVLALGDYL-KVRCHACVGGTVVRDDINKL-KAGVHMVVGTPGRVYDMIDK-RHLRVDDLKLF  174 (401)
T ss_pred             eEEEECCCHHHHHHHHHHHHHHhhhc-CceEEEEECCcCHHHHHHHH-cCCCCEEEECcHHHHHHHHh-CCcccccccEE
Confidence            37999999999999999999998765 78888899998887777766 45799999999999999987 77889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||.+++.+|...+..+++.++++.|++++|||+++++..+...++.+|..+.+...               .....
T Consensus       175 ViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~  239 (401)
T PTZ00424        175 ILDEADEMLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKD---------------ELTLE  239 (401)
T ss_pred             EEecHHHHHhcchHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCC---------------CcccC
Confidence            999999999999999999999999999999999999999999999999999988876554               33455


Q ss_pred             CceEEEEEecC
Q 030094          161 GLHLEVIWNVN  171 (183)
Q Consensus       161 ~l~q~~i~~~~  171 (183)
                      +++++++.++.
T Consensus       240 ~~~~~~~~~~~  250 (401)
T PTZ00424        240 GIRQFYVAVEK  250 (401)
T ss_pred             CceEEEEecCh
Confidence            66666666654

>cd00268 DEADc DEAD-box helicases

Probab=99.88  E-value=1.9e-21  Score=148.53  Aligned_cols=131  Identities=46%  Similarity=0.767  Sum_probs=119.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      ++|++||++|+.|+.+.++.+.+.. ++++..+.|+....+....+ ..+++|+|+||+++..++.+ +..++++++++|
T Consensus        72 viii~p~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~-~~~~~iiv~T~~~l~~~l~~-~~~~~~~l~~lI  148 (203)
T cd00268          72 ALILAPTRELALQIAEVARKLGKHT-NLKVVVIYGGTSIDKQIRKL-KRGPHIVVATPGRLLDLLER-GKLDLSKVKYLV  148 (203)
T ss_pred             EEEEcCCHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHh-cCCCCEEEEChHHHHHHHHc-CCCChhhCCEEE
Confidence            7999999999999999999997765 78899999988877666665 35899999999999999987 668899999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEE
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRV  135 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i  135 (183)
                      +||+|.+.+.++...+..+.+.+++.+|++++|||+++.+..++..++.+|+.|
T Consensus       149 vDE~h~~~~~~~~~~~~~~~~~l~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         149 LDEADRMLDMGFEDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             EeChHHhhccChHHHHHHHHHhCCcccEEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence            999999998889999999999999999999999999999999999999999887

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.

>PRK09401 reverse gyrase; Reviewed

Probab=99.86  E-value=6.1e-21  Score=176.35  Aligned_cols=155  Identities=17%  Similarity=0.163  Sum_probs=119.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcch-----HHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEV-----KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFR   75 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~-----~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~   75 (183)
                      +++||+||||||.|+++.+++++... ++.+..++|+...     +++...+.++++||+||||++|.+++.   .+...
T Consensus       125 ~alIL~PTreLa~Qi~~~l~~l~~~~-~~~~~~~~g~~~~~~~ek~~~~~~l~~~~~~IlV~Tp~rL~~~~~---~l~~~  200 (1176)
T PRK09401        125 KSYIIFPTRLLVEQVVEKLEKFGEKV-GCGVKILYYHSSLKKKEKEEFLERLKEGDFDILVTTSQFLSKNFD---ELPKK  200 (1176)
T ss_pred             eEEEEeccHHHHHHHHHHHHHHhhhc-CceEEEEEccCCcchhHHHHHHHHHhcCCCCEEEECHHHHHHHHH---hcccc
Confidence            48999999999999999999998876 7888888877542     333344444579999999999999875   35667


Q ss_pred             CceEEEEcccchhhc-----------cchH-HHHHHHHHhCCC------------------------CCeEEEEeecCCh
Q 030094           76 NLEILVLDEADRLLD-----------MGFQ-KQISYIISRLPK------------------------LRRTGLFSATQTE  119 (183)
Q Consensus        76 ~l~~lVvDEad~ll~-----------~~~~-~~l~~i~~~l~~------------------------~~Q~v~~SAT~~~  119 (183)
                      +++++|+||||++++           .||. +++..+++.++.                        .+|+++||||+++
T Consensus       201 ~~~~lVvDEaD~~L~~~k~id~~l~~lGF~~~~i~~i~~~i~~~~~~~~~~~~i~~l~~~i~~~~~~~~q~ilfSAT~~~  280 (1176)
T PRK09401        201 KFDFVFVDDVDAVLKSSKNIDKLLYLLGFSEEDIEKAMELIRLKRKYEEIYEKIRELEEKIAELKDKKGVLVVSSATGRP  280 (1176)
T ss_pred             ccCEEEEEChHHhhhcccchhhHHHhCCCCHHHHHHHHHhcccccccchhhhHHHHHHHhhhhcccCCceEEEEeCCCCc
Confidence            799999999999996           5774 788888887764                        6899999999987


Q ss_pred             H-HHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCccCceEEEEEecCcchhhhhh
Q 030094          120 A-VEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMRNHHNL  179 (183)
Q Consensus       120 ~-v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~l~q~~i~~~~~~k~~~ll  179 (183)
                      + +..   ..++++..+.+...               .....++.|.|+.++  +|...+.
T Consensus       281 ~~~~~---~l~~~ll~~~v~~~---------------~~~~rnI~~~yi~~~--~k~~~L~  321 (1176)
T PRK09401        281 RGNRV---KLFRELLGFEVGSP---------------VFYLRNIVDSYIVDE--DSVEKLV  321 (1176)
T ss_pred             cchHH---HHhhccceEEecCc---------------ccccCCceEEEEEcc--cHHHHHH
Confidence            5 332   34566666776655               446788999998776  4444443

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

Probab=99.86  E-value=6.7e-21  Score=169.51  Aligned_cols=131  Identities=18%  Similarity=0.206  Sum_probs=111.1

Q ss_pred             EEE-EeCcHHHHHHHHHHHHHhhhhCC----------------------CceEEEEEcCcchHHHHHHHHhcCCcEEEeC
Q 030094            2 GMI-ISPTRELSSQIYHVAQPFISTLP----------------------DVKSVLLVGGVEVKADVKKIEEEGANLLIGT   58 (183)
Q Consensus         2 alI-l~PtreLa~Qi~~~~~~l~~~~~----------------------~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~T   58 (183)
                      +|| ++||||||.|+++.+++++++++                      ++++..++||.+.+.+...+ ..+|+|||||
T Consensus        64 rLv~~vPtReLa~Qi~~~~~~~~k~l~~~~~~~~~~~~~~~~~~~~~~~~l~v~~l~GG~~~~~q~~~l-~~~p~IIVgT  142 (844)
T TIGR02621        64 RLVYVVNRRTVVDQVTEEAEKIGERLPDVPEVEAALWALCSTRPEKKDRPLAISTLRGQFADNDEWMLD-PHRPAVIVGT  142 (844)
T ss_pred             eEEEeCchHHHHHHHHHHHHHHHHHhcccchhhhhhhhhhccccccccCCeEEEEEECCCChHHHHHhc-CCCCcEEEEC
Confidence            566 56999999999999999998663                      48999999999999898877 5789999999


Q ss_pred             cHHHHHHHHhcCCcC----------------CCCceEEEEcccchhhccchHHHHHHHHHhC--CCC---CeEEEEeecC
Q 030094           59 PGRLYDIMERMDVLD----------------FRNLEILVLDEADRLLDMGFQKQISYIISRL--PKL---RRTGLFSATQ  117 (183)
Q Consensus        59 P~~l~~~l~~~~~~~----------------l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l--~~~---~Q~v~~SAT~  117 (183)
                      +    +++.+ +.++                +++++++|+||||  ++++|.+.+..|++.+  ++.   +|+++||||+
T Consensus       143 ~----D~i~s-r~L~~gYg~~~~~~pi~ag~L~~v~~LVLDEAD--Ld~gF~~~l~~Il~~l~rp~~~rprQtLLFSAT~  215 (844)
T TIGR02621       143 V----DMIGS-RLLFSGYGCGFKSRPLHAGFLGQDALIVHDEAH--LEPAFQELLKQIMNEQQRPPDFLPLRVVELTATS  215 (844)
T ss_pred             H----HHHcC-CccccccccccccccchhhhhccceEEEEehhh--hccccHHHHHHHHHhcccCcccccceEEEEecCC
Confidence            5    67766 5552                7899999999999  6789999999999975  432   6999999999


Q ss_pred             ChHHHHHHHhhCCCCeEEEEccC
Q 030094          118 TEAVEELSKAGLRNPVRVEVRAE  140 (183)
Q Consensus       118 ~~~v~~~~~~~~~~~~~i~~~~~  140 (183)
                      +.++..+...++.+|..+.+..+
T Consensus       216 p~ei~~l~~~~~~~p~~i~V~~~  238 (844)
T TIGR02621       216 RTDGPDRTTLLSAEDYKHPVLKK  238 (844)
T ss_pred             CccHHHHHHHHccCCceeecccc
Confidence            99999999999988887766544

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.

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

Probab=99.82  E-value=4.5e-19  Score=131.23  Aligned_cols=121  Identities=34%  Similarity=0.540  Sum_probs=103.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +++++|+++|+.|+++.+.++... +++++..++|+.....+.......+++|+|+||+++.+++.. +..++.+++++|
T Consensus        47 ~lii~P~~~l~~q~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~-~~~~~~~~~~iV  124 (169)
T PF00270_consen   47 VLIIVPTRALAEQQFERLRKFFSN-TNVRVVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISN-GKINISRLSLIV  124 (169)
T ss_dssp             EEEEESSHHHHHHHHHHHHHHTTT-TTSSEEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHT-TSSTGTTESEEE
T ss_pred             EEEEeecccccccccccccccccc-cccccccccccccccccccccccccccccccCcchhhccccc-cccccccceeec
Confidence            789999999999999999999876 478999999988866343333356799999999999999988 556888899999


Q ss_pred             EcccchhhccchHHHHHHHHHhCC--CCCeEEEEeecCChHHHHH
Q 030094           82 LDEADRLLDMGFQKQISYIISRLP--KLRRTGLFSATQTEAVEEL  124 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~--~~~Q~v~~SAT~~~~v~~~  124 (183)
                      +||+|.+.+.++...+..+++.+.  ++.|++++|||+++.++.+
T Consensus       125 iDE~h~l~~~~~~~~~~~i~~~~~~~~~~~~i~~SAT~~~~~~~~  169 (169)
T PF00270_consen  125 IDEAHHLSDETFRAMLKSILRRLKRFKNIQIILLSATLPSNVEKL  169 (169)
T ss_dssp             EETHHHHHHTTHHHHHHHHHHHSHTTTTSEEEEEESSSTHHHHHH
T ss_pred             cCcccccccccHHHHHHHHHHHhcCCCCCcEEEEeeCCChhHhhC
Confidence            999999998788889999999884  3589999999999777653

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 ....

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

Probab=99.79  E-value=2e-19  Score=147.97  Aligned_cols=154  Identities=29%  Similarity=0.511  Sum_probs=136.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhC--CCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTL--PDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~--~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      .|+|+-|+||||.|++..++++-.+.  |.++..++.||...+.|...+. .|.||+||||+|+.+++.. +.+.+++++
T Consensus       288 ~avivepsrelaEqt~N~i~~Fk~h~~np~~r~lLmiggv~~r~Q~~ql~-~g~~ivvGtpgRl~~~is~-g~~~lt~cr  365 (725)
T KOG0349|consen  288 EAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQLK-DGTHIVVGTPGRLLQPISK-GLVTLTHCR  365 (725)
T ss_pred             ceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHhh-cCceeeecCchhhhhhhhc-cceeeeeeE
Confidence            48999999999999999888886655  5677778999999999999884 6899999999999999988 889999999


Q ss_pred             EEEEcccchhhccchHHHHHHHHHhCCC------CCeEEEEeecCC-hHHHHHHHhhCCCCeEEEEccCCcccccccchh
Q 030094           79 ILVLDEADRLLDMGFQKQISYIISRLPK------LRRTGLFSATQT-EAVEELSKAGLRNPVRVEVRAESKSHHVSASSQ  151 (183)
Q Consensus        79 ~lVvDEad~ll~~~~~~~l~~i~~~l~~------~~Q~v~~SAT~~-~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~  151 (183)
                      ++|+||||.++++++.+.+.++...+|+      ..|.+++|||+. -++..+..+.|.-|..+.+..+           
T Consensus       366 FlvlDead~lL~qgy~d~I~r~h~qip~~tsdg~rlq~~vCsatlh~feVkk~~ervmhfptwVdLkge-----------  434 (725)
T KOG0349|consen  366 FLVLDEADLLLGQGYDDKIYRFHGQIPHMTSDGFRLQSPVCSATLHIFEVKKVGERVMHFPTWVDLKGE-----------  434 (725)
T ss_pred             EEEecchhhhhhcccHHHHHHHhccchhhhcCCcccccceeeeEEeEEEeeehhhhhccCceeEecccc-----------
Confidence            9999999999999999999999999874      469999999985 4688889999999999999888           


Q ss_pred             hcccCCCccCceEEEEEecC
Q 030094          152 QLASSKTPLGLHLEVIWNVN  171 (183)
Q Consensus       152 ~~~~~~~~~~l~q~~i~~~~  171 (183)
                          ...|+++.|.+..+.+
T Consensus       435 ----D~vpetvHhvv~lv~p  450 (725)
T KOG0349|consen  435 ----DLVPETVHHVVKLVCP  450 (725)
T ss_pred             ----cccchhhccceeecCC
Confidence                7888998888876543

>PRK14701 reverse gyrase; Provisional

Probab=99.79  E-value=2.7e-18  Score=162.29  Aligned_cols=154  Identities=19%  Similarity=0.194  Sum_probs=115.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCC-CceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLP-DVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRN   76 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~-~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~   76 (183)
                      ++|||+||||||.|+++.++.++.... ++++..+.|+.+.+++..   .+..+.+||+||||++|.+.+.. . .. .+
T Consensus       124 ~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~-l-~~-~~  200 (1638)
T PRK14701        124 KCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPE-M-KH-LK  200 (1638)
T ss_pred             eEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHH-H-hh-CC
Confidence            489999999999999999999987652 467788889888766543   34445699999999999988765 2 22 78


Q ss_pred             ceEEEEcccchhhc-----------cchHHHHHH----HHH----------------------hCCCCCe-EEEEeecCC
Q 030094           77 LEILVLDEADRLLD-----------MGFQKQISY----IIS----------------------RLPKLRR-TGLFSATQT  118 (183)
Q Consensus        77 l~~lVvDEad~ll~-----------~~~~~~l~~----i~~----------------------~l~~~~Q-~v~~SAT~~  118 (183)
                      ++++|+||||.|++           .||.+++..    +++                      .+++.+| .++||||.+
T Consensus       201 i~~iVVDEAD~ml~~~knid~~L~llGF~~e~~~~~~~il~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ll~~SAT~~  280 (1638)
T PRK14701        201 FDFIFVDDVDAFLKASKNIDRSLQLLGFYEEIIEKAWKIIYLKKQGNIEDAMEKREILNKEIEKIGNKIGCLIVASATGK  280 (1638)
T ss_pred             CCEEEEECceeccccccccchhhhcCCChHHHHHHHHHhhhcccccccchhhhhhhhhhhhhhhcCCCccEEEEEecCCC
Confidence            99999999999986           478777764    432                      2355666 677999999


Q ss_pred             hHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCccCceEEEEEecCcch
Q 030094          119 EAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVNQMR  174 (183)
Q Consensus       119 ~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~l~q~~i~~~~~~k  174 (183)
                      +. ... ..+++++..+.++..               .....++.|.|+.++..+|
T Consensus       281 ~r-~~~-~~l~~~~l~f~v~~~---------------~~~lr~i~~~yi~~~~~~k  319 (1638)
T PRK14701        281 AK-GDR-VKLYRELLGFEVGSG---------------RSALRNIVDVYLNPEKIIK  319 (1638)
T ss_pred             ch-hHH-HHHhhcCeEEEecCC---------------CCCCCCcEEEEEECCHHHH
Confidence            75 112 234578888887666               5567889999988765544

>TIGR01054 rgy reverse gyrase

Probab=99.78  E-value=4.2e-18  Score=157.77  Aligned_cols=148  Identities=22%  Similarity=0.244  Sum_probs=108.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEE---EEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCcCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSV---LLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDF   74 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~---~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l   74 (183)
                      +++||+||||||.|+++.+++++... ++++.   .++||.+..++.   ..+.++++||+||||++|.+++..   +..
T Consensus       123 ~vLIL~PTreLa~Qi~~~l~~l~~~~-~i~~~~i~~~~Gg~~~~e~~~~~~~l~~~~~dIlV~Tp~rL~~~~~~---l~~  198 (1171)
T TIGR01054       123 RCYIILPTTLLVIQVAEKISSLAEKA-GVGTVNIGAYHSRLPTKEKKEFMERIENGDFDILITTTMFLSKNYDE---LGP  198 (1171)
T ss_pred             eEEEEeCHHHHHHHHHHHHHHHHHhc-CCceeeeeeecCCCCHHHHHHHHHHHhcCCCCEEEECHHHHHHHHHH---hcC
Confidence            48999999999999999999998765 55443   466887765543   334445699999999999998865   222


Q ss_pred             CCceEEEEcccchhhc-----------cchHHH-HHHHH----------------------HhCCCCCe--EEEEeec-C
Q 030094           75 RNLEILVLDEADRLLD-----------MGFQKQ-ISYII----------------------SRLPKLRR--TGLFSAT-Q  117 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~-----------~~~~~~-l~~i~----------------------~~l~~~~Q--~v~~SAT-~  117 (183)
                       +++++|+||||.|++           .||.++ ++.++                      +.+++++|  .++|||| .
T Consensus       199 -~~~~iVvDEaD~~L~~~k~vd~il~llGF~~e~i~~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~li~~SAT~~  277 (1171)
T TIGR01054       199 -KFDFIFVDDVDALLKASKNVDKLLKLLGFSEELIEKAWKLIRLRLKLYRALHAKKRLELLEAIPGKKRGCLIVSSATGR  277 (1171)
T ss_pred             -CCCEEEEeChHhhhhccccHHHHHHHcCCCHHHHHHHHHHhhhccccchHHHHHHHHHHHHhhhhccCcEEEEEeCCCC
Confidence             899999999999998           577653 55543                      34456666  5679999 5


Q ss_pred             ChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCccCceEEEEEecC
Q 030094          118 TEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVN  171 (183)
Q Consensus       118 ~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~l~q~~i~~~~  171 (183)
                      +..+.   ..+++++..+.+...               .....++.|.|+.++.
T Consensus       278 p~~~~---~~l~r~ll~~~v~~~---------------~~~~r~I~~~~~~~~~  313 (1171)
T TIGR01054       278 PRGKR---AKLFRELLGFEVGGG---------------SDTLRNVVDVYVEDED  313 (1171)
T ss_pred             ccccH---HHHcccccceEecCc---------------cccccceEEEEEeccc
Confidence            54433   345677777777665               5567889999886654

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.

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

Probab=99.77  E-value=1.1e-17  Score=149.57  Aligned_cols=129  Identities=18%  Similarity=0.233  Sum_probs=98.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHh-cC--CcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMER-MD--VLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~-~~--~~~l~~l   77 (183)
                      .||||+||||||.|+++.++++. . .++++..+.|+.+. ++...+ ..+++|+|+||++|...+-. ..  ...++++
T Consensus        83 ~aL~l~PtraLa~q~~~~l~~l~-~-~~i~v~~~~Gdt~~-~~r~~i-~~~~~IivtTPd~L~~~~L~~~~~~~~~l~~l  158 (742)
T TIGR03817        83 TALYLAPTKALAADQLRAVRELT-L-RGVRPATYDGDTPT-EERRWA-REHARYVLTNPDMLHRGILPSHARWARFLRRL  158 (742)
T ss_pred             EEEEEcChHHHHHHHHHHHHHhc-c-CCeEEEEEeCCCCH-HHHHHH-hcCCCEEEEChHHHHHhhccchhHHHHHHhcC
Confidence            48999999999999999999996 3 37888777777664 344444 45799999999998753321 01  1237899


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhC-------CCCCeEEEEeecCChHHHHHHHhhCCCCeEE
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRL-------PKLRRTGLFSATQTEAVEELSKAGLRNPVRV  135 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l-------~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i  135 (183)
                      +++|+||||.+.+ .|..++..+++++       +.++|+++||||+++..+ +++.++.+|..+
T Consensus       159 ~~vViDEah~~~g-~fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~-~~~~l~g~~~~~  221 (742)
T TIGR03817       159 RYVVIDECHSYRG-VFGSHVALVLRRLRRLCARYGASPVFVLASATTADPAA-AASRLIGAPVVA  221 (742)
T ss_pred             CEEEEeChhhccC-ccHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHH-HHHHHcCCCeEE
Confidence            9999999999976 3777766665554       567899999999999854 678888888655

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.

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

Probab=99.76  E-value=3.8e-19  Score=150.23  Aligned_cols=162  Identities=26%  Similarity=0.302  Sum_probs=133.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhh--hhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCC--cCCCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFI--STLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDV--LDFRN   76 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~--~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~--~~l~~   76 (183)
                      +|+|+.||||||.|+|..+.++.  ... +.++..+.......+....+....+||+|+||.++..++.. +.  +++++
T Consensus       211 ~a~Il~ptreLa~Qi~re~~k~~~~~~t-~~~a~~~~~~~~~~qk~a~~~~~k~dili~TP~ri~~~~~~-~~~~idl~~  288 (593)
T KOG0344|consen  211 RALILSPTRELAAQIYREMRKYSIDEGT-SLRAAQFSKPAYPSQKPAFLSDEKYDILISTPMRIVGLLGL-GKLNIDLSK  288 (593)
T ss_pred             EEEEecchHHHHHHHHHHHHhcCCCCCC-chhhhhcccccchhhccchhHHHHHHHHhcCHHHHHHHhcC-CCccchhhe
Confidence            48999999999999999999997  444 56665555443333333344445689999999999999987 54  78999


Q ss_pred             ceEEEEcccchhhcc-chHHHHHHHHHhCC-CCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcc
Q 030094           77 LEILVLDEADRLLDM-GFQKQISYIISRLP-KLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLA  154 (183)
Q Consensus        77 l~~lVvDEad~ll~~-~~~~~l~~i~~~l~-~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~  154 (183)
                      +.++|+||||.+++. .|..++..|++.+. +...+-+||||++..+++++...+.++..|.++..              
T Consensus       289 V~~lV~dEaD~lfe~~~f~~Qla~I~sac~s~~i~~a~FSat~~~~VEE~~~~i~~~~~~vivg~~--------------  354 (593)
T KOG0344|consen  289 VEWLVVDEADLLFEPEFFVEQLADIYSACQSPDIRVALFSATISVYVEEWAELIKSDLKRVIVGLR--------------  354 (593)
T ss_pred             eeeEeechHHhhhChhhHHHHHHHHHHHhcCcchhhhhhhccccHHHHHHHHHhhccceeEEEecc--------------
Confidence            999999999999998 89999999988874 56678899999999999999999999999999888              


Q ss_pred             cCCCccCceEEEEEecCcc-hhhhhh
Q 030094          155 SSKTPLGLHLEVIWNVNQM-RNHHNL  179 (183)
Q Consensus       155 ~~~~~~~l~q~~i~~~~~~-k~~~ll  179 (183)
                       +....+|.|..++|.++. |+..+.
T Consensus       355 -~sa~~~V~QelvF~gse~~K~lA~r  379 (593)
T KOG0344|consen  355 -NSANETVDQELVFCGSEKGKLLALR  379 (593)
T ss_pred             -hhHhhhhhhhheeeecchhHHHHHH
Confidence             666888999999987655 554443

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.75  E-value=6.7e-17  Score=151.20  Aligned_cols=134  Identities=19%  Similarity=0.213  Sum_probs=104.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhh-----------hCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFIS-----------TLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM   69 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~-----------~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~   69 (183)
                      .+|+|+|+|+|+.|+++.++....           ..+++++...+|+.+..++.+.+ +++|||||+||++|..++.++
T Consensus        39 raLYISPLKALa~Dv~~~L~~pl~~i~~~~~~~g~~~~~i~V~vrtGDt~~~eR~rll-~~ppdILVTTPEsL~~LLtsk  117 (1490)
T PRK09751         39 RILYISPIKALGTDVQRNLQIPLKGIADERRRRGETEVNLRVGIRTGDTPAQERSKLT-RNPPDILITTPESLYLMLTSR  117 (1490)
T ss_pred             EEEEEeChHHHHHHHHHHHHHHHHhhhhhhhhcccccCceEEEEEECCCCHHHHHHHh-cCCCCEEEecHHHHHHHHhhh
Confidence            379999999999999998875221           12378999999998887776665 468999999999999998763


Q ss_pred             CCcCCCCceEEEEcccchhhccc----hHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCC-CCeEEE
Q 030094           70 DVLDFRNLEILVLDEADRLLDMG----FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLR-NPVRVE  136 (183)
Q Consensus        70 ~~~~l~~l~~lVvDEad~ll~~~----~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~-~~~~i~  136 (183)
                      ....+++++++|+||+|.+++..    +...++.+...++++.|+|++|||+++. ++++++... +|+.|.
T Consensus       118 ~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~~~~~QrIgLSATI~n~-eevA~~L~g~~pv~Iv  188 (1490)
T PRK09751        118 ARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLHTSAQRIGLSATVRSA-SDVAAFLGGDRPVTVV  188 (1490)
T ss_pred             hhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhCCCCCeEEEEEeeCCCH-HHHHHHhcCCCCEEEE
Confidence            33568999999999999999753    3455666666667889999999999984 677765433 466654

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.73  E-value=1.1e-16  Score=148.11  Aligned_cols=128  Identities=19%  Similarity=0.265  Sum_probs=103.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHH---HhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l---~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +++|||||++||.|+++.+++....+ ++++..+.|+.+.+++...+   ..+++||+||||+.    +.  +.+.++++
T Consensus       651 qvlvLvPT~eLA~Q~~~~f~~~~~~~-~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~l----L~--~~v~~~~L  723 (1147)
T PRK10689        651 QVAVLVPTTLLAQQHYDNFRDRFANW-PVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKL----LQ--SDVKWKDL  723 (1147)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHhhccC-CceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHH----Hh--CCCCHhhC
Confidence            58999999999999999999876666 68888888888776665433   33579999999953    32  45678899


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccC
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAE  140 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~  140 (183)
                      +++|+||+|++   ++..  ...++.++.++|+++||||+.++...++...+++|..|.....
T Consensus       724 ~lLVIDEahrf---G~~~--~e~lk~l~~~~qvLl~SATpiprtl~l~~~gl~d~~~I~~~p~  781 (1147)
T PRK10689        724 GLLIVDEEHRF---GVRH--KERIKAMRADVDILTLTATPIPRTLNMAMSGMRDLSIIATPPA  781 (1147)
T ss_pred             CEEEEechhhc---chhH--HHHHHhcCCCCcEEEEcCCCCHHHHHHHHhhCCCcEEEecCCC
Confidence            99999999996   3322  3456778889999999999999989999889999998876544

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.71  E-value=3.4e-16  Score=142.25  Aligned_cols=128  Identities=21%  Similarity=0.284  Sum_probs=101.1

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +++|++||++||.|+++.++++.+.+ ++++..+.|+.+.+++.   ..+..+++||+||||.    ++ . +.+.++++
T Consensus       502 qvlvLvPT~~LA~Q~~~~f~~~~~~~-~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~----ll-~-~~v~f~~L  574 (926)
T TIGR00580       502 QVAVLVPTTLLAQQHFETFKERFANF-PVTIELLSRFRSAKEQNEILKELASGKIDILIGTHK----LL-Q-KDVKFKDL  574 (926)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHHhccC-CcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHH----Hh-h-CCCCcccC
Confidence            58999999999999999999988777 78998888876654433   3444457999999993    33 3 46789999


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccC
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAE  140 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~  140 (183)
                      +++|+||+|++     .......++.++.+.|+++||||..++...+....+.++..|.....
T Consensus       575 ~llVIDEahrf-----gv~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~  632 (926)
T TIGR00580       575 GLLIIDEEQRF-----GVKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPE  632 (926)
T ss_pred             CEEEeeccccc-----chhHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCC
Confidence            99999999994     22334556677788999999999988887777777888888775443

All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transacribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families.

>PRK00254 ski2-like helicase; Provisional

Probab=99.68  E-value=4.1e-16  Score=139.61  Aligned_cols=118  Identities=15%  Similarity=0.251  Sum_probs=100.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +|+++|+++||.|+++.+..+. .. ++++..++|+.....+  .+  .++||+|+||+++..++++ +...+++++++|
T Consensus        71 ~l~l~P~~aLa~q~~~~~~~~~-~~-g~~v~~~~Gd~~~~~~--~~--~~~~IiV~Tpe~~~~ll~~-~~~~l~~l~lvV  143 (720)
T PRK00254         71 AVYLVPLKALAEEKYREFKDWE-KL-GLRVAMTTGDYDSTDE--WL--GKYDIIIATAEKFDSLLRH-GSSWIKDVKLVV  143 (720)
T ss_pred             EEEEeChHHHHHHHHHHHHHHh-hc-CCEEEEEeCCCCCchh--hh--ccCCEEEEcHHHHHHHHhC-CchhhhcCCEEE
Confidence            7999999999999999998874 34 7899999998764332  22  4689999999999999876 556689999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHh
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~  127 (183)
                      +||+|.+.+.++...++.++.++++..|++++|||+++. ..++.+
T Consensus       144 iDE~H~l~~~~rg~~le~il~~l~~~~qiI~lSATl~n~-~~la~w  188 (720)
T PRK00254        144 ADEIHLIGSYDRGATLEMILTHMLGRAQILGLSATVGNA-EELAEW  188 (720)
T ss_pred             EcCcCccCCccchHHHHHHHHhcCcCCcEEEEEccCCCH-HHHHHH
Confidence            999999988888999999999999999999999999874 667664

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.67  E-value=1.8e-15  Score=134.63  Aligned_cols=114  Identities=21%  Similarity=0.361  Sum_probs=88.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHH---HHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKAD---VKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~---~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +++|++||++||.|+++.++++.+.. ++++..++|+.+..+.   ...+.++.++|+||||+.+.      ..+.++++
T Consensus       312 q~lilaPT~~LA~Q~~~~l~~l~~~~-~i~v~ll~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~------~~v~~~~l  384 (681)
T PRK10917        312 QAALMAPTEILAEQHYENLKKLLEPL-GIRVALLTGSLKGKERREILEAIASGEADIVIGTHALIQ------DDVEFHNL  384 (681)
T ss_pred             eEEEEeccHHHHHHHHHHHHHHHhhc-CcEEEEEcCCCCHHHHHHHHHHHhCCCCCEEEchHHHhc------ccchhccc
Confidence            58999999999999999999998876 7999999999875443   33454557999999997663      34567899


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHH
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSK  126 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~  126 (183)
                      +++|+||+|++-     ......+...+..+|+++||||..+....+..
T Consensus       385 ~lvVIDE~Hrfg-----~~qr~~l~~~~~~~~iL~~SATp~prtl~~~~  428 (681)
T PRK10917        385 GLVIIDEQHRFG-----VEQRLALREKGENPHVLVMTATPIPRTLAMTA  428 (681)
T ss_pred             ceEEEechhhhh-----HHHHHHHHhcCCCCCEEEEeCCCCHHHHHHHH
Confidence            999999999962     22233344456679999999998877655554

>PRK02362 ski2-like helicase; Provisional

Probab=99.66  E-value=6.7e-16  Score=138.58  Aligned_cols=119  Identities=17%  Similarity=0.262  Sum_probs=96.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+|+++|||+||.|+++.++++.. + ++++..++|+.....+  .+  ..+||+|+||+++..++++ +...+++++++
T Consensus        69 kal~i~P~raLa~q~~~~~~~~~~-~-g~~v~~~tGd~~~~~~--~l--~~~~IiV~Tpek~~~llr~-~~~~l~~v~lv  141 (737)
T PRK02362         69 KALYIVPLRALASEKFEEFERFEE-L-GVRVGISTGDYDSRDE--WL--GDNDIIVATSEKVDSLLRN-GAPWLDDITCV  141 (737)
T ss_pred             cEEEEeChHHHHHHHHHHHHHhhc-C-CCEEEEEeCCcCcccc--cc--CCCCEEEECHHHHHHHHhc-ChhhhhhcCEE
Confidence            379999999999999999998753 3 7899999987654332  22  4689999999999999986 55568899999


Q ss_pred             EEcccchhhccchHHHHHHHHHhC---CCCCeEEEEeecCChHHHHHHHh
Q 030094           81 VLDEADRLLDMGFQKQISYIISRL---PKLRRTGLFSATQTEAVEELSKA  127 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l---~~~~Q~v~~SAT~~~~v~~~~~~  127 (183)
                      |+||+|.+.+.+++..++.++.++   +++.|++++|||+++. ..++.+
T Consensus       142 ViDE~H~l~d~~rg~~le~il~rl~~~~~~~qii~lSATl~n~-~~la~w  190 (737)
T PRK02362        142 VVDEVHLIDSANRGPTLEVTLAKLRRLNPDLQVVALSATIGNA-DELADW  190 (737)
T ss_pred             EEECccccCCCcchHHHHHHHHHHHhcCCCCcEEEEcccCCCH-HHHHHH
Confidence            999999998877888877776554   5678999999999864 555554

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.65  E-value=7.7e-16  Score=140.14  Aligned_cols=124  Identities=20%  Similarity=0.257  Sum_probs=93.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHH-------hh----hhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhc
Q 030094            1 MGMIISPTRELSSQIYHVAQP-------FI----STLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM   69 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~-------l~----~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~   69 (183)
                      ++|+++|||+||.|+++.+..       +.    ...+++++....|+.+..++.+.+ ..+|||+|+||+++..++.+ 
T Consensus        86 ~~LyIsPtraLa~di~~~L~~~l~~i~~~~~~~g~~~~~i~v~v~~Gdt~~~~r~~~l-~~~p~IlVtTPE~L~~ll~~-  163 (876)
T PRK13767         86 YCLYVSPLRALNNDIHRNLEEPLTEIREIAKERGEELPEIRVAIRTGDTSSYEKQKML-KKPPHILITTPESLAILLNS-  163 (876)
T ss_pred             EEEEEcCHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCeeEEEEcCCCCHHHHHHHH-hCCCCEEEecHHHHHHHhcC-
Confidence            389999999999999876553       22    233478899999998877766665 46899999999999988865 


Q ss_pred             CCc--CCCCceEEEEcccchhhccchHHHHHH----HHHhCCCCCeEEEEeecCChHHHHHHHh
Q 030094           70 DVL--DFRNLEILVLDEADRLLDMGFQKQISY----IISRLPKLRRTGLFSATQTEAVEELSKA  127 (183)
Q Consensus        70 ~~~--~l~~l~~lVvDEad~ll~~~~~~~l~~----i~~~l~~~~Q~v~~SAT~~~~v~~~~~~  127 (183)
                      ..+  .+++++++|+||+|.+.+.....++..    +....++..|++++|||+++. ..++++
T Consensus       164 ~~~~~~l~~l~~VVIDE~H~l~~~~RG~~l~~~L~rL~~l~~~~~q~IglSATl~~~-~~va~~  226 (876)
T PRK13767        164 PKFREKLRTVKWVIVDEIHSLAENKRGVHLSLSLERLEELAGGEFVRIGLSATIEPL-EEVAKF  226 (876)
T ss_pred             hhHHHHHhcCCEEEEechhhhccCccHHHHHHHHHHHHHhcCCCCeEEEEecccCCH-HHHHHH
Confidence            443  478999999999999997655544444    344444678999999999873 444443

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.63  E-value=1.3e-14  Score=130.80  Aligned_cols=127  Identities=17%  Similarity=0.119  Sum_probs=94.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .++|+.|||++|.|+++.+.+..+...+..+...+++...      . ..+++|+|+|||+|.+++.+  ..++++++++
T Consensus        47 ~ilvlqPrR~aA~qiA~rva~~~~~~~g~~VGy~vr~~~~------~-s~~t~I~v~T~G~Llr~l~~--d~~L~~v~~V  117 (819)
T TIGR01970        47 KIIMLEPRRLAARSAAQRLASQLGEAVGQTVGYRVRGENK------V-SRRTRLEVVTEGILTRMIQD--DPELDGVGAL  117 (819)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHHhCCCcCcEEEEEEccccc------c-CCCCcEEEECCcHHHHHHhh--CcccccCCEE
Confidence            4799999999999999988654332224556555554331      1 34689999999999999976  4579999999


Q ss_pred             EEcccc-hhhccchHH-HHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEcc
Q 030094           81 VLDEAD-RLLDMGFQK-QISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRA  139 (183)
Q Consensus        81 VvDEad-~ll~~~~~~-~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~  139 (183)
                      |+||+| ++++.++.- .+..+.+.++++.|+++||||++.+.   ...|+.++..|.+..
T Consensus       118 IiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlIlmSATl~~~~---l~~~l~~~~vI~~~g  175 (819)
T TIGR01970       118 IFDEFHERSLDADLGLALALDVQSSLREDLKILAMSATLDGER---LSSLLPDAPVVESEG  175 (819)
T ss_pred             EEeccchhhhccchHHHHHHHHHHhcCCCceEEEEeCCCCHHH---HHHHcCCCcEEEecC
Confidence            999999 477766543 34556667788999999999999763   366787776665543

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.

>PHA02653 RNA helicase NPH-II; Provisional

Probab=99.63  E-value=5.4e-15  Score=130.55  Aligned_cols=125  Identities=15%  Similarity=0.131  Sum_probs=94.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhh--CCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            1 MGMIISPTRELSSQIYHVAQPFIST--LPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~--~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +++|++||||||.|+...+.+..++  +++..+...+||... .+.+.. ..+.+|+|+||+.        ...++++++
T Consensus       224 ~ilvt~PrreLa~qi~~~i~~~vg~~~~~g~~v~v~~Gg~~~-~~~~t~-~k~~~Ilv~T~~L--------~l~~L~~v~  293 (675)
T PHA02653        224 PIVLSLPRVALVRLHSITLLKSLGFDEIDGSPISLKYGSIPD-ELINTN-PKPYGLVFSTHKL--------TLNKLFDYG  293 (675)
T ss_pred             EEEEECcHHHHHHHHHHHHHHHhCccccCCceEEEEECCcch-HHhhcc-cCCCCEEEEeCcc--------cccccccCC
Confidence            3789999999999999998877654  346778888998772 221222 2468999999752        123578899


Q ss_pred             EEEEcccchhhccchHHHHHHHHHhC-CCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEc
Q 030094           79 ILVLDEADRLLDMGFQKQISYIISRL-PKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVR  138 (183)
Q Consensus        79 ~lVvDEad~ll~~~~~~~l~~i~~~l-~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~  138 (183)
                      ++|+||||.+...+  +.+..+++.. ++.+|+++||||++++++.+ ..|+++|..|.+.
T Consensus       294 ~VVIDEaHEr~~~~--DllL~llk~~~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~  351 (675)
T PHA02653        294 TVIIDEVHEHDQIG--DIIIAVARKHIDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIP  351 (675)
T ss_pred             EEEccccccCccch--hHHHHHHHHhhhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeC
Confidence            99999999987654  4555566544 34579999999999998887 5789999998875

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.63  E-value=1.1e-14  Score=131.17  Aligned_cols=126  Identities=13%  Similarity=0.121  Sum_probs=94.1

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +++|++|||++|.|+++.+.+..+...+..+...+++.+..       ..+.+|+|+|||+|.+++..  ...+++++++
T Consensus        50 ~ilvlqPrR~aA~qia~rva~~l~~~~g~~VGy~vr~~~~~-------~~~t~I~v~T~G~Llr~l~~--d~~L~~v~~I  120 (812)
T PRK11664         50 KIIMLEPRRLAARNVAQRLAEQLGEKPGETVGYRMRAESKV-------GPNTRLEVVTEGILTRMIQR--DPELSGVGLV  120 (812)
T ss_pred             eEEEECChHHHHHHHHHHHHHHhCcccCceEEEEecCcccc-------CCCCcEEEEChhHHHHHHhh--CCCcCcCcEE
Confidence            47999999999999999886543332366777777765431       23568999999999999876  4579999999


Q ss_pred             EEcccch-hhccch-HHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEc
Q 030094           81 VLDEADR-LLDMGF-QKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVR  138 (183)
Q Consensus        81 VvDEad~-ll~~~~-~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~  138 (183)
                      |+||+|. .++.++ ...+..+.+.++++.|+++||||++.+  . ...|+.++..|.+.
T Consensus       121 IlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqlilmSATl~~~--~-l~~~~~~~~~I~~~  177 (812)
T PRK11664        121 ILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMSATLDND--R-LQQLLPDAPVIVSE  177 (812)
T ss_pred             EEcCCCccccccchHHHHHHHHHHhCCccceEEEEecCCCHH--H-HHHhcCCCCEEEec
Confidence            9999997 454433 233455667788899999999999865  2 35678777666543

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.60  E-value=1.2e-14  Score=128.34  Aligned_cols=113  Identities=21%  Similarity=0.327  Sum_probs=85.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHH---HHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKA---DVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~---~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +++|++||++||.|+++.++++.+.. ++++..++|+...++   ....+..++++|+||||+.+.      ..+.++++
T Consensus       286 qvlilaPT~~LA~Q~~~~~~~l~~~~-gi~v~lltg~~~~~~r~~~~~~i~~g~~~IiVgT~~ll~------~~~~~~~l  358 (630)
T TIGR00643       286 QVALMAPTEILAEQHYNSLRNLLAPL-GIEVALLTGSLKGKRRKELLETIASGQIHLVVGTHALIQ------EKVEFKRL  358 (630)
T ss_pred             cEEEECCHHHHHHHHHHHHHHHhccc-CcEEEEEecCCCHHHHHHHHHHHhCCCCCEEEecHHHHh------cccccccc
Confidence            58999999999999999999998876 899999999887654   334454567999999998653      24667899


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCC--CCCeEEEEeecCChHHHHH
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLP--KLRRTGLFSATQTEAVEEL  124 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~--~~~Q~v~~SAT~~~~v~~~  124 (183)
                      +++|+||+|++- ..   ....+.+...  ..+|++++|||..++...+
T Consensus       359 ~lvVIDEaH~fg-~~---qr~~l~~~~~~~~~~~~l~~SATp~prtl~l  403 (630)
T TIGR00643       359 ALVIIDEQHRFG-VE---QRKKLREKGQGGFTPHVLVMSATPIPRTLAL  403 (630)
T ss_pred             ceEEEechhhcc-HH---HHHHHHHhcccCCCCCEEEEeCCCCcHHHHH
Confidence            999999999952 11   2222333332  2689999999987765444

>PRK01172 ski2-like helicase; Provisional

Probab=99.59  E-value=1.4e-14  Score=128.98  Aligned_cols=119  Identities=20%  Similarity=0.257  Sum_probs=94.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+++++|+|+||.|+++.++++. .. +.++...+|+......  .+  ..+||+|+||+++..++.+ ....+++++++
T Consensus        67 k~v~i~P~raLa~q~~~~~~~l~-~~-g~~v~~~~G~~~~~~~--~~--~~~dIiv~Tpek~~~l~~~-~~~~l~~v~lv  139 (674)
T PRK01172         67 KSIYIVPLRSLAMEKYEELSRLR-SL-GMRVKISIGDYDDPPD--FI--KRYDVVILTSEKADSLIHH-DPYIINDVGLI  139 (674)
T ss_pred             cEEEEechHHHHHHHHHHHHHHh-hc-CCeEEEEeCCCCCChh--hh--ccCCEEEECHHHHHHHHhC-ChhHHhhcCEE
Confidence            37899999999999999999874 33 7888888887654322  22  3689999999999999876 55668999999


Q ss_pred             EEcccchhhccchHHHHHHHHHh---CCCCCeEEEEeecCChHHHHHHHh
Q 030094           81 VLDEADRLLDMGFQKQISYIISR---LPKLRRTGLFSATQTEAVEELSKA  127 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~---l~~~~Q~v~~SAT~~~~v~~~~~~  127 (183)
                      |+||+|.+.+.++...++.++..   ++++.|++++|||+++. ..++++
T Consensus       140 ViDEaH~l~d~~rg~~le~ll~~~~~~~~~~riI~lSATl~n~-~~la~w  188 (674)
T PRK01172        140 VADEIHIIGDEDRGPTLETVLSSARYVNPDARILALSATVSNA-NELAQW  188 (674)
T ss_pred             EEecchhccCCCccHHHHHHHHHHHhcCcCCcEEEEeCccCCH-HHHHHH
Confidence            99999999877777666666544   45688999999999864 666664

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.57  E-value=3e-13  Score=101.05  Aligned_cols=136  Identities=37%  Similarity=0.589  Sum_probs=110.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +++++||+.++.|..+.+.++.... ........++.....+...+.....+++++||+.+...+.. ......+++++|
T Consensus        57 ~l~~~p~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~t~~~l~~~~~~-~~~~~~~~~~iI  134 (201)
T smart00487       57 VLVLVPTRELAEQWAEELKKLGPSL-GLKVVGLYGGDSKREQLRKLESGKTDILVTTPGRLLDLLEN-DLLELSNVDLVI  134 (201)
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhccC-CeEEEEEeCCcchHHHHHHHhcCCCCEEEeChHHHHHHHHc-CCcCHhHCCEEE
Confidence            6899999999999999998886543 33445555555545555555443349999999999999987 556788899999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEcc
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRA  139 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~  139 (183)
                      +||+|.+....+...+..+++.+++..+.+++|||.++.+......++.++..+....
T Consensus       135 iDE~h~~~~~~~~~~~~~~~~~~~~~~~~v~~saT~~~~~~~~~~~~~~~~~~~~~~~  192 (201)
T smart00487      135 LDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGP  192 (201)
T ss_pred             EECHHHHhcCCcHHHHHHHHHhCCccceEEEEecCCchhHHHHHHHhcCCCEEEeCCc
Confidence            9999999765688899999999988999999999999999999999999887776544

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.56  E-value=1e-13  Score=118.72  Aligned_cols=130  Identities=17%  Similarity=0.224  Sum_probs=91.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCc-CCCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVL-DFRN   76 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~-~l~~   76 (183)
                      .+||++||+||+.|..+.+..+     ++.+..+.|+....+...   .+....++|+++||+++.........+ ...+
T Consensus        53 ~~lVi~P~~~L~~dq~~~l~~~-----gi~~~~l~~~~~~~~~~~i~~~~~~~~~~il~~TPe~l~~~~~~~~~l~~~~~  127 (470)
T TIGR00614        53 ITLVISPLISLMEDQVLQLKAS-----GIPATFLNSSQSKEQQKNVLTDLKDGKIKLLYVTPEKCSASNRLLQTLEERKG  127 (470)
T ss_pred             cEEEEecHHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHcCchhHHHHHHhcCC
Confidence            3799999999999988877654     567777777665543322   334456899999999976432110223 5688


Q ss_pred             ceEEEEcccchhhccc--hHHHHHH---HHHhCCCCCeEEEEeecCChHHHHHHHhhC--CCCeEEE
Q 030094           77 LEILVLDEADRLLDMG--FQKQISY---IISRLPKLRRTGLFSATQTEAVEELSKAGL--RNPVRVE  136 (183)
Q Consensus        77 l~~lVvDEad~ll~~~--~~~~l~~---i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~--~~~~~i~  136 (183)
                      ++++|+||||.+.++|  |.+....   +.+.+ ++.|++++|||.++.+..-+...+  .+|..+.
T Consensus       128 i~~iViDEaH~i~~~g~~fr~~~~~l~~l~~~~-~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~  193 (470)
T TIGR00614       128 ITLIAVDEAHCISQWGHDFRPDYKALGSLKQKF-PNVPIMALTATASPSVREDILRQLNLKNPQIFC  193 (470)
T ss_pred             cCEEEEeCCcccCccccccHHHHHHHHHHHHHc-CCCceEEEecCCCHHHHHHHHHHcCCCCCcEEe
Confidence            9999999999998765  5555544   34444 578899999999998876555543  4665543

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

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.49  E-value=1.2e-13  Score=123.70  Aligned_cols=83  Identities=16%  Similarity=0.305  Sum_probs=74.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhcCCcCCC-----
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMDVLDFR-----   75 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~~~~~l~-----   75 (183)
                      ++||+||||||.|+++.+..+.+++ ++++.+++||.+..++...+   +|||+||||++| .++++. +.+.++     
T Consensus       138 v~IVTpTrELA~Qdae~m~~L~k~l-GLsV~~i~GG~~~~eq~~~y---~~DIVygTPgRLgfDyLrd-~~~~~~~~~~v  212 (970)
T PRK12899        138 VHLVTVNDYLAQRDCEWVGSVLRWL-GLTTGVLVSGSPLEKRKEIY---QCDVVYGTASEFGFDYLRD-NSIATRKEEQV  212 (970)
T ss_pred             eEEEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHHHHHc---CCCEEEECCChhHHHHhhC-CCCCcCHHHhh
Confidence            6899999999999999999999887 89999999999988876554   699999999999 999987 666666     


Q ss_pred             --CceEEEEcccchhh
Q 030094           76 --NLEILVLDEADRLL   89 (183)
Q Consensus        76 --~l~~lVvDEad~ll   89 (183)
                        .++++|+||||.||
T Consensus       213 qr~~~~~IIDEADsmL  228 (970)
T PRK12899        213 GRGFYFAIIDEVDSIL  228 (970)
T ss_pred             cccccEEEEechhhhh
Confidence              45899999999997

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

Probab=99.48  E-value=1.9e-12  Score=118.39  Aligned_cols=125  Identities=21%  Similarity=0.249  Sum_probs=89.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHh-----cCCcEEEeCcHHHHH---HHHhcCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEE-----EGANLLIGTPGRLYD---IMERMDVL   72 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~-----~~~~IiV~TP~~l~~---~l~~~~~~   72 (183)
                      ++|||+|+++|+.+....+..    . ++++..+.|+....++...+..     .+++|+++||++|..   ++.....+
T Consensus       502 iTLVISPLiSLmqDQV~~L~~----~-GI~Aa~L~s~~s~~eq~~ilr~l~s~~g~~~ILyvTPERL~~~d~ll~~L~~L  576 (1195)
T PLN03137        502 ITLVISPLVSLIQDQIMNLLQ----A-NIPAASLSAGMEWAEQLEILQELSSEYSKYKLLYVTPEKVAKSDSLLRHLENL  576 (1195)
T ss_pred             cEEEEeCHHHHHHHHHHHHHh----C-CCeEEEEECCCCHHHHHHHHHHHHhcCCCCCEEEEChHHhhcchHHHHHHHhh
Confidence            479999999999843333332    2 7888999999887777654432     578999999999863   22221112


Q ss_pred             -CCCCceEEEEcccchhhccc--hHHHHHHH--HHhCCCCCeEEEEeecCChHHHHHHHhhCC
Q 030094           73 -DFRNLEILVLDEADRLLDMG--FQKQISYI--ISRLPKLRRTGLFSATQTEAVEELSKAGLR  130 (183)
Q Consensus        73 -~l~~l~~lVvDEad~ll~~~--~~~~l~~i--~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~  130 (183)
                       ....+.++||||||.++++|  |.+....+  +....+..|++++|||.++.+...+...+.
T Consensus       577 ~~~~~LslIVIDEAHcVSqWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~  639 (1195)
T PLN03137        577 NSRGLLARFVIDEAHCVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALG  639 (1195)
T ss_pred             hhccccceeccCcchhhhhcccchHHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcC
Confidence             23558899999999999886  77766653  333335788999999999998875555443

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.47  E-value=3.6e-13  Score=120.56  Aligned_cols=124  Identities=20%  Similarity=0.278  Sum_probs=100.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      ++++||+|.||.+.++.++++.. + ++++...+|+.....+  .+  .+++|+|+||+++..++++ ...-...++++|
T Consensus        79 ~vYivPlkALa~Ek~~~~~~~~~-~-GirV~~~TgD~~~~~~--~l--~~~~ViVtT~EK~Dsl~R~-~~~~~~~V~lvV  151 (766)
T COG1204          79 VVYIVPLKALAEEKYEEFSRLEE-L-GIRVGISTGDYDLDDE--RL--ARYDVIVTTPEKLDSLTRK-RPSWIEEVDLVV  151 (766)
T ss_pred             EEEEeChHHHHHHHHHHhhhHHh-c-CCEEEEecCCcccchh--hh--ccCCEEEEchHHhhHhhhc-CcchhhcccEEE
Confidence            78999999999999999997744 4 8999999998875542  23  4799999999999999987 555778999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCC---CCCeEEEEeecCChHHHHHHHhhCCCCe
Q 030094           82 LDEADRLLDMGFQKQISYIISRLP---KLRRTGLFSATQTEAVEELSKAGLRNPV  133 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~---~~~Q~v~~SAT~~~~v~~~~~~~~~~~~  133 (183)
                      +||+|.+-+..-+..++.|..++.   ...|++..|||+++- .+++.+.-.++.
T Consensus       152 iDEiH~l~d~~RG~~lE~iv~r~~~~~~~~rivgLSATlpN~-~evA~wL~a~~~  205 (766)
T COG1204         152 IDEIHLLGDRTRGPVLESIVARMRRLNELIRIVGLSATLPNA-EEVADWLNAKLV  205 (766)
T ss_pred             EeeeeecCCcccCceehhHHHHHHhhCcceEEEEEeeecCCH-HHHHHHhCCccc
Confidence            999999977655666666665554   347999999999987 888887655554

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

Probab=99.47  E-value=1.7e-12  Score=117.58  Aligned_cols=133  Identities=22%  Similarity=0.258  Sum_probs=100.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCC-CceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHh-cCC--cCCCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLP-DVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMER-MDV--LDFRN   76 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~-~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~-~~~--~~l~~   76 (183)
                      .||+|.||++||+...+.++++...++ ++++....|.....+.. .+..++|||+++||..|..++-. ...  +.+++
T Consensus       117 ~AL~lYPtnALa~DQ~~rl~~~~~~~~~~v~~~~y~Gdt~~~~r~-~~~~~pp~IllTNpdMLh~~llr~~~~~~~~~~~  195 (851)
T COG1205         117 RALLLYPTNALANDQAERLRELISDLPGKVTFGRYTGDTPPEERR-AIIRNPPDILLTNPDMLHYLLLRNHDAWLWLLRN  195 (851)
T ss_pred             cEEEEechhhhHhhHHHHHHHHHHhCCCcceeeeecCCCChHHHH-HHHhCCCCEEEeCHHHHHHHhccCcchHHHHHhc
Confidence            479999999999999999999999886 46666556655544443 44468999999999999995543 111  34788


Q ss_pred             ceEEEEcccchhhccchHHHHHHHHHhC-------CCCCeEEEEeecCChHHHHHHHhhCCCCeEEE
Q 030094           77 LEILVLDEADRLLDMGFQKQISYIISRL-------PKLRRTGLFSATQTEAVEELSKAGLRNPVRVE  136 (183)
Q Consensus        77 l~~lVvDEad~ll~~~~~~~l~~i~~~l-------~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~  136 (183)
                      ++++|+||+|..-+ .|+.+|..+++++       +...|+++.|||+.+. .+++..++.......
T Consensus       196 Lk~lVvDElHtYrG-v~GS~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np-~e~~~~l~~~~f~~~  260 (851)
T COG1205         196 LKYLVVDELHTYRG-VQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANP-GEFAEELFGRDFEVP  260 (851)
T ss_pred             CcEEEEecceeccc-cchhHHHHHHHHHHHHHhccCCCceEEEEeccccCh-HHHHHHhcCCcceee
Confidence            99999999999754 3677776666665       4578999999999998 666666666555543

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

Probab=99.46  E-value=8e-13  Score=110.90  Aligned_cols=131  Identities=17%  Similarity=0.185  Sum_probs=104.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +|+|+||+-|+.|..+.|++.+ ..|.-.++.++|....++....+  ...+|+|+||+.+.+-+.. +.+|+.++.++|
T Consensus        61 vlfLAPTKPLV~Qh~~~~~~v~-~ip~~~i~~ltGev~p~~R~~~w--~~~kVfvaTPQvveNDl~~-Grid~~dv~~li  136 (542)
T COG1111          61 VLFLAPTKPLVLQHAEFCRKVT-GIPEDEIAALTGEVRPEEREELW--AKKKVFVATPQVVENDLKA-GRIDLDDVSLLI  136 (542)
T ss_pred             EEEecCCchHHHHHHHHHHHHh-CCChhheeeecCCCChHHHHHHH--hhCCEEEeccHHHHhHHhc-CccChHHceEEE
Confidence            7999999999999999999997 45678889999988877666655  3579999999999999988 899999999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHH---HHhhCCCCeEEE
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEEL---SKAGLRNPVRVE  136 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~---~~~~~~~~~~i~  136 (183)
                      +||||+-.++.-.-.+.+-.-...+++.++.+|||...+.+.+   ++...-.-+.+.
T Consensus       137 fDEAHRAvGnyAYv~Va~~y~~~~k~~~ilgLTASPGs~~ekI~eV~~nLgIe~vevr  194 (542)
T COG1111         137 FDEAHRAVGNYAYVFVAKEYLRSAKNPLILGLTASPGSDLEKIQEVVENLGIEKVEVR  194 (542)
T ss_pred             echhhhccCcchHHHHHHHHHHhccCceEEEEecCCCCCHHHHHHHHHhCCcceEEEe
Confidence            9999999876555566655555567899999999997765544   444333444444

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.45  E-value=4.4e-13  Score=115.69  Aligned_cols=103  Identities=16%  Similarity=0.177  Sum_probs=79.8

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||||||+||+.|+.+.++++... +...+..+.||....        .+++|+|+||+++.+...    ..+++++++
T Consensus       160 ~vLilvpt~eL~~Q~~~~l~~~~~~-~~~~~~~i~~g~~~~--------~~~~I~VaT~qsl~~~~~----~~~~~~~~i  226 (501)
T PHA02558        160 KVLIIVPTTSLVTQMIDDFVDYRLF-PREAMHKIYSGTAKD--------TDAPIVVSTWQSAVKQPK----EWFDQFGMV  226 (501)
T ss_pred             eEEEEECcHHHHHHHHHHHHHhccc-cccceeEEecCcccC--------CCCCEEEeeHHHHhhchh----hhccccCEE
Confidence            3799999999999999999998643 345555666665421        357999999999876432    246789999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChH
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~  120 (183)
                      |+||||++.+.    .+..++..+++.+|+++||||+.+.
T Consensus       227 IvDEaH~~~~~----~~~~il~~~~~~~~~lGLTATp~~~  262 (501)
T PHA02558        227 IVDECHLFTGK----SLTSIITKLDNCKFKFGLTGSLRDG  262 (501)
T ss_pred             EEEchhcccch----hHHHHHHhhhccceEEEEeccCCCc
Confidence            99999999754    4567777787789999999999754

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.42  E-value=5.9e-12  Score=111.01  Aligned_cols=128  Identities=18%  Similarity=0.163  Sum_probs=89.8

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||++|+++|+.|..+.+..+     ++.+..+.++...++...   .+..+..+++++||+++...... ..+...++
T Consensus        67 ~tlVisPl~sL~~dqv~~l~~~-----gi~~~~~~s~~~~~~~~~~~~~~~~g~~~il~~tPe~l~~~~~~-~~l~~~~l  140 (607)
T PRK11057         67 LTLVVSPLISLMKDQVDQLLAN-----GVAAACLNSTQTREQQLEVMAGCRTGQIKLLYIAPERLMMDNFL-EHLAHWNP  140 (607)
T ss_pred             CEEEEecHHHHHHHHHHHHHHc-----CCcEEEEcCCCCHHHHHHHHHHHhCCCCcEEEEChHHhcChHHH-HHHhhCCC
Confidence            3789999999999988877764     566777777666554433   33345689999999998742222 23445678


Q ss_pred             eEEEEcccchhhccc--hHHHHH---HHHHhCCCCCeEEEEeecCChHHHHHHHhh--CCCCeEE
Q 030094           78 EILVLDEADRLLDMG--FQKQIS---YIISRLPKLRRTGLFSATQTEAVEELSKAG--LRNPVRV  135 (183)
Q Consensus        78 ~~lVvDEad~ll~~~--~~~~l~---~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~--~~~~~~i  135 (183)
                      +++|+||||.+.++|  |.+.+.   .+.+.+ +..|++++|||.++.+..-+...  +.+|...
T Consensus       141 ~~iVIDEaH~i~~~G~~fr~~y~~L~~l~~~~-p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~  204 (607)
T PRK11057        141 ALLAVDEAHCISQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQ  204 (607)
T ss_pred             CEEEEeCccccccccCcccHHHHHHHHHHHhC-CCCcEEEEecCCChhHHHHHHHHhCCCCeEEE
Confidence            999999999998765  555443   344444 46899999999999876544333  4466543

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

Probab=99.41  E-value=8.9e-13  Score=112.20  Aligned_cols=152  Identities=20%  Similarity=0.208  Sum_probs=115.6

Q ss_pred             EEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceE
Q 030094            3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEI   79 (183)
Q Consensus         3 lIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~   79 (183)
                      |+|||--.||+|-|+.+++--+++ ++++..-+|-..++....   .-....+||||||-+.+.++++. + -++.++..
T Consensus       265 lfLvPLVALANQKy~dF~~rYs~L-glkvairVG~srIk~~~~pv~~~t~~dADIIVGTYEGiD~lLRt-g-~~lgdiGt  341 (830)
T COG1202         265 LFLVPLVALANQKYEDFKERYSKL-GLKVAIRVGMSRIKTREEPVVVDTSPDADIIVGTYEGIDYLLRT-G-KDLGDIGT  341 (830)
T ss_pred             EEEehhHHhhcchHHHHHHHhhcc-cceEEEEechhhhcccCCccccCCCCCCcEEEeechhHHHHHHc-C-Ccccccce
Confidence            789999999999999998876777 889988888776654432   11234689999999999999986 4 78999999


Q ss_pred             EEEcccchhhccchHHHHHHHH---HhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccC
Q 030094           80 LVLDEADRLLDMGFQKQISYII---SRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASS  156 (183)
Q Consensus        80 lVvDEad~ll~~~~~~~l~~i~---~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~  156 (183)
                      +|+||+|.+-+..-++.+..++   +.+-+..|.+.+|||..+. +++++.+-.+++..                    .
T Consensus       342 VVIDEiHtL~deERG~RLdGLI~RLr~l~~~AQ~i~LSATVgNp-~elA~~l~a~lV~y--------------------~  400 (830)
T COG1202         342 VVIDEIHTLEDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGNP-EELAKKLGAKLVLY--------------------D  400 (830)
T ss_pred             EEeeeeeeccchhcccchhhHHHHHHHhCCCCeEEEEEeecCCh-HHHHHHhCCeeEee--------------------c
Confidence            9999999987644344444443   3344689999999999988 88898876666554                    2


Q ss_pred             CCccCceEEEEEec-Ccchhhhh
Q 030094          157 KTPLGLHLEVIWNV-NQMRNHHN  178 (183)
Q Consensus       157 ~~~~~l~q~~i~~~-~~~k~~~l  178 (183)
                      ..|..++.+.++|. +.+|.+..
T Consensus       401 ~RPVplErHlvf~~~e~eK~~ii  423 (830)
T COG1202         401 ERPVPLERHLVFARNESEKWDII  423 (830)
T ss_pred             CCCCChhHeeeeecCchHHHHHH
Confidence            34778888888887 44455443

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.41  E-value=7.5e-12  Score=110.09  Aligned_cols=123  Identities=20%  Similarity=0.238  Sum_probs=91.1

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .++|++|+++|+.|..+.++.+     ++.+..+.++.+..+...   .+..+.++|+++||+++...... ..+...++
T Consensus        55 ~~lVisPl~sL~~dq~~~l~~~-----gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~-~~l~~~~l  128 (591)
T TIGR01389        55 LTVVISPLISLMKDQVDQLRAA-----GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFL-NMLQRIPI  128 (591)
T ss_pred             cEEEEcCCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHH-HHHhcCCC
Confidence            3789999999999988877765     567777777766554433   33446789999999998754433 34567789


Q ss_pred             eEEEEcccchhhccc--hHHHHHH---HHHhCCCCCeEEEEeecCChHHHHHHHhhCC
Q 030094           78 EILVLDEADRLLDMG--FQKQISY---IISRLPKLRRTGLFSATQTEAVEELSKAGLR  130 (183)
Q Consensus        78 ~~lVvDEad~ll~~~--~~~~l~~---i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~  130 (183)
                      +++|+||||.+.++|  |.+....   +...+|. .+++++|||.++.+..-+..++.
T Consensus       129 ~~iViDEaH~i~~~g~~frp~y~~l~~l~~~~~~-~~vi~lTAT~~~~~~~~i~~~l~  185 (591)
T TIGR01389       129 ALVAVDEAHCVSQWGHDFRPEYQRLGSLAERFPQ-VPRIALTATADAETRQDIRELLR  185 (591)
T ss_pred             CEEEEeCCcccccccCccHHHHHHHHHHHHhCCC-CCEEEEEeCCCHHHHHHHHHHcC
Confidence            999999999998765  5555444   4455554 45999999999998876666654

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.

>PRK13766 Hef nuclease; Provisional

Probab=99.36  E-value=1.5e-11  Score=111.19  Aligned_cols=123  Identities=20%  Similarity=0.249  Sum_probs=92.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +|||+||++|+.|..+.++++... ++.++..+.|+.+..+....+  .+++|+|+||+.+...+.. +.+++.++.++|
T Consensus        61 vLvl~Pt~~L~~Q~~~~~~~~~~~-~~~~v~~~~g~~~~~~r~~~~--~~~~iiv~T~~~l~~~l~~-~~~~~~~~~liV  136 (773)
T PRK13766         61 VLILAPTKPLVEQHAEFFRKFLNI-PEEKIVVFTGEVSPEKRAELW--EKAKVIVATPQVIENDLIA-GRISLEDVSLLI  136 (773)
T ss_pred             EEEEeCcHHHHHHHHHHHHHHhCC-CCceEEEEeCCCCHHHHHHHH--hCCCEEEECHHHHHHHHHc-CCCChhhCcEEE
Confidence            799999999999999999987643 345777788877655443333  4689999999999888776 778899999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChH---HHHHHHhh
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA---VEELSKAG  128 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~---v~~~~~~~  128 (183)
                      +||||++.+......+........+.++++++|||....   +..+++..
T Consensus       137 vDEaH~~~~~~~~~~i~~~~~~~~~~~~il~lTaTP~~~~~~i~~~~~~L  186 (773)
T PRK13766        137 FDEAHRAVGNYAYVYIAERYHEDAKNPLVLGLTASPGSDEEKIKEVCENL  186 (773)
T ss_pred             EECCccccccccHHHHHHHHHhcCCCCEEEEEEcCCCCCHHHHHHHHHhC
Confidence            999999876544445555555555678899999997543   33444443

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.34  E-value=5.9e-12  Score=112.98  Aligned_cols=85  Identities=18%  Similarity=0.280  Sum_probs=73.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhcCCcCC-----
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMDVLDF-----   74 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~~~~~l-----   74 (183)
                      .++|++||++||.|.++.+..+..++ ++++.+++||.+..++...+   +|||++|||++| .++++.+-.+++     
T Consensus       125 ~V~VvTpn~yLA~qd~e~m~~l~~~l-GLtv~~i~gg~~~~~r~~~y---~~dIvygT~grlgfDyLrd~~~~~~~~~v~  200 (896)
T PRK13104        125 GVHIVTVNDYLAKRDSQWMKPIYEFL-GLTVGVIYPDMSHKEKQEAY---KADIVYGTNNEYGFDYLRDNMAFSLTDKVQ  200 (896)
T ss_pred             CEEEEcCCHHHHHHHHHHHHHHhccc-CceEEEEeCCCCHHHHHHHh---CCCEEEECChhhhHHHHhcCCccchHhhhc
Confidence            37899999999999999999999888 89999999998876664443   699999999999 999987324555     


Q ss_pred             CCceEEEEcccchhh
Q 030094           75 RNLEILVLDEADRLL   89 (183)
Q Consensus        75 ~~l~~lVvDEad~ll   89 (183)
                      +.+.++|+||||.+|
T Consensus       201 r~l~~~IvDEaDsiL  215 (896)
T PRK13104        201 RELNFAIVDEVDSIL  215 (896)
T ss_pred             cccceEEeccHhhhh
Confidence            689999999999997

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.34  E-value=9.2e-11  Score=97.33  Aligned_cols=134  Identities=13%  Similarity=0.091  Sum_probs=89.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhC---CCceEEEEEcCcchH--HH-----------------HHHHHhcCCcEEEeCc
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTL---PDVKSVLLVGGVEVK--AD-----------------VKKIEEEGANLLIGTP   59 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~---~~~~~~~~~g~~~~~--~~-----------------~~~l~~~~~~IiV~TP   59 (183)
                      +++++|+++|+.|.++.++++...+   .+..+..+.|....+  ..                 .+......|+|+++||
T Consensus        42 ~~~~~P~~aL~~~~~~~~~~~~~~~~~~~~~~v~~~~g~~~~d~~~~~~~~~~~~~g~~~~~~~r~~~~~~~p~illT~p  121 (357)
T TIGR03158        42 TIALYPTNALIEDQTEAIKEFVDVFKPERDVNLLHVSKATLKDIKEYANDKVGSSKGEKLYNLLRNPIGTSTPIILLTNP  121 (357)
T ss_pred             EEEEeChHHHHHHHHHHHHHHHHhcCCCCCceEEEecCCchHHHHHhhhhhcccCccchhhhhHHHHHhcCCCCEEEecH
Confidence            6899999999999999999987543   245555555541111  00                 1112234799999999


Q ss_pred             HHHHHHHHhc---CCc----CCCCceEEEEcccchhhccc-----hHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHh
Q 030094           60 GRLYDIMERM---DVL----DFRNLEILVLDEADRLLDMG-----FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (183)
Q Consensus        60 ~~l~~~l~~~---~~~----~l~~l~~lVvDEad~ll~~~-----~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~  127 (183)
                      +.+..+++..   ...    .+.+++++|+||+|.+-..+     +......+++..+...+++++|||+++.+......
T Consensus       122 ~~l~~llr~~~~~~~~~~~~~~~~~~~iV~DE~H~~~~~~~~~~~~~l~~~~~~~~~~~~~~~i~lSAT~~~~~~~~l~~  201 (357)
T TIGR03158       122 DIFVYLTRFAYIDRGDIAAGFYTKFSTVIFDEFHLYDAKQLVGMLFLLAYMQLIRFFECRRKFVFLSATPDPALILRLQN  201 (357)
T ss_pred             HHHHHHHhhhccCcccchhhhhcCCCEEEEecccccCcccchhhhhhhHHHHHHHhhhcCCcEEEEecCCCHHHHHHHHh
Confidence            9998776531   111    25789999999999975322     12234445555555689999999999998888776


Q ss_pred             h--CCCCeEE
Q 030094          128 G--LRNPVRV  135 (183)
Q Consensus       128 ~--~~~~~~i  135 (183)
                      .  +.+|..+
T Consensus       202 ~~~~~~~~~~  211 (357)
T TIGR03158       202 AKQAGVKIAP  211 (357)
T ss_pred             ccccCceeee
Confidence            5  5555433

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.

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=99.33  E-value=5.4e-12  Score=104.36  Aligned_cols=125  Identities=15%  Similarity=0.074  Sum_probs=82.9

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcch------------HHHHHHHHh-----cCCcEEEeCcHHHHH
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEV------------KADVKKIEE-----EGANLLIGTPGRLYD   64 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~------------~~~~~~l~~-----~~~~IiV~TP~~l~~   64 (183)
                      +++++|+++|+.|+++.+..+.+.    .+....|+...            .........     ..++|+|+||+.+..
T Consensus        32 ii~v~P~~~L~~q~~~~l~~~f~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~T~~~l~~  107 (358)
T TIGR01587        32 VIIALPTRATINAMYRRAKELFGS----NLGLLHSSSSFKRIKEMGDSEEFEHLFPLYIHSNDKLFLDPITVCTIDQVLK  107 (358)
T ss_pred             EEEEeehHHHHHHHHHHHHHHhCc----ccEEeeccHHHHHHhccCCchhHHHHHHHHhhchhhhhhCCeeeCCHHHHHH
Confidence            789999999999999999997532    23333333221            011001101     236899999999988


Q ss_pred             HHHhc-CC--cCCC--CceEEEEcccchhhccchHHHHHHHHHhCC-CCCeEEEEeecCChHHHHHHHhhCCC
Q 030094           65 IMERM-DV--LDFR--NLEILVLDEADRLLDMGFQKQISYIISRLP-KLRRTGLFSATQTEAVEELSKAGLRN  131 (183)
Q Consensus        65 ~l~~~-~~--~~l~--~l~~lVvDEad~ll~~~~~~~l~~i~~~l~-~~~Q~v~~SAT~~~~v~~~~~~~~~~  131 (183)
                      .+... +.  ..+.  ..+++|+||+|.+.+.++.. +..+++.++ .+.|++++|||+++.+.+++..+...
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~-l~~~l~~l~~~~~~~i~~SATlp~~l~~~~~~~~~~  179 (358)
T TIGR01587       108 SVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLAL-ILAVLEVLKDNDVPILLMSATLPKFLKEYAEKIGYV  179 (358)
T ss_pred             HHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHH-HHHHHHHHHHcCCCEEEEecCchHHHHHHHhcCCCc
Confidence            76541 11  1111  23789999999998764433 666666554 47899999999998888888766543

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.

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

Probab=99.33  E-value=9e-12  Score=111.25  Aligned_cols=131  Identities=19%  Similarity=0.216  Sum_probs=104.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCc--CCCCce
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL--DFRNLE   78 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~--~l~~l~   78 (183)
                      .||++.|-|+|++.+..-+......+ ++.+..-.|..+..+..+.. +++|||+|+||+.|.-++.. +.+  .+++++
T Consensus        75 ~~lYIsPLkALn~Di~~rL~~~~~~~-G~~v~vRhGDT~~~er~r~~-~~PPdILiTTPEsL~lll~~-~~~r~~l~~vr  151 (814)
T COG1201          75 YALYISPLKALNNDIRRRLEEPLREL-GIEVAVRHGDTPQSEKQKML-KNPPHILITTPESLAILLNS-PKFRELLRDVR  151 (814)
T ss_pred             EEEEeCcHHHHHHHHHHHHHHHHHHc-CCccceecCCCChHHhhhcc-CCCCcEEEeChhHHHHHhcC-HHHHHHhcCCc
Confidence            38999999999999999999999887 89998888877766666565 67999999999999999876 444  489999


Q ss_pred             EEEEcccchhhccchHHH----HHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCC--CeEEE
Q 030094           79 ILVLDEADRLLDMGFQKQ----ISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRN--PVRVE  136 (183)
Q Consensus        79 ~lVvDEad~ll~~~~~~~----l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~--~~~i~  136 (183)
                      ++|+||.|.+.+..-+.+    ++++.+..+ +.|.+..|||..+. ...+++....  +..|.
T Consensus       152 ~VIVDEiHel~~sKRG~~Lsl~LeRL~~l~~-~~qRIGLSATV~~~-~~varfL~g~~~~~~Iv  213 (814)
T COG1201         152 YVIVDEIHALAESKRGVQLALSLERLRELAG-DFQRIGLSATVGPP-EEVAKFLVGFGDPCEIV  213 (814)
T ss_pred             EEEeehhhhhhccccchhhhhhHHHHHhhCc-ccEEEeehhccCCH-HHHHHHhcCCCCceEEE
Confidence            999999999987643433    444444445 89999999999965 7777776665  44443

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.32  E-value=5.5e-12  Score=111.57  Aligned_cols=86  Identities=15%  Similarity=0.178  Sum_probs=73.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhcC-----CcCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMD-----VLDF   74 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~~-----~~~l   74 (183)
                      ++.|++||++||.|.++.+..+.+++ ++++.++.|+.+..++...   ..+||++|||++| .++++.+-     .+.+
T Consensus        99 ~V~VvTpt~~LA~qdae~~~~l~~~L-GLsv~~i~g~~~~~~r~~~---y~~dIvyGT~~rlgfDyLrd~~~~~~~~~~~  174 (745)
T TIGR00963        99 GVHVVTVNDYLAQRDAEWMGQVYRFL-GLSVGLILSGMSPEERREA---YACDITYGTNNELGFDYLRDNMAHSKEEKVQ  174 (745)
T ss_pred             CEEEEcCCHHHHHHHHHHHHHHhccC-CCeEEEEeCCCCHHHHHHh---cCCCEEEECCCchhhHHHhcccccchhhhhc
Confidence            47899999999999999999999988 8999999999886554433   3689999999999 88887621     3568


Q ss_pred             CCceEEEEcccchhhc
Q 030094           75 RNLEILVLDEADRLLD   90 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~   90 (183)
                      +.+.++|+||+|.++-
T Consensus       175 r~l~~aIIDEaDs~LI  190 (745)
T TIGR00963       175 RPFHFAIIDEVDSILI  190 (745)
T ss_pred             cccceeEeecHHHHhH
Confidence            9999999999999974

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.

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.32  E-value=8.1e-11  Score=83.00  Aligned_cols=112  Identities=38%  Similarity=0.609  Sum_probs=84.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      ++|++|++.++.|..+.+......  +..+..+.++.......... ..+.+|+++|++.+...+.. .........++|
T Consensus        33 ~lv~~p~~~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-~~~~~i~i~t~~~~~~~~~~-~~~~~~~~~~ii  108 (144)
T cd00046          33 VLVLAPTRELANQVAERLKELFGE--GIKVGYLIGGTSIKQQEKLL-SGKTDIVVGTPGRLLDELER-LKLSLKKLDLLI  108 (144)
T ss_pred             EEEEcCcHHHHHHHHHHHHHHhhC--CcEEEEEecCcchhHHHHHh-cCCCCEEEECcHHHHHHHHc-CCcchhcCCEEE
Confidence            689999999999999988887643  56777777766655544333 46899999999999988876 444566788999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ  117 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~  117 (183)
                      +||+|.+....+...............+++++|||+
T Consensus       109 iDE~h~~~~~~~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046         109 LDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             EeCHHHHhhcchHHHHHHHHhhCCccceEEEEeccC
Confidence            999999976544433223344456788999999995

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

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.26  E-value=5e-11  Score=110.87  Aligned_cols=115  Identities=20%  Similarity=0.255  Sum_probs=78.9

Q ss_pred             cHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccc-
Q 030094            8 TRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEAD-   86 (183)
Q Consensus         8 treLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad-   86 (183)
                      ++++|.||.+.+..-.+..-+.++    .   .+.+.    ..+++|+++|||+|++.+.. + ..+++++++|+|||| 
T Consensus       131 ArsLA~RVA~El~~~lG~~VGY~v----r---f~~~~----s~~t~I~v~TpG~LL~~l~~-d-~~Ls~~~~IIIDEAHE  197 (1294)
T PRK11131        131 ARTVANRIAEELETELGGCVGYKV----R---FNDQV----SDNTMVKLMTDGILLAEIQQ-D-RLLMQYDTIIIDEAHE  197 (1294)
T ss_pred             HHHHHHHHHHHHhhhhcceeceee----c---Ccccc----CCCCCEEEEChHHHHHHHhc-C-CccccCcEEEecCccc
Confidence            679999999888753222112221    1   11111    35789999999999999976 4 448999999999999 


Q ss_pred             hhhccchHH-HHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEcc
Q 030094           87 RLLDMGFQK-QISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRA  139 (183)
Q Consensus        87 ~ll~~~~~~-~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~  139 (183)
                      ++++.+|.. .+..++... ++.|+++||||++.  +.+.+.|.+.|+ |.+..
T Consensus       198 RsLn~DfLLg~Lk~lL~~r-pdlKvILmSATid~--e~fs~~F~~apv-I~V~G  247 (1294)
T PRK11131        198 RSLNIDFILGYLKELLPRR-PDLKVIITSATIDP--ERFSRHFNNAPI-IEVSG  247 (1294)
T ss_pred             cccccchHHHHHHHhhhcC-CCceEEEeeCCCCH--HHHHHHcCCCCE-EEEcC
Confidence            588887764 344444332 46899999999975  467777666663 55543

>PF06862 DUF1253: Protein of unknown function (DUF1253); InterPro: IPR010678 This family is defined by a C-terminal region of approximately 500 residues, Digestive organ expansion factor (DEF) is thought to Regulate the p53 pathway to control the expansion growth of digestive organs and is required for the expansion growth of intestine, liver and exocrine pancreas, but not endocrine pancreas [, ]

Probab=99.26  E-value=2.1e-10  Score=96.56  Aligned_cols=160  Identities=19%  Similarity=0.216  Sum_probs=110.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCc----eEEEEEc--------------CcchHHHHHHHHhc-------------
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDV----KSVLLVG--------------GVEVKADVKKIEEE-------------   50 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~----~~~~~~g--------------~~~~~~~~~~l~~~-------------   50 (183)
                      +|||+|+|.-|.++.+.+.++......+    +-..-+|              +....++...+..+             
T Consensus        40 VLIL~P~R~~A~~~V~~Li~l~~~~~~~~nk~RF~~efg~~~~~~~~~~~~~~~~~kP~D~~~~F~GN~DD~FrlGik~t  119 (442)
T PF06862_consen   40 VLILLPFRNSALRIVETLISLLPPGKQVENKKRFEEEFGLPEDEDDDEEPPEFKKSKPEDFKALFSGNNDDCFRLGIKFT  119 (442)
T ss_pred             EEEEcccHHHHHHHHHHHHHHcCccchHHHHHHHHHHcCCCccccchhhhccccCCCchhHHHhcCCCccceEEEeEEEe
Confidence            6999999999999999888886431000    0000001              11122222222222             


Q ss_pred             -----------CCcEEEeCcHHHHHHHHh----cCCcC-CCCceEEEEcccchhhccchHHHHHHHHHhCCC--------
Q 030094           51 -----------GANLLIGTPGRLYDIMER----MDVLD-FRNLEILVLDEADRLLDMGFQKQISYIISRLPK--------  106 (183)
Q Consensus        51 -----------~~~IiV~TP~~l~~~l~~----~~~~~-l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~--------  106 (183)
                                 +.|||||+|-.|...+..    ....| +++++++|+|.||.|+-+ .++++..+++.++.        
T Consensus       120 rk~ikLys~Fy~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQ-NW~Hv~~v~~~lN~~P~~~~~~  198 (442)
T PF06862_consen  120 RKSIKLYSDFYSSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQ-NWEHVLHVFEHLNLQPKKSHDT  198 (442)
T ss_pred             cCeeeeecccccCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHh-hHHHHHHHHHHhccCCCCCCCC
Confidence                       489999999999999984    12344 899999999999999855 58888888888742        


Q ss_pred             ----------------CCeEEEEeecCChHHHHHHHhhCCCCe-EEEEccCCcccccccchhhcccCCCccCceEEEEEe
Q 030094          107 ----------------LRRTGLFSATQTEAVEELSKAGLRNPV-RVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWN  169 (183)
Q Consensus       107 ----------------~~Q~v~~SAT~~~~v~~~~~~~~~~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~~~l~q~~i~~  169 (183)
                                      -||++++|+..++++..+.+.++.|.. .+.+......        .+........++|.|...
T Consensus       199 DfsRVR~w~Ldg~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~--------~g~i~~v~~~v~Q~F~r~  270 (442)
T PF06862_consen  199 DFSRVRPWYLDGQAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEA--------SGVISQVVVQVRQVFQRF  270 (442)
T ss_pred             CHHHHHHHHHcCcchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeecccc--------ceeeeccccCCceEEEEe
Confidence                            159999999999999999999888775 4444433210        122356777899999875


Q ss_pred             c
Q 030094          170 V  170 (183)
Q Consensus       170 ~  170 (183)
                      +
T Consensus       271 ~  271 (442)
T PF06862_consen  271 D  271 (442)
T ss_pred             c
Confidence            5

; GO: 0005634 nucleus

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.23  E-value=1.7e-10  Score=102.81  Aligned_cols=112  Identities=17%  Similarity=0.261  Sum_probs=80.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHH---HHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~---l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      ++||++||++|+.|+++.+++..    +.++..+.|+.+..++...   +..+.++|+||||+.+.        ..++++
T Consensus       192 ~vLvLvPt~~L~~Q~~~~l~~~f----g~~v~~~~s~~s~~~r~~~~~~~~~g~~~IVVgTrsal~--------~p~~~l  259 (679)
T PRK05580        192 QALVLVPEIALTPQMLARFRARF----GAPVAVLHSGLSDGERLDEWRKAKRGEAKVVIGARSALF--------LPFKNL  259 (679)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHHh----CCCEEEEECCCCHHHHHHHHHHHHcCCCCEEEeccHHhc--------ccccCC
Confidence            48999999999999999887643    5678889988776555432   33457899999997653        346789


Q ss_pred             eEEEEcccchhhccc-----h-HHHHHHHHHhCCCCCeEEEEeecCChHHHHHH
Q 030094           78 EILVLDEADRLLDMG-----F-QKQISYIISRLPKLRRTGLFSATQTEAVEELS  125 (183)
Q Consensus        78 ~~lVvDEad~ll~~~-----~-~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~  125 (183)
                      +++|+||+|...-.+     | ..++. +.+....+.|++++|||.+.+....+
T Consensus       260 ~liVvDEeh~~s~~~~~~p~y~~r~va-~~ra~~~~~~~il~SATps~~s~~~~  312 (679)
T PRK05580        260 GLIIVDEEHDSSYKQQEGPRYHARDLA-VVRAKLENIPVVLGSATPSLESLANA  312 (679)
T ss_pred             CEEEEECCCccccccCcCCCCcHHHHH-HHHhhccCCCEEEEcCCCCHHHHHHH
Confidence            999999999753211     1 12332 23344578999999999887655543

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.20  E-value=1.9e-10  Score=101.09  Aligned_cols=85  Identities=21%  Similarity=0.275  Sum_probs=66.8

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhcC---------
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMD---------   70 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~~---------   70 (183)
                      +++|++||++||.|.++.+..+..++ ++++.+++||.+..  .+.. ..++||++||...+ .++++.+=         
T Consensus       146 ~v~VvTptreLA~qdae~~~~l~~~l-Glsv~~i~gg~~~~--~r~~-~y~~dIvygT~~e~~FDyLrd~~~~~~~~~~~  221 (656)
T PRK12898        146 PVHVITVNDYLAERDAELMRPLYEAL-GLTVGCVVEDQSPD--ERRA-AYGADITYCTNKELVFDYLRDRLALGQRASDA  221 (656)
T ss_pred             eEEEEcCcHHHHHHHHHHHHHHHhhc-CCEEEEEeCCCCHH--HHHH-HcCCCEEEECCCchhhhhccccccccccccch
Confidence            48999999999999999999999888 99999999997643  3333 35899999999988 44554310         


Q ss_pred             ---------------CcCCCCceEEEEcccchhh
Q 030094           71 ---------------VLDFRNLEILVLDEADRLL   89 (183)
Q Consensus        71 ---------------~~~l~~l~~lVvDEad~ll   89 (183)
                                     ..-.+.+.+.|+||+|.++
T Consensus       222 ~~~~~~l~~~~~~~~~~v~r~~~~aIvDEvDSiL  255 (656)
T PRK12898        222 RLALESLHGRSSRSTQLLLRGLHFAIVDEADSVL  255 (656)
T ss_pred             hhhhhhhccccCchhhhcccccceeEeeccccee
Confidence                           0113567899999999986

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.19  E-value=8.2e-11  Score=105.34  Aligned_cols=86  Identities=19%  Similarity=0.196  Sum_probs=70.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhc-----CCcCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERM-----DVLDF   74 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~-----~~~~l   74 (183)
                      +++|++||++||.|.++.+..+..++ ++++.++.|+.+..++.+..  .+|||++|||+++ .+++..+     ....+
T Consensus       121 ~v~VvTpt~~LA~qd~e~~~~l~~~l-Gl~v~~i~g~~~~~~~r~~~--y~~dIvygT~~~l~fDyLrd~~~~~~~~~~~  197 (790)
T PRK09200        121 GVHLITVNDYLAKRDAEEMGQVYEFL-GLTVGLNFSDIDDASEKKAI--YEADIIYTTNSELGFDYLRDNLADSKEDKVQ  197 (790)
T ss_pred             CeEEEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCcHHHHHHh--cCCCEEEECCccccchhHHhccccchhhhcc
Confidence            47899999999999999999999988 99999999998844444433  4799999999999 4555431     12346


Q ss_pred             CCceEEEEcccchhh
Q 030094           75 RNLEILVLDEADRLL   89 (183)
Q Consensus        75 ~~l~~lVvDEad~ll   89 (183)
                      +.+.++|+||||.++
T Consensus       198 r~~~~~IvDEaDsiL  212 (790)
T PRK09200        198 RPLNYAIIDEIDSIL  212 (790)
T ss_pred             cccceEEEeccccce
Confidence            889999999999987

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.14  E-value=2.2e-10  Score=102.05  Aligned_cols=86  Identities=19%  Similarity=0.225  Sum_probs=67.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcc---hHHHHHHHHhcCCcEEEeCcHHH-HHHHHh-----cCCc
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVE---VKADVKKIEEEGANLLIGTPGRL-YDIMER-----MDVL   72 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~---~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~-----~~~~   72 (183)
                      ++|++||++||.|.++.+..+.+++ ++++..++++..   ...+.+.. ..+|||++|||+++ .+++..     ....
T Consensus       114 V~VVTpn~yLA~Rdae~m~~l~~~L-GLsv~~~~~~s~~~~~~~~~rr~-~y~~dIvygTp~~LgfDyLrD~l~~~~~~~  191 (762)
T TIGR03714       114 AMLVTTNDYLAKRDAEEMGPVYEWL-GLTVSLGVVDDPDEEYDANEKRK-IYNSDIVYTTNSALGFDYLIDNLASNKEGK  191 (762)
T ss_pred             eEEeCCCHHHHHHHHHHHHHHHhhc-CCcEEEEECCCCccccCHHHHHH-hCCCCEEEECchhhhhhHHHHHhhcchhhc
Confidence            7899999999999999999999888 899988877632   33333333 25899999999999 555532     1234


Q ss_pred             CCCCceEEEEcccchhh
Q 030094           73 DFRNLEILVLDEADRLL   89 (183)
Q Consensus        73 ~l~~l~~lVvDEad~ll   89 (183)
                      .++.+.++|+||||.||
T Consensus       192 ~~r~l~~~IVDEaDsIL  208 (762)
T TIGR03714       192 FLRPFNYVIVDEVDSVL  208 (762)
T ss_pred             ccccCcEEEEecHhhHh
Confidence            57889999999999996

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.

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

Probab=99.11  E-value=1.3e-09  Score=94.89  Aligned_cols=114  Identities=19%  Similarity=0.386  Sum_probs=91.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcch---HHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEV---KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~---~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      ||..++||.-||.|.++.+.++...+ ++++..++|....   ++....+.++..||+|||.    .++.  ....++++
T Consensus       313 Q~ALMAPTEILA~QH~~~~~~~l~~~-~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTH----ALiQ--d~V~F~~L  385 (677)
T COG1200         313 QAALMAPTEILAEQHYESLRKWLEPL-GIRVALLTGSLKGKARKEILEQLASGEIDIVVGTH----ALIQ--DKVEFHNL  385 (677)
T ss_pred             eeEEeccHHHHHHHHHHHHHHHhhhc-CCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcc----hhhh--cceeecce
Confidence            68899999999999999999999887 8999999997654   4445566667799999997    4554  57889999


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCC-CCeEEEEeecCChHHHHHHH
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPK-LRRTGLFSATQTEAVEELSK  126 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~-~~Q~v~~SAT~~~~v~~~~~  126 (183)
                      .++|+||-|++     +-+=+..++..+. .+..++||||.-|....+.-
T Consensus       386 gLVIiDEQHRF-----GV~QR~~L~~KG~~~Ph~LvMTATPIPRTLAlt~  430 (677)
T COG1200         386 GLVIIDEQHRF-----GVHQRLALREKGEQNPHVLVMTATPIPRTLALTA  430 (677)
T ss_pred             eEEEEeccccc-----cHHHHHHHHHhCCCCCcEEEEeCCCchHHHHHHH
Confidence            99999999994     4444555666666 68999999998777555544

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

Probab=99.08  E-value=8.7e-10  Score=99.26  Aligned_cols=148  Identities=18%  Similarity=0.231  Sum_probs=107.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCC---cCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDV---LDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~---~~l~~l~   78 (183)
                      .++++|+++||..+++-+.+-.... +++|..++|........  +  ..++|||+||++..-.-++ ..   -.++.++
T Consensus       167 iVYIaPmKALa~Em~~~~~kkl~~~-gi~v~ELTGD~ql~~te--i--~~tqiiVTTPEKwDvvTRk-~~~d~~l~~~V~  240 (1230)
T KOG0952|consen  167 IVYIAPMKALAAEMVDKFSKKLAPL-GISVRELTGDTQLTKTE--I--ADTQIIVTTPEKWDVVTRK-SVGDSALFSLVR  240 (1230)
T ss_pred             EEEEechHHHHHHHHHHHhhhcccc-cceEEEecCcchhhHHH--H--HhcCEEEecccceeeeeee-eccchhhhhhee
Confidence            4789999999998877665544444 89999999988765443  3  2589999999985433222 21   2368899


Q ss_pred             EEEEcccchhhccchHHHHHHHHHhCC-------CCCeEEEEeecCChHHHHHHHhhCCCC-eEEEEccCCcccccccch
Q 030094           79 ILVLDEADRLLDMGFQKQISYIISRLP-------KLRRTGLFSATQTEAVEELSKAGLRNP-VRVEVRAESKSHHVSASS  150 (183)
Q Consensus        79 ~lVvDEad~ll~~~~~~~l~~i~~~l~-------~~~Q~v~~SAT~~~~v~~~~~~~~~~~-~~i~~~~~~~~~~~~~~~  150 (183)
                      ++|+||+|.|-+ .-+.-++.|+.+..       ..-+++.+|||+|+= +.++.+.--|| .-+..-+.          
T Consensus       241 LviIDEVHlLhd-~RGpvlEtiVaRtlr~vessqs~IRivgLSATlPN~-eDvA~fL~vn~~~glfsFd~----------  308 (1230)
T KOG0952|consen  241 LVIIDEVHLLHD-DRGPVLETIVARTLRLVESSQSMIRIVGLSATLPNY-EDVARFLRVNPYAGLFSFDQ----------  308 (1230)
T ss_pred             eEEeeeehhhcC-cccchHHHHHHHHHHHHHhhhhheEEEEeeccCCCH-HHHHHHhcCCCccceeeecc----------
Confidence            999999998754 45777777776653       345799999999976 67776654453 44554455          


Q ss_pred             hhcccCCCccCceEEEEEecCc
Q 030094          151 QQLASSKTPLGLHLEVIWNVNQ  172 (183)
Q Consensus       151 ~~~~~~~~~~~l~q~~i~~~~~  172 (183)
                           ...|..+.|.++.+...
T Consensus       309 -----~yRPvpL~~~~iG~k~~  325 (1230)
T KOG0952|consen  309 -----RYRPVPLTQGFIGIKGK  325 (1230)
T ss_pred             -----cccccceeeeEEeeecc
Confidence                 67788899999888766

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.06  E-value=7e-10  Score=99.49  Aligned_cols=84  Identities=18%  Similarity=0.274  Sum_probs=72.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhcCC-----cCCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMDV-----LDFR   75 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~~~-----~~l~   75 (183)
                      +-|++||++||.|.++.+..+..++ ++++.++.|+.+..++...+   .+||++|||+++ .++++.+-.     ...+
T Consensus       125 V~IvTpn~yLA~rd~e~~~~l~~~L-Glsv~~i~~~~~~~er~~~y---~~dI~ygT~~elgfDyLrd~~~~~~~~~~~r  200 (830)
T PRK12904        125 VHVVTVNDYLAKRDAEWMGPLYEFL-GLSVGVILSGMSPEERREAY---AADITYGTNNEFGFDYLRDNMVFSLEERVQR  200 (830)
T ss_pred             EEEEecCHHHHHHHHHHHHHHHhhc-CCeEEEEcCCCCHHHHHHhc---CCCeEEECCcchhhhhhhcccccchhhhccc
Confidence            5689999999999999999999888 99999999998877766554   599999999999 889876222     2368


Q ss_pred             CceEEEEcccchhh
Q 030094           76 NLEILVLDEADRLL   89 (183)
Q Consensus        76 ~l~~lVvDEad~ll   89 (183)
                      .+.++|+||||.+|
T Consensus       201 ~~~~aIvDEaDsiL  214 (830)
T PRK12904        201 GLNYAIVDEVDSIL  214 (830)
T ss_pred             ccceEEEechhhhe
Confidence            89999999999987

>TIGR00595 priA primosomal protein N'

Probab=99.03  E-value=5.7e-09  Score=90.28  Aligned_cols=112  Identities=19%  Similarity=0.234  Sum_probs=77.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      ++||++|+++|+.|+++.+++..    +.++..+.|+.+..+..+   .+..+.++|+|||+..+.        ..++++
T Consensus        27 ~vLvlvP~i~L~~Q~~~~l~~~f----~~~v~vlhs~~~~~er~~~~~~~~~g~~~IVVGTrsalf--------~p~~~l   94 (505)
T TIGR00595        27 SVLVLVPEIALTPQMIQRFKYRF----GSQVAVLHSGLSDSEKLQAWRKVKNGEILVVIGTRSALF--------LPFKNL   94 (505)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHHh----CCcEEEEECCCCHHHHHHHHHHHHcCCCCEEECChHHHc--------CcccCC
Confidence            48999999999999999887643    456777888776554433   333456899999997653        236788


Q ss_pred             eEEEEcccchhhcc---c---hHHHHHHHHHhCCCCCeEEEEeecCChHHHHHH
Q 030094           78 EILVLDEADRLLDM---G---FQKQISYIISRLPKLRRTGLFSATQTEAVEELS  125 (183)
Q Consensus        78 ~~lVvDEad~ll~~---~---~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~  125 (183)
                      +++|+||+|...-.   +   ...++..... ...+.+++++|||.+.+....+
T Consensus        95 ~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra-~~~~~~vil~SATPsles~~~~  147 (505)
T TIGR00595        95 GLIIVDEEHDSSYKQEEGPRYHARDVAVYRA-KKFNCPVVLGSATPSLESYHNA  147 (505)
T ss_pred             CEEEEECCCccccccccCCCCcHHHHHHHHH-HhcCCCEEEEeCCCCHHHHHHH
Confidence            99999999986421   1   1223333333 3368899999999876655443

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).

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

Probab=98.97  E-value=6.8e-09  Score=94.69  Aligned_cols=140  Identities=26%  Similarity=0.263  Sum_probs=107.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +++..|.++|..|.|..+....... .-.+.+++|..++        +.++.++|-|-+-|.+++.+ +...+..+.++|
T Consensus       165 viYTsPIKALsNQKyrdl~~~fgdv-~~~vGL~TGDv~I--------N~~A~clvMTTEILRnMlyr-g~~~~~~i~~Vi  234 (1041)
T COG4581         165 VIYTSPIKALSNQKYRDLLAKFGDV-ADMVGLMTGDVSI--------NPDAPCLVMTTEILRNMLYR-GSESLRDIEWVV  234 (1041)
T ss_pred             eEeccchhhhhhhHHHHHHHHhhhh-hhhccceecceee--------CCCCceEEeeHHHHHHHhcc-CcccccccceEE
Confidence            5788999999999999888764422 2235667776654        45678999999999999988 778899999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCC---CCeEEEEccCCcccccccchhhcccCCC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLR---NPVRVEVRAESKSHHVSASSQQLASSKT  158 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~---~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (183)
                      +||+|.+-+..-+.-.+.++-.+|+.-|.+++|||+++. .+|..|+-.   .|..+...+.                 .
T Consensus       235 FDEvHyi~D~eRG~VWEE~Ii~lP~~v~~v~LSATv~N~-~EF~~Wi~~~~~~~~~vv~t~~-----------------R  296 (1041)
T COG4581         235 FDEVHYIGDRERGVVWEEVIILLPDHVRFVFLSATVPNA-EEFAEWIQRVHSQPIHVVSTEH-----------------R  296 (1041)
T ss_pred             EEeeeeccccccchhHHHHHHhcCCCCcEEEEeCCCCCH-HHHHHHHHhccCCCeEEEeecC-----------------C
Confidence            999999987666666677888899999999999999998 777777642   4544443332                 4


Q ss_pred             ccCceEEEEEe
Q 030094          159 PLGLHLEVIWN  169 (183)
Q Consensus       159 ~~~l~q~~i~~  169 (183)
                      |..+.||++.-
T Consensus       297 pvPL~~~~~~~  307 (1041)
T COG4581         297 PVPLEHFVYVG  307 (1041)
T ss_pred             CCCeEEEEecC
Confidence            66777776543

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

Probab=98.91  E-value=7.6e-09  Score=91.32  Aligned_cols=124  Identities=14%  Similarity=0.151  Sum_probs=89.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcC-CCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLD-FRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~-l~~l~~l   80 (183)
                      +++++||+-|+.|....+..++.   +-++....||.........+ -..++|+|.||+.|..-+.. +..+ ++.+.++
T Consensus       109 iVF~aP~~pLv~QQ~a~~~~~~~---~~~~T~~l~~~~~~~~r~~i-~~s~~vff~TpQil~ndL~~-~~~~~ls~fs~i  183 (746)
T KOG0354|consen  109 VVFLAPTRPLVNQQIACFSIYLI---PYSVTGQLGDTVPRSNRGEI-VASKRVFFRTPQILENDLKS-GLHDELSDFSLI  183 (746)
T ss_pred             EEEeeCCchHHHHHHHHHhhccC---cccceeeccCccCCCchhhh-hcccceEEeChHhhhhhccc-ccccccceEEEE
Confidence            68999999999999865555542   24556666664332222233 24789999999999999987 5544 5999999


Q ss_pred             EEcccchhhccchHH-HHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCC
Q 030094           81 VLDEADRLLDMGFQK-QISYIISRLPKLRRTGLFSATQTEAVEELSKAGLR  130 (183)
Q Consensus        81 VvDEad~ll~~~~~~-~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~  130 (183)
                      |+||||+-.+..-+. -+...+..-....|++++|||+........+...+
T Consensus       184 v~DE~Hra~kn~~Y~~Vmr~~l~~k~~~~qILgLTASpG~~~~~v~~~I~~  234 (746)
T KOG0354|consen  184 VFDECHRTSKNHPYNNIMREYLDLKNQGNQILGLTASPGSKLEQVQNVIDN  234 (746)
T ss_pred             EEcccccccccccHHHHHHHHHHhhhccccEEEEecCCCccHHHHHHHHHh
Confidence            999999998765444 44466665556669999999999876666655433

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.90  E-value=4e-09  Score=94.92  Aligned_cols=85  Identities=19%  Similarity=0.262  Sum_probs=71.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhcCCcCC-----C
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMDVLDF-----R   75 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~~~~~l-----~   75 (183)
                      +.|++||++||.|..+.+..+..++ ++++.++.++.+..+..   ...+|||++|||+++ .++++.+=.++.     +
T Consensus       126 VhIvT~ndyLA~RD~e~m~~l~~~l-Glsv~~i~~~~~~~~r~---~~Y~~dI~YgT~~e~gfDyLrdnm~~~~~~~vqr  201 (908)
T PRK13107        126 VHVITVNDYLARRDAENNRPLFEFL-GLTVGINVAGLGQQEKK---AAYNADITYGTNNEFGFDYLRDNMAFSPQERVQR  201 (908)
T ss_pred             EEEEeCCHHHHHHHHHHHHHHHHhc-CCeEEEecCCCCHHHHH---hcCCCCeEEeCCCcccchhhhccCccchhhhhcc
Confidence            6899999999999999999999998 99999999987764332   234799999999999 888876214444     7


Q ss_pred             CceEEEEcccchhhc
Q 030094           76 NLEILVLDEADRLLD   90 (183)
Q Consensus        76 ~l~~lVvDEad~ll~   90 (183)
                      .+.+.|+||||.+|-
T Consensus       202 ~~~~aIvDEvDsiLi  216 (908)
T PRK13107        202 PLHYALIDEVDSILI  216 (908)
T ss_pred             ccceeeecchhhhcc
Confidence            889999999999973

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

Probab=98.89  E-value=1.4e-08  Score=93.04  Aligned_cols=128  Identities=20%  Similarity=0.312  Sum_probs=103.1

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      |+.+||||--||+|.|+.++.=.+++ ++++..+..=.+.+++..   .+..+..||||||.    .++.  +.+.++++
T Consensus       645 QVAvLVPTTlLA~QHy~tFkeRF~~f-PV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTH----rLL~--kdv~FkdL  717 (1139)
T COG1197         645 QVAVLVPTTLLAQQHYETFKERFAGF-PVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTH----RLLS--KDVKFKDL  717 (1139)
T ss_pred             eEEEEcccHHhHHHHHHHHHHHhcCC-CeeEEEecccCCHHHHHHHHHHHhcCCccEEEech----HhhC--CCcEEecC
Confidence            68899999999999999999888888 699988876666555544   55668899999997    5554  57889999


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccC
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAE  140 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~  140 (183)
                      .++|+||=|++ +....+.    ++.+..+.-++-+|||.-|+..+++-.-+++-..|....+
T Consensus       718 GLlIIDEEqRF-GVk~KEk----LK~Lr~~VDvLTLSATPIPRTL~Msm~GiRdlSvI~TPP~  775 (1139)
T COG1197         718 GLLIIDEEQRF-GVKHKEK----LKELRANVDVLTLSATPIPRTLNMSLSGIRDLSVIATPPE  775 (1139)
T ss_pred             CeEEEechhhc-CccHHHH----HHHHhccCcEEEeeCCCCcchHHHHHhcchhhhhccCCCC
Confidence            99999999994 3334444    4455567889999999999999999988888888876655

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.89  E-value=2.8e-09  Score=90.29  Aligned_cols=131  Identities=23%  Similarity=0.254  Sum_probs=94.3

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEE--------EEEcC--------cchHHHHHHHHh----------------
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSV--------LLVGG--------VEVKADVKKIEE----------------   49 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~--------~~~g~--------~~~~~~~~~l~~----------------   49 (183)
                      +|||||+||-|..+.+.+..+..+..+-+..        .-++|        ....++.+.+..                
T Consensus       296 VLivvpfRe~A~riVn~lis~l~G~~q~k~~V~Nk~RF~~eys~~te~~~~~~~kP~D~~~lf~GNtDD~FriGl~ftkK  375 (698)
T KOG2340|consen  296 VLIVVPFRESAYRIVNLLISLLSGDDQGKSEVWNKKRFEGEYSGPTELPPPRAKKPEDFEELFSGNTDDAFRIGLAFTKK  375 (698)
T ss_pred             EEEEecchHHHHHHHHHHHHHhcCccccchhhhhhhhhchhcCCCcccCCCCCCCchhHHHHhcCCCcchhhhhHHHHHH
Confidence            7999999999999999998884332121111        11111        011122221111                


Q ss_pred             --------cCCcEEEeCcHHHHHHHHhcC----CcC-CCCceEEEEcccchhhccchHHHHHHHHHhCCC---C------
Q 030094           50 --------EGANLLIGTPGRLYDIMERMD----VLD-FRNLEILVLDEADRLLDMGFQKQISYIISRLPK---L------  107 (183)
Q Consensus        50 --------~~~~IiV~TP~~l~~~l~~~~----~~~-l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~---~------  107 (183)
                              ...||+||+|..|..++.+++    .+| ++++.++|+|.||.++.+ .++++..|+.++..   +      
T Consensus       376 tikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~Q-NwEhl~~ifdHLn~~P~k~h~~Df  454 (698)
T KOG2340|consen  376 TIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQ-NWEHLLHIFDHLNLQPSKQHDVDF  454 (698)
T ss_pred             HHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHh-hHHHHHHHHHHhhcCcccccCCCh
Confidence                    358999999999999998422    244 799999999999999876 48888899988742   1      


Q ss_pred             ---------------CeEEEEeecCChHHHHHHHhhCCCCe
Q 030094          108 ---------------RRTGLFSATQTEAVEELSKAGLRNPV  133 (183)
Q Consensus       108 ---------------~Q~v~~SAT~~~~v~~~~~~~~~~~~  133 (183)
                                     +|+++||+--.+....+...++.|..
T Consensus       455 SRVR~wyL~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N~~  495 (698)
T KOG2340|consen  455 SRVRMWYLDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQNMA  495 (698)
T ss_pred             hheehheeccHHHHHHHHHHHHhhccHHHHHHHHHhhhhhc
Confidence                           49999999999999999999988764

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

Probab=98.76  E-value=3e-08  Score=90.95  Aligned_cols=154  Identities=18%  Similarity=0.160  Sum_probs=106.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcC-CCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLD-FRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~-l~~l~~l   80 (183)
                      .+.++|.+.|++.+...+.+-...+ +++|.-.+|......+.    -.+.+|+||||+.-...-++.+..+ .+-++.+
T Consensus       367 IVYIAPmKaLvqE~VgsfSkRla~~-GI~V~ElTgD~~l~~~q----ieeTqVIV~TPEK~DiITRk~gdraY~qlvrLl  441 (1674)
T KOG0951|consen  367 IVYIAPMKALVQEMVGSFSKRLAPL-GITVLELTGDSQLGKEQ----IEETQVIVTTPEKWDIITRKSGDRAYEQLVRLL  441 (1674)
T ss_pred             EEEEeeHHHHHHHHHHHHHhhcccc-CcEEEEecccccchhhh----hhcceeEEeccchhhhhhcccCchhHHHHHHHH
Confidence            4679999999997777555544566 89999999987644332    2467899999998544433312222 3567889


Q ss_pred             EEcccchhhccchHHHHHHHHHhCC-------CCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLP-------KLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQL  153 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~-------~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~  153 (183)
                      |+||.|.+-+ .-++.+++|..+..       ..++.+.+|||+|+- ...+.-...+|.-+..-+.             
T Consensus       442 IIDEIHLLhD-dRGpvLESIVaRt~r~ses~~e~~RlVGLSATLPNy-~DV~~Fl~v~~~glf~fd~-------------  506 (1674)
T KOG0951|consen  442 IIDEIHLLHD-DRGPVLESIVARTFRRSESTEEGSRLVGLSATLPNY-EDVASFLRVDPEGLFYFDS-------------  506 (1674)
T ss_pred             hhhhhhhccc-ccchHHHHHHHHHHHHhhhcccCceeeeecccCCch-hhhHHHhccCcccccccCc-------------
Confidence            9999998744 35666666655542       367899999999976 4444433345554554455             


Q ss_pred             ccCCCccCceEEEEEecCcchhhh
Q 030094          154 ASSKTPLGLHLEVIWNVNQMRNHH  177 (183)
Q Consensus       154 ~~~~~~~~l~q~~i~~~~~~k~~~  177 (183)
                        .+.|..++|.||.+...+..++
T Consensus       507 --syRpvPL~qq~Igi~ek~~~~~  528 (1674)
T KOG0951|consen  507 --SYRPVPLKQQYIGITEKKPLKR  528 (1674)
T ss_pred             --ccCcCCccceEeccccCCchHH
Confidence              6789999999999887665554

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=98.75  E-value=2.9e-07  Score=86.38  Aligned_cols=120  Identities=20%  Similarity=0.212  Sum_probs=79.5

Q ss_pred             EeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCc-chHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEc
Q 030094            5 ISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGV-EVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLD   83 (183)
Q Consensus         5 l~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~-~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvD   83 (183)
                      .-|-|--|..+.+-+.+-.    +..+...+|.. ..+.+.    +.+..|.++|||.|+..+.. + -.+++++++|+|
T Consensus       117 tQPRRlAA~svA~RvA~el----g~~lG~~VGY~vR~~~~~----s~~T~I~~~TdGiLLr~l~~-d-~~L~~~~~IIID  186 (1283)
T TIGR01967       117 TQPRRLAARTVAQRIAEEL----GTPLGEKVGYKVRFHDQV----SSNTLVKLMTDGILLAETQQ-D-RFLSRYDTIIID  186 (1283)
T ss_pred             CCccHHHHHHHHHHHHHHh----CCCcceEEeeEEcCCccc----CCCceeeeccccHHHHHhhh-C-cccccCcEEEEc
Confidence            3466666665554333332    33444445532 222221    34689999999999999876 3 358999999999


Q ss_pred             ccc-hhhccchHHH-HHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEc
Q 030094           84 EAD-RLLDMGFQKQ-ISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVR  138 (183)
Q Consensus        84 Ead-~ll~~~~~~~-l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~  138 (183)
                      ||| ++++.+|.-. +..++... ++.|++++|||++.  ..+.+.|...|+ |.+.
T Consensus       187 EaHERsL~~D~LL~lLk~il~~r-pdLKlIlmSATld~--~~fa~~F~~apv-I~V~  239 (1283)
T TIGR01967       187 EAHERSLNIDFLLGYLKQLLPRR-PDLKIIITSATIDP--ERFSRHFNNAPI-IEVS  239 (1283)
T ss_pred             CcchhhccchhHHHHHHHHHhhC-CCCeEEEEeCCcCH--HHHHHHhcCCCE-EEEC
Confidence            999 5888877654 66665544 47899999999974  567776655554 4443

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.

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

Probab=98.69  E-value=7.9e-08  Score=86.34  Aligned_cols=138  Identities=25%  Similarity=0.238  Sum_probs=109.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +++-.|-+.|..|-++.++.-...     +.+++|....        +..+..+|-|-+-|..++.+ +.--.++++++|
T Consensus       343 ~iYTSPIKALSNQKfRDFk~tF~D-----vgLlTGDvqi--------nPeAsCLIMTTEILRsMLYr-gadliRDvE~VI  408 (1248)
T KOG0947|consen  343 TIYTSPIKALSNQKFRDFKETFGD-----VGLLTGDVQI--------NPEASCLIMTTEILRSMLYR-GADLIRDVEFVI  408 (1248)
T ss_pred             eEecchhhhhccchHHHHHHhccc-----cceeecceee--------CCCcceEeehHHHHHHHHhc-ccchhhccceEE
Confidence            567789999999999988886432     2377776553        33467999999999999988 554578999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCC-CCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLR-NPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      +||+|-+-+..-+.-.+.++=.+|+..++|++|||.|+. .+|+.|.-+ .-..|++...               ...|.
T Consensus       409 FDEVHYiND~eRGvVWEEViIMlP~HV~~IlLSATVPN~-~EFA~WIGRtK~K~IyViST---------------~kRPV  472 (1248)
T KOG0947|consen  409 FDEVHYINDVERGVVWEEVIIMLPRHVNFILLSATVPNT-LEFADWIGRTKQKTIYVIST---------------SKRPV  472 (1248)
T ss_pred             EeeeeecccccccccceeeeeeccccceEEEEeccCCCh-HHHHHHhhhccCceEEEEec---------------CCCcc
Confidence            999999977666666677788899999999999999998 788888766 4456666666               56788


Q ss_pred             CceEEEEEe
Q 030094          161 GLHLEVIWN  169 (183)
Q Consensus       161 ~l~q~~i~~  169 (183)
                      .++||+..-
T Consensus       473 PLEh~l~t~  481 (1248)
T KOG0947|consen  473 PLEHYLYTK  481 (1248)
T ss_pred             ceEEEEEec
Confidence            888887654

>PF14617 CMS1: U3-containing 90S pre-ribosomal complex subunit

Probab=98.51  E-value=2.5e-07  Score=72.98  Aligned_cols=82  Identities=24%  Similarity=0.446  Sum_probs=67.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcC-cchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGG-VEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~-~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +|||+++-..|..+.+.++.+...  +.+++-+.+. ...+++...+.....+|.||||+||..+++. +.+.+++++.+
T Consensus       129 ~lvvs~SalRa~dl~R~l~~~~~k--~~~v~KLFaKH~Kl~eqv~~L~~~~~~i~vGTP~Rl~kLle~-~~L~l~~l~~i  205 (252)
T PF14617_consen  129 VLVVSSSALRAADLIRALRSFKGK--DCKVAKLFAKHIKLEEQVKLLKKTRVHIAVGTPGRLSKLLEN-GALSLSNLKRI  205 (252)
T ss_pred             EEEEcchHHHHHHHHHHHHhhccC--CchHHHHHHhhccHHHHHHHHHhCCceEEEeChHHHHHHHHc-CCCCcccCeEE
Confidence            689999999999888888887321  2344444443 4788999999878899999999999999988 99999999999


Q ss_pred             EEcccc
Q 030094           81 VLDEAD   86 (183)
Q Consensus        81 VvDEad   86 (183)
                      |+|--+
T Consensus       206 vlD~s~  211 (252)
T PF14617_consen  206 VLDWSY  211 (252)
T ss_pred             EEcCCc
Confidence            999753

>PF04851 ResIII: Type III restriction enzyme, res subunit; InterPro: IPR006935 This entry represents a domain found in the N terminus of several proteins, including helicases, the R subunit (HsdR) of type I restriction endonucleases (3

Probab=98.50  E-value=7.4e-07  Score=66.10  Aligned_cols=110  Identities=17%  Similarity=0.121  Sum_probs=68.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEE-----------EcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLL-----------VGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMD   70 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~-----------~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~   70 (183)
                      +++++|+..|+.|..+.+..+....  ......           ..................++++.|...+........
T Consensus        53 ~l~~~p~~~l~~Q~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~  130 (184)
T PF04851_consen   53 VLIVAPNISLLEQWYDEFDDFGSEK--YNFFEKSIKPAYDSKEFISIQDDISDKSESDNNDKDIILTTYQSLQSDIKEEK  130 (184)
T ss_dssp             EEEEESSHHHHHHHHHHHHHHSTTS--EEEEE--GGGCCE-SEEETTTTEEEHHHHHCBSS-SEEEEEHHHHHHHHHH--
T ss_pred             eeEecCHHHHHHHHHHHHHHhhhhh--hhhcccccccccccccccccccccccccccccccccchhhHHHHHHhhccccc
Confidence            6899999999999999997665432  111111           111111111122334578999999999998876411


Q ss_pred             C----------cCCCCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC
Q 030094           71 V----------LDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        71 ~----------~~l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      .          .......++|+||||+.-+..-   ...+++  .+..-++++|||+.
T Consensus       131 ~~~~~~~~~~~~~~~~~~~vI~DEaH~~~~~~~---~~~i~~--~~~~~~l~lTATp~  183 (184)
T PF04851_consen  131 KIDESARRSYKLLKNKFDLVIIDEAHHYPSDSS---YREIIE--FKAAFILGLTATPF  183 (184)
T ss_dssp             -------GCHHGGGGSESEEEEETGGCTHHHHH---HHHHHH--SSCCEEEEEESS-S
T ss_pred             ccccchhhhhhhccccCCEEEEehhhhcCCHHH---HHHHHc--CCCCeEEEEEeCcc
Confidence            1          1234567999999999865431   334444  56778999999975

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 ....

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

Probab=98.45  E-value=4.4e-07  Score=80.00  Aligned_cols=135  Identities=22%  Similarity=0.202  Sum_probs=99.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +++-.|-++|..|-|+.+..=.+     .+.+.+|.-.+        +-.+.-+|-|-+-|..++.+ ++--++.+.++|
T Consensus       175 VIYTSPIKALSNQKYREl~~EF~-----DVGLMTGDVTI--------nP~ASCLVMTTEILRsMLYR-GSEvmrEVaWVI  240 (1041)
T KOG0948|consen  175 VIYTSPIKALSNQKYRELLEEFK-----DVGLMTGDVTI--------NPDASCLVMTTEILRSMLYR-GSEVMREVAWVI  240 (1041)
T ss_pred             EEeeChhhhhcchhHHHHHHHhc-----ccceeecceee--------CCCCceeeeHHHHHHHHHhc-cchHhheeeeEE
Confidence            46678999999999998776433     35566675553        23456789999999999988 777789999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCC---CCeEEEEccCCcccccccchhhcccCCC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLR---NPVRVEVRAESKSHHVSASSQQLASSKT  158 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~---~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (183)
                      +||+|-|-|..-+--.+.=+=.+|++.+.+|+|||+|+. .+|+.|...   .|..|-..+                 +.
T Consensus       241 FDEIHYMRDkERGVVWEETIIllP~~vr~VFLSATiPNA-~qFAeWI~~ihkQPcHVVYTd-----------------yR  302 (1041)
T KOG0948|consen  241 FDEIHYMRDKERGVVWEETIILLPDNVRFVFLSATIPNA-RQFAEWICHIHKQPCHVVYTD-----------------YR  302 (1041)
T ss_pred             eeeehhccccccceeeeeeEEeccccceEEEEeccCCCH-HHHHHHHHHHhcCCceEEeec-----------------CC
Confidence            999999987543333333334568999999999999998 788887654   676554333                 34


Q ss_pred             ccCceEEEEE
Q 030094          159 PLGLHLEVIW  168 (183)
Q Consensus       159 ~~~l~q~~i~  168 (183)
                      |-.++||.+.
T Consensus       303 PTPLQHyifP  312 (1041)
T KOG0948|consen  303 PTPLQHYIFP  312 (1041)
T ss_pred             CCcceeeeec
Confidence            7778888554

>PRK09694 helicase Cas3; Provisional

Probab=98.43  E-value=1.8e-06  Score=78.94  Aligned_cols=125  Identities=14%  Similarity=0.136  Sum_probs=78.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhh-CCCceEEEEEcCcchHHHH---------------------HHHHh-----cCCcE
Q 030094            2 GMIISPTRELSSQIYHVAQPFIST-LPDVKSVLLVGGVEVKADV---------------------KKIEE-----EGANL   54 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~-~~~~~~~~~~g~~~~~~~~---------------------~~l~~-----~~~~I   54 (183)
                      .++..||+..+.|+++.+.++.+. ++...+.+..|+.......                     ..+.+     --.+|
T Consensus       334 i~~aLPT~Atan~m~~Rl~~~~~~~f~~~~v~L~Hg~a~l~~~~~~~~~~~~~~~~~~~~~~~~~~w~~~~~kr~llapi  413 (878)
T PRK09694        334 IIFALPTQATANAMLSRLEALASKLFPSPNLILAHGNSRFNHLFQSLKSRAATEQGQEEAWVQCCEWLSQSNKRVFLGQI  413 (878)
T ss_pred             EEEECcHHHHHHHHHHHHHHHHHHhcCCCceEeecCcchhhhhhhhhhcccccccccchhhhHHHHHHhhhhhhhhcCCE
Confidence            468899999999999998875542 2345667777665422110                     11110     12689


Q ss_pred             EEeCcHHHHHHHHhcCCcCCCCc----eEEEEcccchhhccchHHHHHHHHHhCC-CCCeEEEEeecCChHHHH-HHHh
Q 030094           55 LIGTPGRLYDIMERMDVLDFRNL----EILVLDEADRLLDMGFQKQISYIISRLP-KLRRTGLFSATQTEAVEE-LSKA  127 (183)
Q Consensus        55 iV~TP~~l~~~l~~~~~~~l~~l----~~lVvDEad~ll~~~~~~~l~~i~~~l~-~~~Q~v~~SAT~~~~v~~-~~~~  127 (183)
                      +|||+.-++...-..+...++..    +.+|+||+|.+ +......+..+++.+. ....++++|||+|....+ +.+.
T Consensus       414 ~V~TiDQlL~a~l~~kh~~lR~~~La~svvIiDEVHAy-D~ym~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L~~a  491 (878)
T PRK09694        414 GVCTIDQVLISVLPVKHRFIRGFGLGRSVLIVDEVHAY-DAYMYGLLEAVLKAQAQAGGSVILLSATLPATLKQKLLDT  491 (878)
T ss_pred             EEcCHHHHHHHHHccchHHHHHHhhccCeEEEechhhC-CHHHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHH
Confidence            99999887744332122222222    58999999997 4334455566665543 356799999999988664 3443

>COG1110 Reverse gyrase [DNA replication, recombination, and repair]

Probab=98.42  E-value=2e-06  Score=78.12  Aligned_cols=87  Identities=21%  Similarity=0.344  Sum_probs=63.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCc-c---hHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGV-E---VKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~-~---~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      ++|++||+-|+.|+++-+++++.......+...+-+. +   .++-...+.+++.||+|+|.+-|..-++...   -.+.
T Consensus       128 ~yii~PT~~Lv~Q~~~kl~~~~e~~~~~~~~~~yh~~l~~~ekee~le~i~~gdfdIlitTs~FL~k~~e~L~---~~kF  204 (1187)
T COG1110         128 VYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEELS---KLKF  204 (1187)
T ss_pred             EEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHHhc---ccCC
Confidence            6899999999999999999998765224444433332 2   3334456666789999999988877766522   2346


Q ss_pred             eEEEEcccchhhcc
Q 030094           78 EILVLDEADRLLDM   91 (183)
Q Consensus        78 ~~lVvDEad~ll~~   91 (183)
                      +++.+|++|.++..
T Consensus       205 dfifVDDVDA~Lka  218 (1187)
T COG1110         205 DFIFVDDVDAILKA  218 (1187)
T ss_pred             CEEEEccHHHHHhc
Confidence            79999999999864

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

Probab=98.42  E-value=1.2e-06  Score=74.74  Aligned_cols=102  Identities=20%  Similarity=0.270  Sum_probs=66.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcC-CcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEG-ANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~-~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +||||||++|+.|..+.+.+....  + .....+|+...        +.. ..|.|+|-+.+...-.. ..+..++..++
T Consensus        83 ~Lvlv~~~~L~~Qw~~~~~~~~~~--~-~~~g~~~~~~~--------~~~~~~i~vat~qtl~~~~~l-~~~~~~~~~li  150 (442)
T COG1061          83 TLVLVPTKELLDQWAEALKKFLLL--N-DEIGIYGGGEK--------ELEPAKVTVATVQTLARRQLL-DEFLGNEFGLI  150 (442)
T ss_pred             EEEEECcHHHHHHHHHHHHHhcCC--c-cccceecCcee--------ccCCCcEEEEEhHHHhhhhhh-hhhcccccCEE
Confidence            699999999999998766665422  1 12233333332        112 36999999988874211 23444578899


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCCh
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~  119 (183)
                      |+||+|++....+......+....+    .+.+|||+..
T Consensus       151 I~DE~Hh~~a~~~~~~~~~~~~~~~----~LGLTATp~R  185 (442)
T COG1061         151 IFDEVHHLPAPSYRRILELLSAAYP----RLGLTATPER  185 (442)
T ss_pred             EEEccccCCcHHHHHHHHhhhcccc----eeeeccCcee
Confidence            9999999976655554444333332    8999999763

>TIGR00603 rad25 DNA repair helicase rad25

Probab=98.36  E-value=2e-06  Score=76.99  Aligned_cols=106  Identities=11%  Similarity=0.128  Sum_probs=70.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhc-------CCcCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM-------DVLDF   74 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~-------~~~~l   74 (183)
                      +|||||+.+|+.|..+.+.+++. .+...+..+.|+....     . ....+|+|+|...+.....+.       ..+.-
T Consensus       301 tLILvps~~Lv~QW~~ef~~~~~-l~~~~I~~~tg~~k~~-----~-~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~  373 (732)
T TIGR00603       301 CLVLCTSAVSVEQWKQQFKMWST-IDDSQICRFTSDAKER-----F-HGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTN  373 (732)
T ss_pred             EEEEeCcHHHHHHHHHHHHHhcC-CCCceEEEEecCcccc-----c-ccCCcEEEEEHHHhhcccccchhhhHHHHHhcc
Confidence            69999999999999999998853 3345566666643211     1 124689999998775332210       11223


Q ss_pred             CCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCCh
Q 030094           75 RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~  119 (183)
                      ....++|+||+|++-.    .....++..++ .+..+++|||+..
T Consensus       374 ~~~gLII~DEvH~lpA----~~fr~il~~l~-a~~RLGLTATP~R  413 (732)
T TIGR00603       374 REWGLILLDEVHVVPA----AMFRRVLTIVQ-AHCKLGLTATLVR  413 (732)
T ss_pred             ccCCEEEEEccccccH----HHHHHHHHhcC-cCcEEEEeecCcc
Confidence            4677999999999843    33444555553 4567999999863

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).

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

Probab=98.34  E-value=5.9e-06  Score=72.15  Aligned_cols=128  Identities=17%  Similarity=0.223  Sum_probs=92.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      .|||.|--.|.....+.++..     +++++.+.+.-+.++...   .+..+..+++--+|++|..---. +.+.-..+.
T Consensus        60 TLVVSPLiSLM~DQV~~l~~~-----Gi~A~~lnS~l~~~e~~~v~~~l~~g~~klLyisPErl~~~~f~-~~L~~~~i~  133 (590)
T COG0514          60 TLVVSPLISLMKDQVDQLEAA-----GIRAAYLNSTLSREERQQVLNQLKSGQLKLLYISPERLMSPRFL-ELLKRLPIS  133 (590)
T ss_pred             EEEECchHHHHHHHHHHHHHc-----CceeehhhcccCHHHHHHHHHHHhcCceeEEEECchhhcChHHH-HHHHhCCCc
Confidence            689999999998666655554     678888887766554433   34345589999999998654322 234456788


Q ss_pred             EEEEcccchhhccc--hHHHHHHH---HHhCCCCCeEEEEeecCChHHHHHHHhhCC--CCeEEE
Q 030094           79 ILVLDEADRLLDMG--FQKQISYI---ISRLPKLRRTGLFSATQTEAVEELSKAGLR--NPVRVE  136 (183)
Q Consensus        79 ~lVvDEad~ll~~~--~~~~l~~i---~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~--~~~~i~  136 (183)
                      ++|+||||.+..+|  |.++...+   ...+| +..++.++||-++.+..-+...+.  +|..+.
T Consensus       134 l~vIDEAHCiSqWGhdFRP~Y~~lg~l~~~~~-~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~  197 (590)
T COG0514         134 LVAIDEAHCISQWGHDFRPDYRRLGRLRAGLP-NPPVLALTATATPRVRDDIREQLGLQDANIFR  197 (590)
T ss_pred             eEEechHHHHhhcCCccCHhHHHHHHHHhhCC-CCCEEEEeCCCChHHHHHHHHHhcCCCcceEE
Confidence            99999999999886  77766655   44454 778999999999998887766544  554443

>TIGR00348 hsdR type I site-specific deoxyribonuclease, HsdR family

Probab=98.22  E-value=1.2e-05  Score=71.92  Aligned_cols=107  Identities=14%  Similarity=0.107  Sum_probs=66.3

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHh-cCCcCCCCc-eE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMER-MDVLDFRNL-EI   79 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~-~~~~~l~~l-~~   79 (183)
                      +|||||+.+|..|..+.+..+....  .     .+..+...-...+......|+|+|.+++...+.. ...+...+- -+
T Consensus       296 vl~lvdR~~L~~Q~~~~f~~~~~~~--~-----~~~~s~~~L~~~l~~~~~~iivtTiQk~~~~~~~~~~~~~~~~~~~l  368 (667)
T TIGR00348       296 VFFVVDRRELDYQLMKEFQSLQKDC--A-----ERIESIAELKRLLEKDDGGIIITTIQKFDKKLKEEEEKFPVDRKEVV  368 (667)
T ss_pred             EEEEECcHHHHHHHHHHHHhhCCCC--C-----cccCCHHHHHHHHhCCCCCEEEEEhHHhhhhHhhhhhccCCCCCCEE
Confidence            6899999999999999998875321  1     1112222222334344578999999999865432 011211111 17


Q ss_pred             EEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCCh
Q 030094           80 LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (183)
Q Consensus        80 lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~  119 (183)
                      +|+||||+.-..++.   ..+.+.+| +...++||||.-.
T Consensus       369 vIvDEaHrs~~~~~~---~~l~~~~p-~a~~lGfTaTP~~  404 (667)
T TIGR00348       369 VIFDEAHRSQYGELA---KNLKKALK-NASFFGFTGTPIF  404 (667)
T ss_pred             EEEEcCccccchHHH---HHHHhhCC-CCcEEEEeCCCcc
Confidence            999999996432222   22234554 5789999999853

Members of this family are assumed to differ from each other in DNA site specificity.

>PF07652 Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR011492 This is the Flavivirus DEAD domain

Probab=98.19  E-value=7.8e-06  Score=59.09  Aligned_cols=106  Identities=10%  Similarity=0.152  Sum_probs=62.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      .|||.|||-+|..+++.++..     +++..  .....  .   .. .++--|=|.|.+.+.+.+-+  .....+.+++|
T Consensus        36 vLvL~PTRvva~em~~aL~~~-----~~~~~--t~~~~--~---~~-~g~~~i~vMc~at~~~~~~~--p~~~~~yd~II  100 (148)
T PF07652_consen   36 VLVLAPTRVVAEEMYEALKGL-----PVRFH--TNARM--R---TH-FGSSIIDVMCHATYGHFLLN--PCRLKNYDVII  100 (148)
T ss_dssp             EEEEESSHHHHHHHHHHTTTS-----SEEEE--STTSS----------SSSSEEEEEHHHHHHHHHT--SSCTTS-SEEE
T ss_pred             EEEecccHHHHHHHHHHHhcC-----CcccC--ceeee--c---cc-cCCCcccccccHHHHHHhcC--cccccCccEEE
Confidence            689999999999887766543     33332  11111  0   11 24556778899998887755  45578899999


Q ss_pred             Ecccchhhcc--chHHHHHHHHHhCCCCCeEEEEeecCChHHHHH
Q 030094           82 LDEADRLLDM--GFQKQISYIISRLPKLRRTGLFSATQTEAVEEL  124 (183)
Q Consensus        82 vDEad~ll~~--~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~  124 (183)
                      +||+|..-..  .+...+.....  .....++++|||.|.....+
T Consensus       101 ~DEcH~~Dp~sIA~rg~l~~~~~--~g~~~~i~mTATPPG~~~~f  143 (148)
T PF07652_consen  101 MDECHFTDPTSIAARGYLRELAE--SGEAKVIFMTATPPGSEDEF  143 (148)
T ss_dssp             ECTTT--SHHHHHHHHHHHHHHH--TTS-EEEEEESS-TT---SS
T ss_pred             EeccccCCHHHHhhheeHHHhhh--ccCeeEEEEeCCCCCCCCCC
Confidence            9999996322  13344444433  23467999999999875433

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 ....

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

Probab=98.02  E-value=2.6e-05  Score=73.27  Aligned_cols=113  Identities=12%  Similarity=0.062  Sum_probs=71.9

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhc----CCcCCCCc
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM----DVLDFRNL   77 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~----~~~~l~~l   77 (183)
                      +|||||+++|+.|..+.+..+.... ......+++.....+   ........|+|+|.+++...+...    ..+.+.+.
T Consensus       466 VLfLvDR~~L~~Qa~~~F~~~~~~~-~~~~~~i~~i~~L~~---~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~f  541 (1123)
T PRK11448        466 ILFLVDRSALGEQAEDAFKDTKIEG-DQTFASIYDIKGLED---KFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQY  541 (1123)
T ss_pred             EEEEecHHHHHHHHHHHHHhccccc-ccchhhhhchhhhhh---hcccCCCCEEEEEHHHHHHhhhccccccccCCCCcc
Confidence            6899999999999999988863211 111111222111111   111345789999999987765321    12456778


Q ss_pred             eEEEEcccchhhcc---------------chHHHHHHHHHhCCCCCeEEEEeecCChH
Q 030094           78 EILVLDEADRLLDM---------------GFQKQISYIISRLPKLRRTGLFSATQTEA  120 (183)
Q Consensus        78 ~~lVvDEad~ll~~---------------~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~  120 (183)
                      .++|+||||+-...               .+......++..+  +.-.++||||....
T Consensus       542 dlIIiDEaHRs~~~d~~~~~~~~~~~~~~~~~~~yr~iL~yF--dA~~IGLTATP~r~  597 (1123)
T PRK11448        542 DCIIVDEAHRGYTLDKEMSEGELQFRDQLDYVSKYRRVLDYF--DAVKIGLTATPALH  597 (1123)
T ss_pred             cEEEEECCCCCCccccccccchhccchhhhHHHHHHHHHhhc--CccEEEEecCCccc
Confidence            89999999996310               1235566677765  35679999998644

>PF00176 SNF2_N: SNF2 family N-terminal domain; InterPro: IPR000330 This domain is found in proteins involved in a variety of processes including transcription regulation (e

Probab=97.96  E-value=2.5e-05  Score=62.44  Aligned_cols=110  Identities=20%  Similarity=0.214  Sum_probs=66.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHh--cCCcCCCCceE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMER--MDVLDFRNLEI   79 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~--~~~~~l~~l~~   79 (183)
                      +||+||+ .+..|..+.+.+.+... .+++....|+.......... ....+++|+|.+.+......  ...+.--+...
T Consensus        61 ~LIv~P~-~l~~~W~~E~~~~~~~~-~~~v~~~~~~~~~~~~~~~~-~~~~~vvi~ty~~~~~~~~~~~~~~l~~~~~~~  137 (299)
T PF00176_consen   61 TLIVVPS-SLLSQWKEEIEKWFDPD-SLRVIIYDGDSERRRLSKNQ-LPKYDVVITTYETLRKARKKKDKEDLKQIKWDR  137 (299)
T ss_dssp             EEEEE-T-TTHHHHHHHHHHHSGT--TS-EEEESSSCHHHHTTSSS-CCCSSEEEEEHHHHH--TSTHTTHHHHTSEEEE
T ss_pred             eeEeecc-chhhhhhhhhccccccc-cccccccccccccccccccc-cccceeeecccccccccccccccccccccccee
Confidence            6999999 77788888888887432 56776666655222221111 24689999999988811000  01111234789


Q ss_pred             EEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecC
Q 030094           80 LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ  117 (183)
Q Consensus        80 lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~  117 (183)
                      +|+||+|.+-  +........+..+. ....+++|||.
T Consensus       138 vIvDEaH~~k--~~~s~~~~~l~~l~-~~~~~lLSgTP  172 (299)
T PF00176_consen  138 VIVDEAHRLK--NKDSKRYKALRKLR-ARYRWLLSGTP  172 (299)
T ss_dssp             EEETTGGGGT--TTTSHHHHHHHCCC-ECEEEEE-SS-
T ss_pred             EEEecccccc--cccccccccccccc-cceEEeecccc
Confidence            9999999983  23334444455554 67788999995

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.

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=97.93  E-value=3.8e-05  Score=69.90  Aligned_cols=85  Identities=18%  Similarity=0.203  Sum_probs=66.1

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhc-----CCcCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERM-----DVLDF   74 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~-----~~~~l   74 (183)
                      ++-|++||.-||.|-++.+..+..++ ++++.++.++.+.++....+   .+||+.||..-+ .++++.+     ...-.
T Consensus       125 ~VhvvT~ndyLA~RD~e~m~~l~~~l-Gl~v~~i~~~~~~~err~~Y---~~dI~YGT~~e~gFDYLrD~~~~~~~~~vq  200 (913)
T PRK13103        125 GVHVVTVNDYLARRDANWMRPLYEFL-GLSVGIVTPFQPPEEKRAAY---AADITYGTNNEFGFDYLRDNMAFSLDDKFQ  200 (913)
T ss_pred             CEEEEeCCHHHHHHHHHHHHHHhccc-CCEEEEECCCCCHHHHHHHh---cCCEEEEcccccccchhhccceechhhhcc
Confidence            46789999999999999999999888 99999998877655554443   599999999886 3334320     11123


Q ss_pred             CCceEEEEcccchhh
Q 030094           75 RNLEILVLDEADRLL   89 (183)
Q Consensus        75 ~~l~~lVvDEad~ll   89 (183)
                      +.+.+.|+||+|.+|
T Consensus       201 r~l~~aIVDEvDsiL  215 (913)
T PRK13103        201 RELNFAVIDEVDSIL  215 (913)
T ss_pred             cccceeEechhhhee
Confidence            788999999999987

>KOG0949 consensus Predicted helicase, DEAD-box superfamily [General function prediction only]

Probab=97.90  E-value=3.6e-05  Score=69.98  Aligned_cols=114  Identities=15%  Similarity=0.129  Sum_probs=75.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhc--CCcCCCCceE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM--DVLDFRNLEI   79 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~--~~~~l~~l~~   79 (183)
                      +|.++||+.|+.|+...+......-.-.+...+.|....+.+.+.   -+|+|+|+-|+.+-.++-..  ..-...++++
T Consensus       559 VIyvaPtKaLVnQvsa~VyaRF~~~t~~rg~sl~g~ltqEYsinp---~nCQVLITvPecleslLlspp~~q~~cerIRy  635 (1330)
T KOG0949|consen  559 VIYVAPTKALVNQVSANVYARFDTKTFLRGVSLLGDLTQEYSINP---WNCQVLITVPECLESLLLSPPHHQKFCERIRY  635 (1330)
T ss_pred             EEEecchHHHhhhhhHHHHHhhccCccccchhhHhhhhHHhcCCc---hhceEEEEchHHHHHHhcCchhhhhhhhcceE
Confidence            578999999999998776665422112344444554444444332   37999999999998888651  1234688999


Q ss_pred             EEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChH
Q 030094           80 LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (183)
Q Consensus        80 lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~  120 (183)
                      +|+||+|.+-...-..-.+.++-..  .|-++.+|||+.+.
T Consensus       636 iIfDEVH~iG~~ed~l~~Eqll~li--~CP~L~LSATigN~  674 (1330)
T KOG0949|consen  636 IIFDEVHLIGNEEDGLLWEQLLLLI--PCPFLVLSATIGNP  674 (1330)
T ss_pred             EEechhhhccccccchHHHHHHHhc--CCCeeEEecccCCH
Confidence            9999999984332122222233333  47789999999876

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=97.80  E-value=0.00028  Score=65.74  Aligned_cols=107  Identities=15%  Similarity=0.185  Sum_probs=70.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH--HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK--KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEI   79 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~--~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~   79 (183)
                      .|||||. .+..|..+.+.+++   |.+++..+.|.........  .+.....+|+|+|.+.+.....   .+.--...+
T Consensus       222 ~LIVvP~-SlL~nW~~Ei~kw~---p~l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~---~L~k~~W~~  294 (1033)
T PLN03142        222 HMVVAPK-STLGNWMNEIRRFC---PVLRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKT---ALKRFSWRY  294 (1033)
T ss_pred             EEEEeCh-HHHHHHHHHHHHHC---CCCceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHH---HhccCCCCE
Confidence            5899996 44566777776654   6778888887654332221  2223568999999988765432   233335679


Q ss_pred             EEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC
Q 030094           80 LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        80 lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      +|+||||.+=+  ....+...++.+. ....+++|+|.-
T Consensus       295 VIvDEAHrIKN--~~Sklskalr~L~-a~~RLLLTGTPl  330 (1033)
T PLN03142        295 IIIDEAHRIKN--ENSLLSKTMRLFS-TNYRLLITGTPL  330 (1033)
T ss_pred             EEEcCccccCC--HHHHHHHHHHHhh-cCcEEEEecCCC
Confidence            99999999843  3445566666664 445678899963

>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]

Probab=97.69  E-value=0.0004  Score=61.98  Aligned_cols=111  Identities=22%  Similarity=0.276  Sum_probs=73.9

Q ss_pred             EEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH--HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK--KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         3 lIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~--~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      ||+||-.-|..    ....+.++.|++.+...+|.........  .+..+..||+|+|-+..+.-  . ..+.--..+++
T Consensus       221 LVi~P~StL~N----W~~Ef~rf~P~l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~d--k-~~lk~~~W~yl  293 (971)
T KOG0385|consen  221 LVIAPKSTLDN----WMNEFKRFTPSLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKD--K-SFLKKFNWRYL  293 (971)
T ss_pred             EEEeeHhhHHH----HHHHHHHhCCCcceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhh--H-HHHhcCCceEE
Confidence            78999777654    4455556678999999999875433322  23345789999998765443  1 23444567899


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeec-CChHHHH
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT-QTEAVEE  123 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT-~~~~v~~  123 (183)
                      |+||||++=+  -...+..+++.+......++ +.| +.+.+.+
T Consensus       294 vIDEaHRiKN--~~s~L~~~lr~f~~~nrLLl-TGTPLQNNL~E  334 (971)
T KOG0385|consen  294 VIDEAHRIKN--EKSKLSKILREFKTDNRLLL-TGTPLQNNLHE  334 (971)
T ss_pred             Eechhhhhcc--hhhHHHHHHHHhcccceeEe-eCCcccccHHH
Confidence            9999999843  45666688888865555555 555 4544443

>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=97.65  E-value=0.00051  Score=63.04  Aligned_cols=87  Identities=23%  Similarity=0.332  Sum_probs=60.9

Q ss_pred             CEEEEeCcHHHHHHH-HHHHHHhhhhCCCceEEEEEcCcch------HHHH-----------------------------
Q 030094            1 MGMIISPTRELSSQI-YHVAQPFISTLPDVKSVLLVGGVEV------KADV-----------------------------   44 (183)
Q Consensus         1 ~alIl~PtreLa~Qi-~~~~~~l~~~~~~~~~~~~~g~~~~------~~~~-----------------------------   44 (183)
                      .++|++||++|+.|+ .+.+..+.+.+ ++++..+.|+.+.      .+..                             
T Consensus       293 ~vvI~t~T~~Lq~Ql~~~~i~~l~~~~-~~~~~~~kg~~~ylcl~k~~~~l~~~~~~~~~~~~~~~il~Wl~~T~tGD~~  371 (820)
T PRK07246        293 QIIVSVPTKILQDQIMAEEVKAIQEVF-HIDCHSLKGPQNYLKLDAFYDSLQQNDDNRLVNRYKMQLLVWLTETETGDLD  371 (820)
T ss_pred             cEEEEeCcHHHHHHHHHHHHHHHHHhc-CCcEEEEECCcccccHHHHHHHhhccCcchHHHHHHHHHHHHHhcCCCCCHh
Confidence            479999999999999 57788887776 6778777766431      0000                             


Q ss_pred             ------------HHH-----------------------HhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccchhh
Q 030094           45 ------------KKI-----------------------EEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLL   89 (183)
Q Consensus        45 ------------~~l-----------------------~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~ll   89 (183)
                                  ..+                       ....+||+|++..-|...+.. +. .+-.-+.+|+||||++-
T Consensus       372 El~~~~~~~~~w~~i~~~~~~~~~cp~~~~cf~~~ar~~a~~AdivItNHall~~~~~~-~~-~~p~~~~lIiDEAH~l~  449 (820)
T PRK07246        372 EIKQKQRYAAYFDQLKHDGNLSQSSLFYDYDFWKRSYEKAKTARLLITNHAYFLTRVQD-DK-DFARNKVLVFDEAQKLM  449 (820)
T ss_pred             hccCCccccHHHHHhhccCCCCCCCCcchhhHHHHHHHHHHhCCEEEEchHHHHHHHhh-cc-CCCCCCEEEEECcchhH
Confidence                        000                       001379999999988777654 32 24567899999999986


Q ss_pred             c
Q 030094           90 D   90 (183)
Q Consensus        90 ~   90 (183)
                      +
T Consensus       450 ~  450 (820)
T PRK07246        450 L  450 (820)
T ss_pred             H
Confidence            3

>TIGR03117 cas_csf4 CRISPR-associated DEAD/DEAH-box helicase Csf4

Probab=97.60  E-value=0.00064  Score=60.45  Aligned_cols=40  Identities=23%  Similarity=0.180  Sum_probs=30.2

Q ss_pred             cCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccchhhc
Q 030094           50 EGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLD   90 (183)
Q Consensus        50 ~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~ll~   90 (183)
                      ..+||+|+++.-|...++....+ +-....+|+||||++-+
T Consensus       181 ~~AdivItNHalL~~~~~~~~~i-LP~~~~lIiDEAH~L~d  220 (636)
T TIGR03117       181 RRCRILFCTHAMLGLAFRDKWGL-LPQPDILIVDEAHLFEQ  220 (636)
T ss_pred             ccCCEEEECHHHHHHHhhhhcCC-CCCCCEEEEeCCcchHH
Confidence            45799999999888766542233 34478999999999864

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.

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

Probab=97.46  E-value=0.0028  Score=58.68  Aligned_cols=129  Identities=22%  Similarity=0.274  Sum_probs=87.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhc--CCcEEEeCcHHHHHHHHhc-CCcCCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEE--GANLLIGTPGRLYDIMERM-DVLDFR   75 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~--~~~IiV~TP~~l~~~l~~~-~~~~l~   75 (183)
                      .|||.|-..|....   +..+.+.  ++....+.++....++..   .+..+  ..+|+--||+.+..--... ...++.
T Consensus       307 tvVISPL~SLm~DQ---v~~L~~~--~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~  381 (941)
T KOG0351|consen  307 TVVISPLISLMQDQ---VTHLSKK--GIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLY  381 (941)
T ss_pred             eEEeccHHHHHHHH---HHhhhhc--CcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhcc
Confidence            58999999998844   4445322  788888888877765444   34344  5899999999876543221 123355


Q ss_pred             C---ceEEEEcccchhhccc--hHHHHHH---HHHhCCCCCeEEEEeecCChHHHHHHHhh--CCCCeEEE
Q 030094           76 N---LEILVLDEADRLLDMG--FQKQISY---IISRLPKLRRTGLFSATQTEAVEELSKAG--LRNPVRVE  136 (183)
Q Consensus        76 ~---l~~lVvDEad~ll~~~--~~~~l~~---i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~--~~~~~~i~  136 (183)
                      .   +..+|+||||....+|  |+++-++   +..+.+. .-++..+||-+..+..=+-..  +++|..+.
T Consensus       382 ~~~~lal~vIDEAHCVSqWgHdFRp~Yk~l~~l~~~~~~-vP~iALTATAT~~v~~DIi~~L~l~~~~~~~  451 (941)
T KOG0351|consen  382 ARGLLALFVIDEAHCVSQWGHDFRPSYKRLGLLRIRFPG-VPFIALTATATERVREDVIRSLGLRNPELFK  451 (941)
T ss_pred             CCCeeEEEEecHHHHhhhhcccccHHHHHHHHHHhhCCC-CCeEEeehhccHHHHHHHHHHhCCCCcceec
Confidence            5   8899999999998775  6655554   3444443 678999999999887644444  55776543

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

Probab=97.41  E-value=0.00058  Score=57.49  Aligned_cols=130  Identities=21%  Similarity=0.210  Sum_probs=86.1

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhc--CCcEEEeCcHHHHH-----HHHhcC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEE--GANLLIGTPGRLYD-----IMERMD   70 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~--~~~IiV~TP~~l~~-----~l~~~~   70 (183)
                      +.||+.|--.|.....+.+.+|     .+.+..+.+..+..+..+   .+...  +..++--||+.-..     +++  +
T Consensus        63 ITIV~SPLiALIkDQiDHL~~L-----KVp~~SLNSKlSt~ER~ri~~DL~~ekp~~K~LYITPE~AAt~~FQ~lLn--~  135 (641)
T KOG0352|consen   63 ITIVISPLIALIKDQIDHLKRL-----KVPCESLNSKLSTVERSRIMGDLAKEKPTIKMLYITPEGAATDGFQKLLN--G  135 (641)
T ss_pred             eEEEehHHHHHHHHHHHHHHhc-----CCchhHhcchhhHHHHHHHHHHHHhcCCceeEEEEchhhhhhhhHHHHHH--H
Confidence            3578889888887666666665     566666666666554444   33333  35688889986322     221  1


Q ss_pred             CcCCCCceEEEEcccchhhccc--hHHHHHHHH---HhCCCCCeEEEEeecCChHHHH--HHHhhCCCCeEEEEc
Q 030094           71 VLDFRNLEILVLDEADRLLDMG--FQKQISYII---SRLPKLRRTGLFSATQTEAVEE--LSKAGLRNPVRVEVR  138 (183)
Q Consensus        71 ~~~l~~l~~lVvDEad~ll~~~--~~~~l~~i~---~~l~~~~Q~v~~SAT~~~~v~~--~~~~~~~~~~~i~~~  138 (183)
                      -.+-+.+.++|+||||..-.+|  |.++...+-   +.+ ...-.+.++||-+++|.+  +....+++|+-|.-.
T Consensus       136 L~~r~~L~Y~vVDEAHCVSQWGHDFRPDYL~LG~LRS~~-~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkT  209 (641)
T KOG0352|consen  136 LANRDVLRYIVVDEAHCVSQWGHDFRPDYLTLGSLRSVC-PGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKT  209 (641)
T ss_pred             HhhhceeeeEEechhhhHhhhccccCcchhhhhhHHhhC-CCCceEEeecccChhHHHHHHHHHhhcCcHHhccC
Confidence            2234668899999999998775  666655543   233 356678889999999886  445667899877643

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=97.30  E-value=0.00081  Score=60.25  Aligned_cols=85  Identities=14%  Similarity=0.153  Sum_probs=64.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHH-HHHHhc-----CCcCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-DIMERM-----DVLDF   74 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~-~~l~~~-----~~~~l   74 (183)
                      ++-|++||.-||.|-++.+..+..++ ++++.++.++.+.++....   ..|||.=||...+- ++++.+     ...-.
T Consensus       121 ~VhvvT~NdyLA~RDae~m~~ly~~L-GLsvg~i~~~~~~~err~a---Y~~DItYgTn~e~gFDyLRDnm~~~~~~~v~  196 (764)
T PRK12326        121 RVHVITVNDYLARRDAEWMGPLYEAL-GLTVGWITEESTPEERRAA---YACDVTYASVNEIGFDVLRDQLVTDVADLVS  196 (764)
T ss_pred             CeEEEcCCHHHHHHHHHHHHHHHHhc-CCEEEEECCCCCHHHHHHH---HcCCCEEcCCcccccccchhhhccChHhhcC
Confidence            36789999999999999999999998 9999999887775544433   36899999998752 233220     11224


Q ss_pred             CCceEEEEcccchhh
Q 030094           75 RNLEILVLDEADRLL   89 (183)
Q Consensus        75 ~~l~~lVvDEad~ll   89 (183)
                      +...+.|+||+|.+|
T Consensus       197 R~~~faIVDEvDSiL  211 (764)
T PRK12326        197 PNPDVAIIDEADSVL  211 (764)
T ss_pred             Cccceeeecchhhhe
Confidence            667899999999987

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=97.26  E-value=0.00091  Score=60.66  Aligned_cols=85  Identities=16%  Similarity=0.140  Sum_probs=65.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHH-HHHHhc-----CCcCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-DIMERM-----DVLDF   74 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~-~~l~~~-----~~~~l   74 (183)
                      ++-|++||.-||.|-++.+..+..++ ++++.++.|+.+.++....   ..+||+-||...+- ++++.+     ...-.
T Consensus       123 ~v~vvT~neyLA~Rd~e~~~~~~~~L-Gl~vg~i~~~~~~~~r~~~---y~~dI~Y~t~~e~gfDyLRD~m~~~~~~~v~  198 (796)
T PRK12906        123 GVHVVTVNEYLSSRDATEMGELYRWL-GLTVGLNLNSMSPDEKRAA---YNCDITYSTNSELGFDYLRDNMVVYKEQMVQ  198 (796)
T ss_pred             CeEEEeccHHHHHhhHHHHHHHHHhc-CCeEEEeCCCCCHHHHHHH---hcCCCeecCCccccccchhhccccchhhhhc
Confidence            46789999999999999999999998 9999999887665554433   36899999998863 333321     11123


Q ss_pred             CCceEEEEcccchhh
Q 030094           75 RNLEILVLDEADRLL   89 (183)
Q Consensus        75 ~~l~~lVvDEad~ll   89 (183)
                      +...+.|+||+|.+|
T Consensus       199 r~~~~aIvDEvDSiL  213 (796)
T PRK12906        199 RPLNYAIVDEVDSIL  213 (796)
T ss_pred             cCcceeeeccchhee
Confidence            567899999999987

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=97.21  E-value=0.0016  Score=60.56  Aligned_cols=126  Identities=19%  Similarity=0.205  Sum_probs=67.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH----HHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV----KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~----~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +||+||+ .|..|....+.+..    ++....+.++ ......    +..  ...+++|+|.+.+...-.....+.-...
T Consensus       202 vLIVvP~-sL~~QW~~El~~kF----~l~~~i~~~~-~~~~~~~~~~~pf--~~~~~vI~S~~~l~~~~~~~~~l~~~~w  273 (956)
T PRK04914        202 VLILVPE-TLQHQWLVEMLRRF----NLRFSLFDEE-RYAEAQHDADNPF--ETEQLVICSLDFLRRNKQRLEQALAAEW  273 (956)
T ss_pred             EEEEcCH-HHHHHHHHHHHHHh----CCCeEEEcCc-chhhhcccccCcc--ccCcEEEEEHHHhhhCHHHHHHHhhcCC
Confidence            6899998 78998888775432    3333333322 211110    111  1357999998776541110011222456


Q ss_pred             eEEEEcccchhhcc-chHHHHHHHHHhCC-CCCeEEEEeecCCh-HHH-HHHHhhCCCCeEE
Q 030094           78 EILVLDEADRLLDM-GFQKQISYIISRLP-KLRRTGLFSATQTE-AVE-ELSKAGLRNPVRV  135 (183)
Q Consensus        78 ~~lVvDEad~ll~~-~~~~~l~~i~~~l~-~~~Q~v~~SAT~~~-~v~-~~~~~~~~~~~~i  135 (183)
                      +++|+||||++-.. +....-...++.+. +....+++|||.-. ... .+..-.+-+|..+
T Consensus       274 dlvIvDEAH~lk~~~~~~s~~y~~v~~La~~~~~~LLLTATP~q~~~~e~falL~lLdP~~f  335 (956)
T PRK04914        274 DLLVVDEAHHLVWSEEAPSREYQVVEQLAEVIPGVLLLTATPEQLGQESHFARLRLLDPDRF  335 (956)
T ss_pred             CEEEEechhhhccCCCCcCHHHHHHHHHhhccCCEEEEEcCcccCCcHHHHHhhhhhCCCcC
Confidence            79999999998521 01111122233332 34578999999863 233 3333344466554

>KOG0389 consensus SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics]

Probab=97.19  E-value=0.0048  Score=55.47  Aligned_cols=116  Identities=15%  Similarity=0.225  Sum_probs=73.9

Q ss_pred             EEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhc---CCcEEEeCcHHHHHHHHhcCC-cCCCCce
Q 030094            3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEE---GANLLIGTPGRLYDIMERMDV-LDFRNLE   78 (183)
Q Consensus         3 lIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~---~~~IiV~TP~~l~~~l~~~~~-~~l~~l~   78 (183)
                      ||+||+.-|    ..+++.+.+.+|.+++-..+|...-..+.+.....   ..||+++|-.-...-=.. +. +.-.++.
T Consensus       452 LVVvPsSTl----eNWlrEf~kwCPsl~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdD-Rsflk~~~~n  526 (941)
T KOG0389|consen  452 LVVVPSSTL----ENWLREFAKWCPSLKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDD-RSFLKNQKFN  526 (941)
T ss_pred             EEEecchhH----HHHHHHHHHhCCceEEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHH-HHHHHhcccc
Confidence            799997665    46777788888999999999988766666655432   579999997432110000 00 1134566


Q ss_pred             EEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeec-CChHHHHHHH
Q 030094           79 ILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT-QTEAVEELSK  126 (183)
Q Consensus        79 ~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT-~~~~v~~~~~  126 (183)
                      ++|+||+|.|=+.+ .....+++. ++ ..+.++++.| +.+.+.+++.
T Consensus       527 ~viyDEgHmLKN~~-SeRy~~LM~-I~-An~RlLLTGTPLQNNL~ELiS  572 (941)
T KOG0389|consen  527 YVIYDEGHMLKNRT-SERYKHLMS-IN-ANFRLLLTGTPLQNNLKELIS  572 (941)
T ss_pred             EEEecchhhhhccc-hHHHHHhcc-cc-ccceEEeeCCcccccHHHHHH
Confidence            99999999985543 223333333 22 4556777777 4666676665

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.17  E-value=0.0017  Score=59.39  Aligned_cols=84  Identities=17%  Similarity=0.162  Sum_probs=66.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-----HHHHHh-cCCcCCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-----YDIMER-MDVLDFR   75 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-----~~~l~~-~~~~~l~   75 (183)
                      +-|++++..||.+=.+.+..+..++ ++++.++.++.+..+...   ..+|||+-||+..+     .+.+.. ....-.+
T Consensus       129 VhVVTvNdYLA~RDae~m~~vy~~L-GLtvg~i~~~~~~~err~---aY~~DItYgTn~e~gFDYLRDnm~~~~~~~vqR  204 (939)
T PRK12902        129 VHVVTVNDYLARRDAEWMGQVHRFL-GLSVGLIQQDMSPEERKK---NYACDITYATNSELGFDYLRDNMATDISEVVQR  204 (939)
T ss_pred             eEEEeCCHHHHHhHHHHHHHHHHHh-CCeEEEECCCCChHHHHH---hcCCCeEEecCCcccccchhhhhcccccccccC
Confidence            5789999999999999999999998 999998877665544332   35899999999987     444432 1223457


Q ss_pred             CceEEEEcccchhh
Q 030094           76 NLEILVLDEADRLL   89 (183)
Q Consensus        76 ~l~~lVvDEad~ll   89 (183)
                      .+.+.|+||+|.+|
T Consensus       205 ~~~faIVDEvDSIL  218 (939)
T PRK12902        205 PFNYCVIDEVDSIL  218 (939)
T ss_pred             ccceEEEeccccee
Confidence            78899999999987

>PRK14873 primosome assembly protein PriA; Provisional

Probab=97.15  E-value=0.0034  Score=56.32  Aligned_cols=113  Identities=9%  Similarity=0.168  Sum_probs=75.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      ++|||+|...|+.|+.+.++...+   +-.+..+.++.+..+..+   .+..+.+.|+|||-..+.        .-++++
T Consensus       190 ~vLvLvPEi~lt~q~~~rl~~~f~---~~~v~~lhS~l~~~~R~~~w~~~~~G~~~IViGtRSAvF--------aP~~~L  258 (665)
T PRK14873        190 GALVVVPDQRDVDRLEAALRALLG---AGDVAVLSAGLGPADRYRRWLAVLRGQARVVVGTRSAVF--------APVEDL  258 (665)
T ss_pred             eEEEEecchhhHHHHHHHHHHHcC---CCcEEEECCCCCHHHHHHHHHHHhCCCCcEEEEcceeEE--------eccCCC
Confidence            589999999999999998876542   255777887776555444   333566899999953221        236789


Q ss_pred             eEEEEcccchh-hccc-----hHHHHHHHHHhCCCCCeEEEEeecCChHHHHHH
Q 030094           78 EILVLDEADRL-LDMG-----FQKQISYIISRLPKLRRTGLFSATQTEAVEELS  125 (183)
Q Consensus        78 ~~lVvDEad~l-l~~~-----~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~  125 (183)
                      .++|+||=|.- ....     +..++...... ..+..+++-|||.+-+....+
T Consensus       259 gLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~-~~~~~lvLgSaTPSles~~~~  311 (665)
T PRK14873        259 GLVAIWDDGDDLLAEPRAPYPHAREVALLRAH-QHGCALLIGGHARTAEAQALV  311 (665)
T ss_pred             CEEEEEcCCchhhcCCCCCCccHHHHHHHHHH-HcCCcEEEECCCCCHHHHHHH
Confidence            99988887643 2221     22333332222 357899999999997765543

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

Probab=97.12  E-value=0.00093  Score=60.87  Aligned_cols=113  Identities=15%  Similarity=0.176  Sum_probs=71.9

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhc-CCcCCCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM-DVLDFRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~-~~~~l~~l~~l   80 (183)
                      ++.+.|.-.-++.-...+..+.-.. ++.+-..+|+.......     +.-++-|||=++-..+++.. ..=++..++++
T Consensus       272 ~llilp~vsiv~Ek~~~l~~~~~~~-G~~ve~y~g~~~p~~~~-----k~~sv~i~tiEkanslin~lie~g~~~~~g~v  345 (1008)
T KOG0950|consen  272 VLLILPYVSIVQEKISALSPFSIDL-GFPVEEYAGRFPPEKRR-----KRESVAIATIEKANSLINSLIEQGRLDFLGMV  345 (1008)
T ss_pred             eeEecceeehhHHHHhhhhhhcccc-CCcchhhcccCCCCCcc-----cceeeeeeehHhhHhHHHHHHhcCCccccCcE
Confidence            3444455444444444444444343 56665555554432221     23579999998866665431 12246778999


Q ss_pred             EEcccchhhccchHHHHHHHHHhC-----CCCCeEEEEeecCChH
Q 030094           81 VLDEADRLLDMGFQKQISYIISRL-----PKLRRTGLFSATQTEA  120 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l-----~~~~Q~v~~SAT~~~~  120 (183)
                      |+||.|.+.+.+-+..++.++..+     ....|+|.+|||+++.
T Consensus       346 vVdElhmi~d~~rg~~lE~~l~k~~y~~~~~~~~iIGMSATi~N~  390 (1008)
T KOG0950|consen  346 VVDELHMIGDKGRGAILELLLAKILYENLETSVQIIGMSATIPNN  390 (1008)
T ss_pred             EEeeeeeeeccccchHHHHHHHHHHHhccccceeEeeeecccCCh
Confidence            999999999888777777776554     2235799999999865

>KOG0387 consensus Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription; Replication, recombination and repair]

Probab=97.11  E-value=0.0042  Score=55.85  Aligned_cols=115  Identities=18%  Similarity=0.187  Sum_probs=69.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcch------------HHHHHHHHhcCCcEEEeCcHHHHHHHHhc
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEV------------KADVKKIEEEGANLLIGTPGRLYDIMERM   69 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~------------~~~~~~l~~~~~~IiV~TP~~l~~~l~~~   69 (183)
                      ||||||.--+ .   +.++++..-.|.+++..++|..+.            +..........-+|+|+|-..+.-.  . 
T Consensus       258 aLIVCP~Tii-~---qW~~E~~~w~p~~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~--~-  330 (923)
T KOG0387|consen  258 ALIVCPATII-H---QWMKEFQTWWPPFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQ--G-  330 (923)
T ss_pred             eEEEccHHHH-H---HHHHHHHHhCcceEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhccc--C-
Confidence            7999996543 3   344445555678999999876552            1111111113457999997654332  1 


Q ss_pred             CCcCCCCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeec-CChHHHHHHH
Q 030094           70 DVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT-QTEAVEELSK  126 (183)
Q Consensus        70 ~~~~l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT-~~~~v~~~~~  126 (183)
                      ..+.-....++|+||.|.+-+.  ...+..-...++ ..+.+.+|.| +.+.+.++-+
T Consensus       331 d~l~~~~W~y~ILDEGH~IrNp--ns~islackki~-T~~RiILSGTPiQNnL~ELws  385 (923)
T KOG0387|consen  331 DDLLGILWDYVILDEGHRIRNP--NSKISLACKKIR-TVHRIILSGTPIQNNLTELWS  385 (923)
T ss_pred             cccccccccEEEecCcccccCC--ccHHHHHHHhcc-ccceEEeeCccccchHHHHHH
Confidence            3455566789999999998653  344444456664 4555556666 5666666554

>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=97.04  E-value=0.0065  Score=48.56  Aligned_cols=84  Identities=14%  Similarity=0.226  Sum_probs=63.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHH-HHHhc---CCc--CCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYD-IMERM---DVL--DFR   75 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~-~l~~~---~~~--~l~   75 (183)
                      +-|++.+..||.+=++.+..+...+ ++++....++.+.++.....   .+||+-||...+.- +++..   +.-  -..
T Consensus       121 V~vvT~NdyLA~RD~~~~~~~y~~L-Glsv~~~~~~~~~~~r~~~Y---~~dI~Y~t~~~~~fD~Lrd~~~~~~~~~~~r  196 (266)
T PF07517_consen  121 VHVVTSNDYLAKRDAEEMRPFYEFL-GLSVGIITSDMSSEERREAY---AADIVYGTNSEFGFDYLRDNLALSKNEQVQR  196 (266)
T ss_dssp             EEEEESSHHHHHHHHHHHHHHHHHT-T--EEEEETTTEHHHHHHHH---HSSEEEEEHHHHHHHHHHHTT-SSGGG--SS
T ss_pred             cEEEeccHHHhhccHHHHHHHHHHh-hhccccCccccCHHHHHHHH---hCcccccccchhhHHHHHHHHhhccchhccC
Confidence            4588999999999999999999998 99999999988865544333   57999999998753 44431   111  147


Q ss_pred             CceEEEEcccchhh
Q 030094           76 NLEILVLDEADRLL   89 (183)
Q Consensus        76 ~l~~lVvDEad~ll   89 (183)
                      ...++|+||+|.++
T Consensus       197 ~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  197 GFDFAIVDEVDSIL  210 (266)
T ss_dssp             SSSEEEECTHHHHT
T ss_pred             CCCEEEEeccceEE
Confidence            88899999999987

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 ....

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=96.95  E-value=0.0025  Score=58.10  Aligned_cols=84  Identities=17%  Similarity=0.140  Sum_probs=64.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHH-HHHHhc-----CCcCCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-DIMERM-----DVLDFR   75 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~-~~l~~~-----~~~~l~   75 (183)
                      +-|++++..||.+-++.+..+.+++ ++++.++.++.+..+....   ..+||.-||...+- ++++.+     ...-.+
T Consensus       120 VhVvT~NdyLA~RD~e~m~pvy~~L-GLsvg~i~~~~~~~err~a---Y~~DItYgTn~e~gFDyLRDnm~~~~~~~v~r  195 (870)
T CHL00122        120 VHIVTVNDYLAKRDQEWMGQIYRFL-GLTVGLIQEGMSSEERKKN---YLKDITYVTNSELGFDYLRDNMALSLSDVVQR  195 (870)
T ss_pred             eEEEeCCHHHHHHHHHHHHHHHHHc-CCceeeeCCCCChHHHHHh---cCCCCEecCCccccccchhhccCcChHHhhcc
Confidence            5789999999999999999999998 9999998887776554433   46899999997543 333320     111246


Q ss_pred             CceEEEEcccchhh
Q 030094           76 NLEILVLDEADRLL   89 (183)
Q Consensus        76 ~l~~lVvDEad~ll   89 (183)
                      .+.+.|+||+|.+|
T Consensus       196 ~~~faIVDEvDSiL  209 (870)
T CHL00122        196 PFNYCIIDEVDSIL  209 (870)
T ss_pred             ccceeeeecchhhe
Confidence            78899999999987

>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative

Probab=96.94  E-value=0.0083  Score=55.48  Aligned_cols=39  Identities=28%  Similarity=0.256  Sum_probs=28.5

Q ss_pred             CCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccchhhc
Q 030094           51 GANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLD   90 (183)
Q Consensus        51 ~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~ll~   90 (183)
                      .+||+|++..-|...+.....+.+ .-+++|+||||+|.+
T Consensus       416 ~AdivItNHa~L~~~~~~~~~ilp-~~~~lIiDEAH~L~d  454 (850)
T TIGR01407       416 QAQILITNHAYLITRLVDNPELFP-SFRDLIIDEAHHLPD  454 (850)
T ss_pred             cCCEEEecHHHHHHHhhcccccCC-CCCEEEEECcchHHH
Confidence            479999999888777644233333 337999999999964

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.

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=96.94  E-value=0.013  Score=53.05  Aligned_cols=112  Identities=19%  Similarity=0.241  Sum_probs=77.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHH---HHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~---l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +||||||--.|--|+.+.++...    +.+++.+.++-+..+....   ...+...|+|||=..+..        -++++
T Consensus       247 qvLvLVPEI~Ltpq~~~rf~~rF----g~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF~--------Pf~~L  314 (730)
T COG1198         247 QVLVLVPEIALTPQLLARFKARF----GAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALFL--------PFKNL  314 (730)
T ss_pred             EEEEEeccccchHHHHHHHHHHh----CCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhcC--------chhhc
Confidence            58999999999999988777764    4677778777665544443   335779999999532222        36779


Q ss_pred             eEEEEcccchhh-c--cc---hHHHHHHHHHhCCCCCeEEEEeecCChHHHHHH
Q 030094           78 EILVLDEADRLL-D--MG---FQKQISYIISRLPKLRRTGLFSATQTEAVEELS  125 (183)
Q Consensus        78 ~~lVvDEad~ll-~--~~---~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~  125 (183)
                      .++|+||=|--- .  .+   +..++.-... -..++.+++-|||.+-+....+
T Consensus       315 GLIIvDEEHD~sYKq~~~prYhARdvA~~Ra-~~~~~pvvLgSATPSLES~~~~  367 (730)
T COG1198         315 GLIIVDEEHDSSYKQEDGPRYHARDVAVLRA-KKENAPVVLGSATPSLESYANA  367 (730)
T ss_pred             cEEEEeccccccccCCcCCCcCHHHHHHHHH-HHhCCCEEEecCCCCHHHHHhh
Confidence            999999988742 1  11   2344433333 3368999999999886654444

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

Probab=96.92  E-value=0.027  Score=51.80  Aligned_cols=83  Identities=17%  Similarity=0.167  Sum_probs=58.8

Q ss_pred             cCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccchh-hccch-HHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHh
Q 030094           50 EGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRL-LDMGF-QKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (183)
Q Consensus        50 ~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~l-l~~~~-~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~  127 (183)
                      ....|-+-|.|.|+..+.+  ...++.+.++|+||||.= ++.++ ...+..++...+.+-.++.+|||+..+   -...
T Consensus       138 ~~Trik~mTdGiLlrei~~--D~~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIimSATld~~---rfs~  212 (845)
T COG1643         138 PRTRIKVMTDGILLREIQN--DPLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMSATLDAE---RFSA  212 (845)
T ss_pred             CCceeEEeccHHHHHHHhh--CcccccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEEecccCHH---HHHH
Confidence            3567999999999999976  456899999999999973 23333 234455566666678899999999943   3445


Q ss_pred             hCCCCeEEEE
Q 030094          128 GLRNPVRVEV  137 (183)
Q Consensus       128 ~~~~~~~i~~  137 (183)
                      |+.++-.+.+
T Consensus       213 ~f~~apvi~i  222 (845)
T COG1643         213 YFGNAPVIEI  222 (845)
T ss_pred             HcCCCCEEEe
Confidence            5665444433

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

Probab=96.90  E-value=0.017  Score=48.25  Aligned_cols=122  Identities=18%  Similarity=0.237  Sum_probs=82.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHH--hcCCcEEEeCcHHHHH---HHHh-cCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIE--EEGANLLIGTPGRLYD---IMER-MDV   71 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~--~~~~~IiV~TP~~l~~---~l~~-~~~   71 (183)
                      ++|++||--.|.....-.++.+     ++....+....+.++..+   .+.  +....++-.||+++..   +|.+ .+.
T Consensus       136 ~alvi~plislmedqil~lkql-----gi~as~lnansske~~k~v~~~i~nkdse~kliyvtpekiaksk~~mnkleka  210 (695)
T KOG0353|consen  136 FALVICPLISLMEDQILQLKQL-----GIDASMLNANSSKEEAKRVEAAITNKDSEFKLIYVTPEKIAKSKKFMNKLEKA  210 (695)
T ss_pred             ceEeechhHHHHHHHHHHHHHh-----CcchhhccCcccHHHHHHHHHHHcCCCceeEEEEecHHHHHHHHHHHHHHHHH
Confidence            5899999999998776777777     455555555555443332   111  2346789999999854   2322 135


Q ss_pred             cCCCCceEEEEcccchhhccc--hHHHHH--HHHHhCCCCCeEEEEeecCChHHHHHHHh
Q 030094           72 LDFRNLEILVLDEADRLLDMG--FQKQIS--YIISRLPKLRRTGLFSATQTEAVEELSKA  127 (183)
Q Consensus        72 ~~l~~l~~lVvDEad~ll~~~--~~~~l~--~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~  127 (183)
                      +....++.+.+||+|....+|  |.++..  .++++--+..-++.++||-++.+..=++.
T Consensus       211 ~~~~~~~~iaidevhccsqwghdfr~dy~~l~ilkrqf~~~~iigltatatn~vl~d~k~  270 (695)
T KOG0353|consen  211 LEAGFFKLIAIDEVHCCSQWGHDFRPDYKALGILKRQFKGAPIIGLTATATNHVLDDAKD  270 (695)
T ss_pred             hhcceeEEEeecceeehhhhCcccCcchHHHHHHHHhCCCCceeeeehhhhcchhhHHHH
Confidence            677889999999999998765  555443  34444446778999999998887665543

>COG4096 HsdR Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=96.84  E-value=0.003  Score=57.02  Aligned_cols=103  Identities=17%  Similarity=0.225  Sum_probs=69.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhc----CCcCCCCc
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM----DVLDFRNL   77 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~----~~~~l~~l   77 (183)
                      +|+|+-.+.|+.|.+..+..+.   |.-.......+...        ...++|.|+|-.++...+...    ..+.+...
T Consensus       218 VLFLaDR~~Lv~QA~~af~~~~---P~~~~~n~i~~~~~--------~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~F  286 (875)
T COG4096         218 VLFLADRNALVDQAYGAFEDFL---PFGTKMNKIEDKKG--------DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFF  286 (875)
T ss_pred             eeEEechHHHHHHHHHHHHHhC---CCccceeeeecccC--------CcceeEEEeehHHHHhhhhccccccccCCCCce
Confidence            5899999999999999877764   44444333332221        124799999999999888762    24567778


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHH
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV  121 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v  121 (183)
                      .++|+||||+-.    ...-+.|+..+..-+|.+  +||..+.+
T Consensus       287 DlIvIDEaHRgi----~~~~~~I~dYFdA~~~gL--TATP~~~~  324 (875)
T COG4096         287 DLIVIDEAHRGI----YSEWSSILDYFDAATQGL--TATPKETI  324 (875)
T ss_pred             eEEEechhhhhH----HhhhHHHHHHHHHHHHhh--ccCccccc
Confidence            999999999953    334446666663323322  66666543

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

Probab=96.84  E-value=0.023  Score=52.49  Aligned_cols=122  Identities=15%  Similarity=0.089  Sum_probs=78.4

Q ss_pred             EeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcc
Q 030094            5 ISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDE   84 (183)
Q Consensus         5 l~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDE   84 (183)
                      =-|-|--|..+++.+..=.....+-.|..-++..+..       .....++.||-|.|++.+..  .-.+.++.++|+||
T Consensus       225 TQPRRIsAIsvAeRVa~ER~~~~g~~VGYqvrl~~~~-------s~~t~L~fcTtGvLLr~L~~--~~~l~~vthiivDE  295 (924)
T KOG0920|consen  225 TQPRRISAISVAERVAKERGESLGEEVGYQVRLESKR-------SRETRLLFCTTGVLLRRLQS--DPTLSGVTHIIVDE  295 (924)
T ss_pred             cCCchHHHHHHHHHHHHHhccccCCeeeEEEeeeccc-------CCceeEEEecHHHHHHHhcc--CcccccCceeeeee
Confidence            3477777777776665543222233344333333221       12367999999999999875  45688999999999


Q ss_pred             cchhh-ccchHH-HHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEcc
Q 030094           85 ADRLL-DMGFQK-QISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRA  139 (183)
Q Consensus        85 ad~ll-~~~~~~-~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~  139 (183)
                      +|.=- +.+|.- .++.++.. .+.-+++++|||+.   .+..+.|+..+-.|.+..
T Consensus       296 VHER~i~~DflLi~lk~lL~~-~p~LkvILMSAT~d---ae~fs~YF~~~pvi~i~g  348 (924)
T KOG0920|consen  296 VHERSINTDFLLILLKDLLPR-NPDLKVILMSATLD---AELFSDYFGGCPVITIPG  348 (924)
T ss_pred             EEEccCCcccHHHHHHHHhhh-CCCceEEEeeeecc---hHHHHHHhCCCceEeecC
Confidence            99742 233433 33333433 36789999999999   455666666666666654

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

Probab=96.84  E-value=0.018  Score=47.52  Aligned_cols=102  Identities=22%  Similarity=0.309  Sum_probs=66.6

Q ss_pred             EEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEE
Q 030094            3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVL   82 (183)
Q Consensus         3 lIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVv   82 (183)
                      .|-.|--+.+..++..++.   .+++..+.+++|+++-.        ....++|+|-..|++.-+   .+     +++++
T Consensus       148 ciASPRvDVclEl~~Rlk~---aF~~~~I~~Lyg~S~~~--------fr~plvVaTtHQLlrFk~---aF-----D~liI  208 (441)
T COG4098         148 CIASPRVDVCLELYPRLKQ---AFSNCDIDLLYGDSDSY--------FRAPLVVATTHQLLRFKQ---AF-----DLLII  208 (441)
T ss_pred             EEecCcccchHHHHHHHHH---hhccCCeeeEecCCchh--------ccccEEEEehHHHHHHHh---hc-----cEEEE
Confidence            3556777777766654444   45568899999977631        236789999887776643   34     48999


Q ss_pred             cccchhhccchHHHHHHHH-HhCCCCCeEEEEeecCChHHHHH
Q 030094           83 DEADRLLDMGFQKQISYII-SRLPKLRRTGLFSATQTEAVEEL  124 (183)
Q Consensus        83 DEad~ll~~~~~~~l~~i~-~~l~~~~Q~v~~SAT~~~~v~~~  124 (183)
                      ||+|..== .-...+.... +...+..-++++|||.+.+.+.=
T Consensus       209 DEVDAFP~-~~d~~L~~Av~~ark~~g~~IylTATp~k~l~r~  250 (441)
T COG4098         209 DEVDAFPF-SDDQSLQYAVKKARKKEGATIYLTATPTKKLERK  250 (441)
T ss_pred             eccccccc-cCCHHHHHHHHHhhcccCceEEEecCChHHHHHH
Confidence            99999621 1122333333 33345678999999999776543

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=96.60  E-value=0.0071  Score=55.02  Aligned_cols=136  Identities=16%  Similarity=0.127  Sum_probs=81.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH-------------HHHhcCCcEEEeCcHHHHHHHHh
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK-------------KIEEEGANLLIGTPGRLYDIMER   68 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~-------------~l~~~~~~IiV~TP~~l~~~l~~   68 (183)
                      .+.+.|+|.+..++++.++...... .+......|.........             ........+.++||..+......
T Consensus       249 ~i~vlP~~t~ie~~~~r~~~~~~~~-~~~~~~~h~~~~~~~~~~~~~~~~~~~~~~ds~~~~~~~~~~~~~~~~~~~~~~  327 (733)
T COG1203         249 VIYVLPFRTIIEDMYRRAKEIFGLF-SVIGKSLHSSSKEPLLLEPDQDILLTLTTNDSYKKLLLALIVVTPIQILIFSVK  327 (733)
T ss_pred             EEEEccHHHHHHHHHHHHHhhhccc-ccccccccccccchhhhccccccceeEEecccccceeccccccCHhHhhhhhcc
Confidence            4678999999999999999876543 222221222221110000             01112245667777665553222


Q ss_pred             cCCcC-CC--CceEEEEcccchhhccchHHHHHHHHHhCC-CCCeEEEEeecCChHHHHHHHhhCCCCeEEEEc
Q 030094           69 MDVLD-FR--NLEILVLDEADRLLDMGFQKQISYIISRLP-KLRRTGLFSATQTEAVEELSKAGLRNPVRVEVR  138 (183)
Q Consensus        69 ~~~~~-l~--~l~~lVvDEad~ll~~~~~~~l~~i~~~l~-~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~  138 (183)
                      ...+. +.  .-..+|+||+|.+-+......+..++..+. .+.-++++|||+|+..++.....+.+...+...
T Consensus       328 ~~~~~~~~~l~~S~vIlDE~h~~~~~~~~~~l~~~i~~l~~~g~~ill~SATlP~~~~~~l~~~~~~~~~~~~~  401 (733)
T COG1203         328 GFKFEFLALLLTSLVILDEVHLYADETMLAALLALLEALAEAGVPVLLMSATLPPFLKEKLKKALGKGREVVEN  401 (733)
T ss_pred             ccchHHHHHHHhhchhhccHHhhcccchHHHHHHHHHHHHhCCCCEEEEecCCCHHHHHHHHHHHhcccceecc
Confidence            11111 11  225789999999876534444444444443 367899999999999999999888777666554

>KOG0391 consensus SNF2 family DNA-dependent ATPase [General function prediction only]

Probab=96.50  E-value=0.0095  Score=55.90  Aligned_cols=108  Identities=17%  Similarity=0.238  Sum_probs=66.7

Q ss_pred             EEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH--HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK--KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         3 lIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~--~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      ||+|||.-+-. ....+++.   +|++++...+|...-....+  +.+.+..||.|++-..+..-+   ..|.-++.+++
T Consensus       669 LIVVpTsviLn-WEMElKRw---cPglKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~---~AFkrkrWqyL  741 (1958)
T KOG0391|consen  669 LIVVPTSVILN-WEMELKRW---CPGLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDL---TAFKRKRWQYL  741 (1958)
T ss_pred             eEEeechhhhh-hhHHHhhh---CCcceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHH---HHHHhhcccee
Confidence            79999976543 33445554   57899999998655333322  222345689999886665544   34666889999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeec-CChH
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT-QTEA  120 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT-~~~~  120 (183)
                      |+|||+.+=  +|...-...+-.++..+ .++++.| +.+.
T Consensus       742 vLDEaqnIK--nfksqrWQAllnfnsqr-RLLLtgTPLqNs  779 (1958)
T KOG0391|consen  742 VLDEAQNIK--NFKSQRWQALLNFNSQR-RLLLTGTPLQNS  779 (1958)
T ss_pred             ehhhhhhhc--chhHHHHHHHhccchhh-eeeecCCchhhH
Confidence            999999984  34443333333443344 4444555 4444

>PRK10689 transcription-repair coupling factor; Provisional

Probab=96.41  E-value=0.057  Score=51.51  Aligned_cols=78  Identities=14%  Similarity=0.221  Sum_probs=61.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +++|++|+++-+..+++.+.+.   .|+.++..+.|+.+.++..   ....++..+|+|||-     .+.  .++|+.++
T Consensus       811 qv~vf~n~i~~ie~la~~L~~~---~p~~~v~~lHG~m~q~eRe~im~~Fr~Gk~~VLVaTd-----Iie--rGIDIP~v  880 (1147)
T PRK10689        811 QVYYLYNDVENIQKAAERLAEL---VPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----IIE--TGIDIPTA  880 (1147)
T ss_pred             eEEEEECCHHHHHHHHHHHHHh---CCCCcEEEEeCCCCHHHHHHHHHHHHhcCCCEEEECc-----hhh--cccccccC
Confidence            5789999999888777766665   4678888999987655433   344567899999994     565  48999999


Q ss_pred             eEEEEcccchh
Q 030094           78 EILVLDEADRL   88 (183)
Q Consensus        78 ~~lVvDEad~l   88 (183)
                      .++|++.+|++
T Consensus       881 ~~VIi~~ad~f  891 (1147)
T PRK10689        881 NTIIIERADHF  891 (1147)
T ss_pred             CEEEEecCCCC
Confidence            99999999874

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=96.37  E-value=0.015  Score=53.43  Aligned_cols=89  Identities=13%  Similarity=0.051  Sum_probs=72.1

Q ss_pred             CCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC------hHHHHH
Q 030094           51 GANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT------EAVEEL  124 (183)
Q Consensus        51 ~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~------~~v~~~  124 (183)
                      .-.|+++||..|..-+-. +.++++.+..+|+||||++.+......+-++.+.-++..-+.+|||...      .++...
T Consensus         7 ~ggi~~~T~rIl~~DlL~-~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr~~n~~gfIkafSdsP~~~~~g~~~l~~v   85 (814)
T TIGR00596         7 EGGIFSITSRILVVDLLT-GIIPPELITGILVLRADRIIESSQEAFILRLYRQKNKTGFIKAFSDNPEAFTMGFSPLETK   85 (814)
T ss_pred             cCCEEEEechhhHhHHhc-CCCCHHHccEEEEeecccccccccHHHHHHHHHHhCCCcceEEecCCCcccccchHHHHHH
Confidence            357999999998766656 7899999999999999999988778888888888888888999999976      457777


Q ss_pred             HHhhCCCCeEEEEccC
Q 030094          125 SKAGLRNPVRVEVRAE  140 (183)
Q Consensus       125 ~~~~~~~~~~i~~~~~  140 (183)
                      ++...-.-+.+.-...
T Consensus        86 mk~L~i~~v~l~prf~  101 (814)
T TIGR00596        86 MRNLFLRHVYLWPRFH  101 (814)
T ss_pred             HHHhCcCeEEEeCCCc
Confidence            7776655566654433

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

>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=96.27  E-value=0.0058  Score=54.39  Aligned_cols=126  Identities=17%  Similarity=0.158  Sum_probs=72.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHH----HHHhcCC-cCCCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYD----IMERMDV-LDFRN   76 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~----~l~~~~~-~~l~~   76 (183)
                      .||+||-+- ..|.+..+.+-.... -++|...+|....+...+.+.  ..||+|+|..-+..    -.+..+. --+-.
T Consensus       386 TLII~PaSl-i~qW~~Ev~~rl~~n-~LsV~~~HG~n~r~i~~~~L~--~YDvViTTY~lva~~~~~e~~~~~~~spL~~  461 (901)
T KOG4439|consen  386 TLIICPASL-IHQWEAEVARRLEQN-ALSVYLYHGPNKREISAKELR--KYDVVITTYNLVANKPDDELEEGKNSSPLAR  461 (901)
T ss_pred             eEEeCcHHH-HHHHHHHHHHHHhhc-ceEEEEecCCccccCCHHHHh--hcceEEEeeeccccCCchhhhcccCccHHHH
Confidence            489999654 455555444433343 689999998876655566663  57999999855444    1111011 11333


Q ss_pred             c--eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeec-CChHHHHHHH--hhCCCCeE
Q 030094           77 L--EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT-QTEAVEELSK--AGLRNPVR  134 (183)
Q Consensus        77 l--~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT-~~~~v~~~~~--~~~~~~~~  134 (183)
                      +  .-+|+||||.+-+.  ..+-...+..+...++ +++|+| +.+....+..  .|++.|-+
T Consensus       462 I~W~RVILDEAH~IrN~--~tq~S~AVC~L~a~~R-WclTGTPiqNn~~DvysLlrFLr~~pF  521 (901)
T KOG4439|consen  462 IAWSRVILDEAHNIRNS--NTQCSKAVCKLSAKSR-WCLTGTPIQNNLWDVYSLLRFLRCPPF  521 (901)
T ss_pred             hhHHHhhhhhhhhhccc--chhHHHHHHHHhhcce-eecccCccccchhHHHHHHHHhcCCCc
Confidence            3  35899999998543  3333344455544444 445565 4555455444  35555543

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=96.23  E-value=0.026  Score=52.65  Aligned_cols=78  Identities=14%  Similarity=0.244  Sum_probs=61.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +++|+||+.+-+..+++.++++   .|+.++..+.|+.+.++..   ....++..+|+|||-     .+.  .++|..++
T Consensus       662 qv~if~n~i~~~e~l~~~L~~~---~p~~~v~~lHG~m~~~eRe~im~~F~~Gk~~ILVaT~-----iie--~GIDIp~v  731 (926)
T TIGR00580       662 QVFYVHNRIESIEKLATQLREL---VPEARIAIAHGQMTENELEEVMLEFYKGEFQVLVCTT-----IIE--TGIDIPNA  731 (926)
T ss_pred             eEEEEECCcHHHHHHHHHHHHh---CCCCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEECC-----hhh--cccccccC
Confidence            5789999999988888777765   3578999999987654433   344567899999995     565  48999999


Q ss_pred             eEEEEcccchh
Q 030094           78 EILVLDEADRL   88 (183)
Q Consensus        78 ~~lVvDEad~l   88 (183)
                      .++|++.+|+.
T Consensus       732 ~~VIi~~a~~~  742 (926)
T TIGR00580       732 NTIIIERADKF  742 (926)
T ss_pred             CEEEEecCCCC
Confidence            99999999874

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.

>KOG0392 consensus SNF2 family DNA-dependent ATPase domain-containing protein [Transcription]

Probab=96.10  E-value=0.034  Score=52.45  Aligned_cols=119  Identities=18%  Similarity=0.212  Sum_probs=75.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||+||+- |+--...++.+   ++|.+++...+|+...+...+.- -++.+|+|++-..+.+-+..   +.-...-++|
T Consensus      1034 SLIVCPsT-LtGHW~~E~~k---f~pfL~v~~yvg~p~~r~~lR~q-~~~~~iiVtSYDv~RnD~d~---l~~~~wNYcV 1105 (1549)
T KOG0392|consen 1034 SLIVCPST-LTGHWKSEVKK---FFPFLKVLQYVGPPAERRELRDQ-YKNANIIVTSYDVVRNDVDY---LIKIDWNYCV 1105 (1549)
T ss_pred             eEEECCch-hhhHHHHHHHH---hcchhhhhhhcCChHHHHHHHhh-ccccceEEeeHHHHHHHHHH---HHhcccceEE
Confidence            68999964 45544444444   45667888888877655554433 24689999998776532221   1112344899


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecC-ChHHH---HHHHhhCCC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ-TEAVE---ELSKAGLRN  131 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~-~~~v~---~~~~~~~~~  131 (183)
                      +||-|.+=  +-...+...++.+..+++.|+ |.|. .+.+.   .+....|+.
T Consensus      1106 LDEGHVik--N~ktkl~kavkqL~a~hRLIL-SGTPIQNnvleLWSLFdFLMPG 1156 (1549)
T KOG0392|consen 1106 LDEGHVIK--NSKTKLTKAVKQLRANHRLIL-SGTPIQNNVLELWSLFDFLMPG 1156 (1549)
T ss_pred             ecCcceec--chHHHHHHHHHHHhhcceEEe-eCCCcccCHHHHHHHHHHhccc
Confidence            99999984  346777777888866666665 6664 45444   445555553

>COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]

Probab=96.05  E-value=0.06  Score=50.53  Aligned_cols=108  Identities=13%  Similarity=0.150  Sum_probs=71.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce-EE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE-IL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~-~l   80 (183)
                      +++||=.++|-.|+.+.+..+.....  ...   ...+..+-.+.+.+..-.|+|+|=+++.............+-. .+
T Consensus       306 v~fvvDR~dLd~Q~~~~f~~~~~~~~--~~~---~~~s~~~Lk~~l~~~~~~ii~TTIQKf~~~~~~~~~~~~~~~~ivv  380 (962)
T COG0610         306 VLFVVDRKDLDDQTSDEFQSFGKVAF--NDP---KAESTSELKELLEDGKGKIIVTTIQKFNKAVKEDELELLKRKNVVV  380 (962)
T ss_pred             EEEEechHHHHHHHHHHHHHHHHhhh--hcc---cccCHHHHHHHHhcCCCcEEEEEecccchhhhcccccccCCCcEEE
Confidence            58899999999999999999975432  111   3344444444453333489999999999988762122233333 67


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      |+||||+-   .++..-..+-..+ ++...++|+.|.-
T Consensus       381 I~DEaHRS---Q~G~~~~~~~~~~-~~a~~~gFTGTPi  414 (962)
T COG0610         381 IIDEAHRS---QYGELAKLLKKAL-KKAIFIGFTGTPI  414 (962)
T ss_pred             EEechhhc---cccHHHHHHHHHh-ccceEEEeeCCcc
Confidence            99999995   2333333334444 4588999999964

>KOG3089 consensus Predicted DEAD-box-containing helicase [General function prediction only]

Probab=96.00  E-value=0.014  Score=45.04  Aligned_cols=44  Identities=30%  Similarity=0.565  Sum_probs=36.8

Q ss_pred             HHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEccc
Q 030094           41 KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEA   85 (183)
Q Consensus        41 ~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEa   85 (183)
                      +++.........++-||||+|+.++++. +++..+.++++|+|=.
T Consensus       186 ~~~~k~~k~~~v~~gIgTp~Ri~~lv~~-~~f~~~~lk~iIlD~s  229 (271)
T KOG3089|consen  186 QAQVKLLKKRVVHLGIGTPGRIKELVKQ-GGFNLSPLKFIILDWS  229 (271)
T ss_pred             HHHHHHHhhcceeEeecCcHHHHHHHHh-cCCCCCcceeEEeecc
Confidence            4555555566789999999999999998 7899999999998853

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

Probab=95.73  E-value=0.38  Score=42.89  Aligned_cols=83  Identities=16%  Similarity=0.117  Sum_probs=53.6

Q ss_pred             CCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccchhh-ccc-hHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhh
Q 030094           51 GANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLL-DMG-FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAG  128 (183)
Q Consensus        51 ~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~ll-~~~-~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~  128 (183)
                      ...|..-|-|.|++-+-.  .-.++.-.++|+||||.=- ..+ ....++.+++.- ++-.++++|||+.   .+..+.|
T Consensus       140 ~TrikymTDG~LLRE~l~--Dp~LskYsvIIlDEAHERsl~TDiLlGlLKki~~~R-~~LklIimSATld---a~kfS~y  213 (674)
T KOG0922|consen  140 DTRIKYMTDGMLLREILK--DPLLSKYSVIILDEAHERSLHTDILLGLLKKILKKR-PDLKLIIMSATLD---AEKFSEY  213 (674)
T ss_pred             ceeEEEecchHHHHHHhc--CCccccccEEEEechhhhhhHHHHHHHHHHHHHhcC-CCceEEEEeeeec---HHHHHHH
Confidence            457899999999887754  4567889999999999721 111 122333333332 3458999999999   3345566


Q ss_pred             CCCCeEEEEcc
Q 030094          129 LRNPVRVEVRA  139 (183)
Q Consensus       129 ~~~~~~i~~~~  139 (183)
                      +.+.-.+.+..
T Consensus       214 F~~a~i~~i~G  224 (674)
T KOG0922|consen  214 FNNAPILTIPG  224 (674)
T ss_pred             hcCCceEeecC
Confidence            66644444433

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=95.55  E-value=0.34  Score=43.71  Aligned_cols=114  Identities=11%  Similarity=0.267  Sum_probs=73.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHH---HHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKAD---VKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~---~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      ++|.|+|++.|..+.+.+...     ++.+..+.|+....+.   ...+..+..+|+|||     ..+.  .++++..++
T Consensus       445 vLIf~~tk~~ae~L~~~L~~~-----gi~~~~lh~~~~~~eR~~~l~~fr~G~i~VLV~t-----~~L~--rGfDiP~v~  512 (655)
T TIGR00631       445 VLVTTLTKKMAEDLTDYLKEL-----GIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGI-----NLLR--EGLDLPEVS  512 (655)
T ss_pred             EEEEECCHHHHHHHHHHHhhh-----ccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEc-----Chhc--CCeeeCCCc
Confidence            689999999999998887765     5677777776554333   334445779999999     3554  589999999


Q ss_pred             EEEEcccchhhccchHHHHHHHHHhCCC--CCeEEEEeecCChHHHHHHHh
Q 030094           79 ILVLDEADRLLDMGFQKQISYIISRLPK--LRRTGLFSATQTEAVEELSKA  127 (183)
Q Consensus        79 ~lVvDEad~ll~~~~~~~l~~i~~~l~~--~~Q~v~~SAT~~~~v~~~~~~  127 (183)
                      ++|+-++|..--......+-+...+..+  ....+++--..+..+...+..
T Consensus       513 lVvi~DadifG~p~~~~~~iqriGRagR~~~G~vi~~~~~~~~~~~~ai~~  563 (655)
T TIGR00631       513 LVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQKAIEE  563 (655)
T ss_pred             EEEEeCcccccCCCCHHHHHHHhcCCCCCCCCEEEEEEcCCCHHHHHHHHH
Confidence            9999888884211112222233333222  335666666676555544443

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

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=95.50  E-value=0.022  Score=53.17  Aligned_cols=72  Identities=22%  Similarity=0.062  Sum_probs=46.2

Q ss_pred             CCcEEEeCcHHHHHHHHhc--CCcCCC--C--ceEEEEcccchhhccchHHHHHHHHHhCC-CCCeEEEEeecCChHHHH
Q 030094           51 GANLLIGTPGRLYDIMERM--DVLDFR--N--LEILVLDEADRLLDMGFQKQISYIISRLP-KLRRTGLFSATQTEAVEE  123 (183)
Q Consensus        51 ~~~IiV~TP~~l~~~l~~~--~~~~l~--~--l~~lVvDEad~ll~~~~~~~l~~i~~~l~-~~~Q~v~~SAT~~~~v~~  123 (183)
                      ...++|||+.-++......  +...+.  .  =+.+|+||+|..-. .....+..+++-.. -...++++|||+|+.+..
T Consensus       562 ~apv~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaYD~-~~~~~L~rlL~w~~~lG~~VlLmSATLP~~l~~  640 (1110)
T TIGR02562       562 AAPVLVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDYEP-EDLPALLRLVQLAGLLGSRVLLSSATLPPALVK  640 (1110)
T ss_pred             cCCeEEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccCCH-HHHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHH
Confidence            3689999999988876321  111111  1  15799999999632 22334444444222 257889999999998654

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.

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=95.37  E-value=0.09  Score=44.61  Aligned_cols=71  Identities=15%  Similarity=0.212  Sum_probs=53.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|+|++-|..+++.+...     +.++..+.|+...+++..   ....+.++|+|||.     .+.  .++|+.++
T Consensus       257 ~~lVF~~t~~~~~~l~~~L~~~-----g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTd-----v~~--rGiDip~v  324 (423)
T PRK04837        257 RAIIFANTKHRCEEIWGHLAAD-----GHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATD-----VAA--RGLHIPAV  324 (423)
T ss_pred             eEEEEECCHHHHHHHHHHHHhC-----CCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEec-----hhh--cCCCcccc
Confidence            3799999999999888877653     678888898876544433   44457899999994     454  57999999


Q ss_pred             eEEEEc
Q 030094           78 EILVLD   83 (183)
Q Consensus        78 ~~lVvD   83 (183)
                      +++|.-
T Consensus       325 ~~VI~~  330 (423)
T PRK04837        325 THVFNY  330 (423)
T ss_pred             CEEEEe
Confidence            988743

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=95.33  E-value=0.15  Score=45.31  Aligned_cols=73  Identities=12%  Similarity=0.200  Sum_probs=55.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|+|++.|.++++.+.+.     ++++..+.|+.+..+...   ...++..+|+|+|.     .+.  .++|+.++
T Consensus       259 k~LVF~nt~~~ae~l~~~L~~~-----g~~v~~lhg~l~~~eR~~il~~Fr~G~~~VLVaTd-----v~a--rGIDip~V  326 (572)
T PRK04537        259 RTMVFVNTKAFVERVARTLERH-----GYRVGVLSGDVPQKKRESLLNRFQKGQLEILVATD-----VAA--RGLHIDGV  326 (572)
T ss_pred             cEEEEeCCHHHHHHHHHHHHHc-----CCCEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEeh-----hhh--cCCCccCC
Confidence            3799999999999998877654     578889998876544433   34456789999994     554  47999999


Q ss_pred             eEEEEccc
Q 030094           78 EILVLDEA   85 (183)
Q Consensus        78 ~~lVvDEa   85 (183)
                      .++|.-+.
T Consensus       327 ~~VInyd~  334 (572)
T PRK04537        327 KYVYNYDL  334 (572)
T ss_pred             CEEEEcCC
Confidence            98886443

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=95.26  E-value=0.37  Score=43.24  Aligned_cols=81  Identities=20%  Similarity=0.358  Sum_probs=55.4

Q ss_pred             CEEEEeCcHHHH-----HHHHHHHHHhhhhCCCceEEEEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCc
Q 030094            1 MGMIISPTRELS-----SQIYHVAQPFISTLPDVKSVLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVL   72 (183)
Q Consensus         1 ~alIl~PtreLa-----~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~   72 (183)
                      +++|+||+.+-.     ....+.+..+...+++.++..+.|+.+.++..   +....+..+|+|||.     .+.  .++
T Consensus       450 q~~v~~~~i~~s~~~~~~~a~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~-----vie--~Gv  522 (630)
T TIGR00643       450 QAYVVYPLIEESEKLDLKAAEALYERLKKAFPKYNVGLLHGRMKSDEKEAVMEEFREGEVDILVATT-----VIE--VGV  522 (630)
T ss_pred             cEEEEEccccccccchHHHHHHHHHHHHhhCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECc-----eee--cCc
Confidence            578899976421     22223334444444688999999987654443   344456799999995     444  589


Q ss_pred             CCCCceEEEEcccchh
Q 030094           73 DFRNLEILVLDEADRL   88 (183)
Q Consensus        73 ~l~~l~~lVvDEad~l   88 (183)
                      |+.++.++|+..++..
T Consensus       523 DiP~v~~VIi~~~~r~  538 (630)
T TIGR00643       523 DVPNATVMVIEDAERF  538 (630)
T ss_pred             ccCCCcEEEEeCCCcC
Confidence            9999999999888874

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=95.21  E-value=0.39  Score=43.51  Aligned_cols=81  Identities=17%  Similarity=0.333  Sum_probs=55.6

Q ss_pred             CEEEEeCcHHH-----HHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCc
Q 030094            1 MGMIISPTREL-----SSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVL   72 (183)
Q Consensus         1 ~alIl~PtreL-----a~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~   72 (183)
                      +++|+||+.+-     .....+.+..+...+++.++..+.|+.+.++...   ...++..+|+|||.     .+.  .++
T Consensus       473 q~~v~~~~ie~s~~l~~~~~~~~~~~L~~~~~~~~v~~lHG~m~~~eR~~i~~~F~~g~~~ILVaT~-----vie--~Gi  545 (681)
T PRK10917        473 QAYVVCPLIEESEKLDLQSAEETYEELQEAFPELRVGLLHGRMKPAEKDAVMAAFKAGEIDILVATT-----VIE--VGV  545 (681)
T ss_pred             cEEEEEcccccccchhHHHHHHHHHHHHHHCCCCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEECc-----cee--eCc
Confidence            57899996431     1122334444544555688999999876544433   34456789999995     454  479


Q ss_pred             CCCCceEEEEcccchh
Q 030094           73 DFRNLEILVLDEADRL   88 (183)
Q Consensus        73 ~l~~l~~lVvDEad~l   88 (183)
                      |..++.++|+..+++.
T Consensus       546 Dip~v~~VIi~~~~r~  561 (681)
T PRK10917        546 DVPNATVMVIENAERF  561 (681)
T ss_pred             ccCCCcEEEEeCCCCC
Confidence            9999999999999874

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=95.05  E-value=0.59  Score=42.85  Aligned_cols=123  Identities=12%  Similarity=0.123  Sum_probs=77.3

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +|++...+.|+.+....++.-  +++++....-.++....       ....+-++..-+.|.++-    .-.+++.+++|
T Consensus        81 VLvVShRrSL~~sL~~rf~~~--~l~gFv~Y~d~~~~~i~-------~~~~~rLivqIdSL~R~~----~~~l~~yDvVI  147 (824)
T PF02399_consen   81 VLVVSHRRSLTKSLAERFKKA--GLSGFVNYLDSDDYIID-------GRPYDRLIVQIDSLHRLD----GSLLDRYDVVI  147 (824)
T ss_pred             EEEEEhHHHHHHHHHHHHhhc--CCCcceeeecccccccc-------ccccCeEEEEehhhhhcc----cccccccCEEE
Confidence            578889999999888766653  22344443333322211       123466666666665542    23466788999


Q ss_pred             EcccchhhccchHHHHHH-------HHHhCCCCCeEEEEeecCChHHHHHHHhhCCC-CeEEEE
Q 030094           82 LDEADRLLDMGFQKQISY-------IISRLPKLRRTGLFSATQTEAVEELSKAGLRN-PVRVEV  137 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~-------i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~-~~~i~~  137 (183)
                      +||+...++.-|.+.|++       +...+.+...+|++-|++++..-+|+....++ ++.+.+
T Consensus       148 IDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tvdFl~~~Rp~~~i~vI~  211 (824)
T PF02399_consen  148 IDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTVDFLASCRPDENIHVIV  211 (824)
T ss_pred             EehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHHHHHHHhCCCCcEEEEE
Confidence            999999987533222222       22333456789999999999999999987653 334433

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

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

Probab=94.84  E-value=0.18  Score=44.17  Aligned_cols=69  Identities=14%  Similarity=0.236  Sum_probs=54.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|.|+..|..++..+.+.     ++++..++|+.+..+..+   ...++..+|+|||-     ...  .++|..++
T Consensus       275 ~~IVF~~tk~~~~~l~~~l~~~-----g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTD-----vaa--RGiDi~~v  342 (513)
T COG0513         275 RVIVFVRTKRLVEELAESLRKR-----GFKVAALHGDLPQEERDRALEKFKDGELRVLVATD-----VAA--RGLDIPDV  342 (513)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHC-----CCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEec-----hhh--ccCCcccc
Confidence            3899999999999987766665     688999999987554444   44567899999994     443  58999999


Q ss_pred             eEEE
Q 030094           78 EILV   81 (183)
Q Consensus        78 ~~lV   81 (183)
                      .++|
T Consensus       343 ~~Vi  346 (513)
T COG0513         343 SHVI  346 (513)
T ss_pred             ceeE
Confidence            9886

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=94.78  E-value=0.19  Score=43.39  Aligned_cols=73  Identities=16%  Similarity=0.274  Sum_probs=55.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|+.-|.++++.+.+.     ++++..+.|+.+.++...   ....+.++|+|||-     .+.  .++|+.+++
T Consensus       229 ~IIF~~s~~~~e~la~~L~~~-----g~~~~~~H~~l~~~eR~~i~~~F~~g~~~vLVaT~-----~~~--~GID~p~V~  296 (470)
T TIGR00614       229 GIIYCPSRKKSEQVTASLQNL-----GIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATV-----AFG--MGINKPDVR  296 (470)
T ss_pred             eEEEECcHHHHHHHHHHHHhc-----CCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEec-----hhh--ccCCcccce
Confidence            589999999999998887764     677888888877554433   34457899999995     343  579999999


Q ss_pred             EEEEcccc
Q 030094           79 ILVLDEAD   86 (183)
Q Consensus        79 ~lVvDEad   86 (183)
                      ++|.-..-
T Consensus       297 ~VI~~~~P  304 (470)
T TIGR00614       297 FVIHYSLP  304 (470)
T ss_pred             EEEEeCCC
Confidence            99865543

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

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=94.76  E-value=0.22  Score=42.76  Aligned_cols=70  Identities=16%  Similarity=0.212  Sum_probs=52.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|+|++-|..+++.+.+.     ++.+..+.|+.+..+...   ...++..+|+|||-     .+.  .++|+.++
T Consensus       247 ~~lVF~~t~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTd-----v~~--rGiDip~v  314 (456)
T PRK10590        247 QVLVFTRTKHGANHLAEQLNKD-----GIRSAAIHGNKSQGARTRALADFKSGDIRVLVATD-----IAA--RGLDIEEL  314 (456)
T ss_pred             cEEEEcCcHHHHHHHHHHHHHC-----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcc-----HHh--cCCCcccC
Confidence            3699999999999888877653     677888898877544433   34456789999994     454  47999999


Q ss_pred             eEEEE
Q 030094           78 EILVL   82 (183)
Q Consensus        78 ~~lVv   82 (183)
                      .++|.
T Consensus       315 ~~VI~  319 (456)
T PRK10590        315 PHVVN  319 (456)
T ss_pred             CEEEE
Confidence            98874

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=94.60  E-value=0.18  Score=42.87  Aligned_cols=69  Identities=13%  Similarity=0.237  Sum_probs=53.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-|..+++.+...     ++++..+.|+.+..+...   ...++..+|+|||-     .+.  .++|+.++.
T Consensus       248 ~lVF~~s~~~~~~l~~~L~~~-----~~~~~~l~g~~~~~~R~~~l~~f~~G~~~vLVaTd-----~~~--~GiDip~v~  315 (434)
T PRK11192        248 SIVFVRTRERVHELAGWLRKA-----GINCCYLEGEMVQAKRNEAIKRLTDGRVNVLVATD-----VAA--RGIDIDDVS  315 (434)
T ss_pred             EEEEeCChHHHHHHHHHHHhC-----CCCEEEecCCCCHHHHHHHHHHHhCCCCcEEEEcc-----ccc--cCccCCCCC
Confidence            799999999999998887663     678888888876554433   44457799999994     443  578999999


Q ss_pred             EEEE
Q 030094           79 ILVL   82 (183)
Q Consensus        79 ~lVv   82 (183)
                      ++|.
T Consensus       316 ~VI~  319 (434)
T PRK11192        316 HVIN  319 (434)
T ss_pred             EEEE
Confidence            8874

>PRK05580 primosome assembly protein PriA; Validated

Probab=94.57  E-value=0.85  Score=41.38  Aligned_cols=98  Identities=15%  Similarity=0.185  Sum_probs=61.5

Q ss_pred             HHHHHHHHHHHhhhhCCCceEEEEEcCcc-----hHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEccc
Q 030094           11 LSSQIYHVAQPFISTLPDVKSVLLVGGVE-----VKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEA   85 (183)
Q Consensus        11 La~Qi~~~~~~l~~~~~~~~~~~~~g~~~-----~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEa   85 (183)
                      =+.++.+.+++   .+|+.++..+.+...     .+.......++.++|+|||.     ++.  +++|+.++.++++-.|
T Consensus       438 G~e~~~e~l~~---~fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~-----~ia--kG~d~p~v~lV~il~a  507 (679)
T PRK05580        438 GTERLEEELAE---LFPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQ-----MLA--KGHDFPNVTLVGVLDA  507 (679)
T ss_pred             cHHHHHHHHHH---hCCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEECh-----hhc--cCCCCCCcCEEEEEcC
Confidence            34455555544   457788877776543     33334556567899999997     343  5799999999999999


Q ss_pred             chhhccc-h------HHHHHHHHHhCC---CCCeEEEEeecCC
Q 030094           86 DRLLDMG-F------QKQISYIISRLP---KLRRTGLFSATQT  118 (183)
Q Consensus        86 d~ll~~~-~------~~~l~~i~~~l~---~~~Q~v~~SAT~~  118 (183)
                      |..+... |      ...+.....+.+   +....++.|....
T Consensus       508 D~~l~~pdfra~Er~~~~l~q~~GRagR~~~~g~viiqT~~p~  550 (679)
T PRK05580        508 DLGLFSPDFRASERTFQLLTQVAGRAGRAEKPGEVLIQTYHPE  550 (679)
T ss_pred             chhccCCccchHHHHHHHHHHHHhhccCCCCCCEEEEEeCCCC
Confidence            9987542 2      122333333332   3456676666554

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=94.50  E-value=0.2  Score=43.02  Aligned_cols=72  Identities=15%  Similarity=0.278  Sum_probs=54.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-|..+++.+...     ++.+..++|+.+..++..   ...++..+|+|||-     .+.  .++|+.++.
T Consensus       245 ~lVF~~t~~~~~~l~~~L~~~-----~~~v~~~hg~~~~~eR~~~l~~F~~g~~~vLVaTd-----v~~--rGiDi~~v~  312 (460)
T PRK11776        245 CVVFCNTKKECQEVADALNAQ-----GFSALALHGDLEQRDRDQVLVRFANRSCSVLVATD-----VAA--RGLDIKALE  312 (460)
T ss_pred             eEEEECCHHHHHHHHHHHHhC-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEec-----ccc--cccchhcCC
Confidence            799999999999998877664     677888899877554433   33456789999994     444  479999999


Q ss_pred             EEEEccc
Q 030094           79 ILVLDEA   85 (183)
Q Consensus        79 ~lVvDEa   85 (183)
                      ++|.-+.
T Consensus       313 ~VI~~d~  319 (460)
T PRK11776        313 AVINYEL  319 (460)
T ss_pred             eEEEecC
Confidence            8885443

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=94.29  E-value=0.28  Score=44.04  Aligned_cols=70  Identities=16%  Similarity=0.282  Sum_probs=52.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHH---HHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKAD---VKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~---~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|+|+.-+.++++.+...     ++.+..+.|+.+..+.   ...+..+..+|+|||-     .+.  .++|+.++
T Consensus       247 ~~IVF~~tk~~a~~l~~~L~~~-----g~~~~~lhgd~~q~~R~~il~~Fr~G~~~ILVATd-----v~a--rGIDip~V  314 (629)
T PRK11634        247 AAIIFVRTKNATLEVAEALERN-----GYNSAALNGDMNQALREQTLERLKDGRLDILIATD-----VAA--RGLDVERI  314 (629)
T ss_pred             CEEEEeccHHHHHHHHHHHHhC-----CCCEEEeeCCCCHHHHHHHHHHHhCCCCCEEEEcc-----hHh--cCCCcccC
Confidence            4799999999999988877653     5678888887665443   3344567899999994     454  46888888


Q ss_pred             eEEEE
Q 030094           78 EILVL   82 (183)
Q Consensus        78 ~~lVv   82 (183)
                      .++|.
T Consensus       315 ~~VI~  319 (629)
T PRK11634        315 SLVVN  319 (629)
T ss_pred             CEEEE
Confidence            88774

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=94.12  E-value=0.31  Score=42.04  Aligned_cols=71  Identities=13%  Similarity=0.154  Sum_probs=53.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|++++-|..+++.+.+.     ++++..+.|+...+++..   ...++...|+|+|.     .+.  .++|+.++
T Consensus       337 ~~IVF~~s~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~R~~~~~~Fr~G~~~vLvaT~-----~l~--~GIDi~~v  404 (475)
T PRK01297        337 RVMVFANRKDEVRRIEERLVKD-----GINAAQLSGDVPQHKRIKTLEGFREGKIRVLVATD-----VAG--RGIHIDGI  404 (475)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHhCCCCcEEEEcc-----ccc--cCCcccCC
Confidence            3799999999999988777553     567788888776554433   44456789999994     554  47999999


Q ss_pred             eEEEEc
Q 030094           78 EILVLD   83 (183)
Q Consensus        78 ~~lVvD   83 (183)
                      .++|.-
T Consensus       405 ~~VI~~  410 (475)
T PRK01297        405 SHVINF  410 (475)
T ss_pred             CEEEEe
Confidence            988854

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=94.03  E-value=0.53  Score=44.23  Aligned_cols=39  Identities=23%  Similarity=0.319  Sum_probs=29.0

Q ss_pred             CCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccchhhc
Q 030094           51 GANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLD   90 (183)
Q Consensus        51 ~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~ll~   90 (183)
                      .+||+|++..-|...+...+.+ +-.-+++|+||||++-+
T Consensus       431 ~AdivItNHalLl~dl~~~~~i-lp~~~~lViDEAH~l~d  469 (928)
T PRK08074        431 FADLVITNHALLLTDLTSEEPL-LPSYEHIIIDEAHHFEE  469 (928)
T ss_pred             cCCEEEECHHHHHHHHhhhccc-CCCCCeEEEECCchHHH
Confidence            3799999999887776441222 34468999999999964

>PTZ00110 helicase; Provisional

Probab=94.02  E-value=0.35  Score=42.67  Aligned_cols=69  Identities=10%  Similarity=0.156  Sum_probs=52.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-|..+.+.++..     ++.+..+.|+....++.   ....++...|+|||.     .+.  .++|+.++.
T Consensus       380 ~LIF~~t~~~a~~l~~~L~~~-----g~~~~~ihg~~~~~eR~~il~~F~~G~~~ILVaTd-----v~~--rGIDi~~v~  447 (545)
T PTZ00110        380 ILIFVETKKGADFLTKELRLD-----GWPALCIHGDKKQEERTWVLNEFKTGKSPIMIATD-----VAS--RGLDVKDVK  447 (545)
T ss_pred             EEEEecChHHHHHHHHHHHHc-----CCcEEEEECCCcHHHHHHHHHHHhcCCCcEEEEcc-----hhh--cCCCcccCC
Confidence            799999999999888877642     56778888887755443   344456789999994     444  579999999


Q ss_pred             EEEE
Q 030094           79 ILVL   82 (183)
Q Consensus        79 ~lVv   82 (183)
                      ++|.
T Consensus       448 ~VI~  451 (545)
T PTZ00110        448 YVIN  451 (545)
T ss_pred             EEEE
Confidence            9885

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=93.97  E-value=1.2  Score=40.30  Aligned_cols=75  Identities=12%  Similarity=0.323  Sum_probs=56.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHH---HHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKAD---VKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~---~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      ++|+|+|+.-|..+.+.+...     ++++..+.|+....+.   ......++.+|+|||-     .+.  .++++..++
T Consensus       449 viIf~~t~~~ae~L~~~L~~~-----gi~~~~~h~~~~~~~R~~~l~~f~~g~i~vlV~t~-----~L~--rGfdlp~v~  516 (652)
T PRK05298        449 VLVTTLTKRMAEDLTDYLKEL-----GIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGIN-----LLR--EGLDIPEVS  516 (652)
T ss_pred             EEEEeCCHHHHHHHHHHHhhc-----ceeEEEEECCCCHHHHHHHHHHHHcCCceEEEEeC-----HHh--CCccccCCc
Confidence            789999999999888877664     6778888777654333   2344456789999994     454  589999999


Q ss_pred             EEEEcccchh
Q 030094           79 ILVLDEADRL   88 (183)
Q Consensus        79 ~lVvDEad~l   88 (183)
                      ++|+=|++..
T Consensus       517 lVii~d~eif  526 (652)
T PRK05298        517 LVAILDADKE  526 (652)
T ss_pred             EEEEeCCccc
Confidence            9988778753

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

Probab=93.84  E-value=0.26  Score=47.04  Aligned_cols=111  Identities=21%  Similarity=0.356  Sum_probs=77.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      |+.++|..+.+...++...+-.....+.++.-+.|..+.+-..  +  ..-+|+|+||++...+ +     ....++++|
T Consensus      1189 ~vyi~p~~~i~~~~~~~w~~~f~~~~G~~~~~l~ge~s~~lkl--~--~~~~vii~tpe~~d~l-q-----~iQ~v~l~i 1258 (1674)
T KOG0951|consen 1189 AVYIAPLEEIADEQYRDWEKKFSKLLGLRIVKLTGETSLDLKL--L--QKGQVIISTPEQWDLL-Q-----SIQQVDLFI 1258 (1674)
T ss_pred             EEEecchHHHHHHHHHHHHHhhccccCceEEecCCccccchHH--h--hhcceEEechhHHHHH-h-----hhhhcceEe
Confidence            6789999999986666554433333478888888776654332  2  3468999999986655 2     456788999


Q ss_pred             Ecccchhhccc------hHHHHHHHHHhCCCCCeEEEEeecCChHHHHH
Q 030094           82 LDEADRLLDMG------FQKQISYIISRLPKLRRTGLFSATQTEAVEEL  124 (183)
Q Consensus        82 vDEad~ll~~~------~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~  124 (183)
                      .||+|.+-+..      ... ++.|...+-++.+.+.+|..+.+. +.+
T Consensus      1259 ~d~lh~igg~~g~v~evi~S-~r~ia~q~~k~ir~v~ls~~lana-~d~ 1305 (1674)
T KOG0951|consen 1259 VDELHLIGGVYGAVYEVICS-MRYIASQLEKKIRVVALSSSLANA-RDL 1305 (1674)
T ss_pred             eehhhhhcccCCceEEEEee-HHHHHHHHHhheeEEEeehhhccc-hhh
Confidence            99999875321      123 667777777788888888888766 444

>PTZ00424 helicase 45; Provisional

Probab=93.74  E-value=0.35  Score=40.46  Aligned_cols=70  Identities=14%  Similarity=0.212  Sum_probs=52.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-|..+.+.+...     ++.+..+.|+.+..++..   ...++..+|+|||.     .+.  .++|+..+.
T Consensus       270 ~ivF~~t~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~R~~i~~~f~~g~~~vLvaT~-----~l~--~GiDip~v~  337 (401)
T PTZ00424        270 AIIYCNTRRKVDYLTKKMHER-----DFTVSCMHGDMDQKDRDLIMREFRSGSTRVLITTD-----LLA--RGIDVQQVS  337 (401)
T ss_pred             EEEEecCcHHHHHHHHHHHHC-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCCEEEEcc-----ccc--CCcCcccCC
Confidence            689999999998887766543     677888899877554433   34456799999994     444  579999999


Q ss_pred             EEEEc
Q 030094           79 ILVLD   83 (183)
Q Consensus        79 ~lVvD   83 (183)
                      ++|.-
T Consensus       338 ~VI~~  342 (401)
T PTZ00424        338 LVINY  342 (401)
T ss_pred             EEEEE
Confidence            88853

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=93.68  E-value=0.25  Score=44.58  Aligned_cols=110  Identities=19%  Similarity=0.203  Sum_probs=59.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      .||+||+--+.. ....+.+.... ..+.+...+|   ...+...+  .++||+++|++.+..     ..+.--..-.+|
T Consensus       192 tLivcp~s~~~q-W~~elek~~~~-~~l~v~v~~g---r~kd~~el--~~~dVVltTy~il~~-----~~l~~i~w~Rii  259 (674)
T KOG1001|consen  192 TLIVCPTSLLTQ-WKTELEKVTEE-DKLSIYVYHG---RTKDKSEL--NSYDVVLTTYDILKN-----SPLVKIKWLRIV  259 (674)
T ss_pred             eeEecchHHHHH-HHHHHhccCCc-cceEEEEecc---cccccchh--cCCceEEeeHHHhhc-----ccccceeEEEEE
Confidence            478888765544 44444555433 2577777777   22223333  468899999976653     111112223579


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecC-ChHHHHHHH
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ-TEAVEELSK  126 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~-~~~v~~~~~  126 (183)
                      +||||.+-+..  .+.....-.+...++. .+++|. ...+.++..
T Consensus       260 ldea~~ikn~~--tq~~~a~~~L~a~~RW-cLtgtPiqn~~~~lys  302 (674)
T KOG1001|consen  260 LDEAHTIKNKD--TQIFKAVCQLDAKYRW-CLTGTPIQNNLDELYS  302 (674)
T ss_pred             eccccccCCcc--hHhhhhheeeccceee-eecCChhhhhHHHHHH
Confidence            99999985433  2233333333334444 445554 444555544

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

Probab=93.62  E-value=3.2  Score=34.64  Aligned_cols=111  Identities=21%  Similarity=0.310  Sum_probs=81.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEc-CcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVG-GVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g-~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+|.+|+-|.+.|+...+++..   |..+++.+.+ .....+....++++..+|+|+|-     .+++  ++.+.+++.+
T Consensus       308 ~liF~p~I~~~eq~a~~lk~~~---~~~~i~~Vhs~d~~R~EkV~~fR~G~~~lLiTTT-----ILER--GVTfp~vdV~  377 (441)
T COG4098         308 VLIFFPEIETMEQVAAALKKKL---PKETIASVHSEDQHRKEKVEAFRDGKITLLITTT-----ILER--GVTFPNVDVF  377 (441)
T ss_pred             EEEEecchHHHHHHHHHHHhhC---CccceeeeeccCccHHHHHHHHHcCceEEEEEee-----hhhc--ccccccceEE
Confidence            5899999999999999885543   4556555544 44577888888888899999995     6665  7889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCC-----CeEEEEeecCChHHHHHH
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKL-----RRTGLFSATQTEAVEELS  125 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~-----~Q~v~~SAT~~~~v~~~~  125 (183)
                      |++--|.++.   ...+-.|..+.++.     --+++|---.+.++.+..
T Consensus       378 Vlgaeh~vfT---esaLVQIaGRvGRs~~~PtGdv~FFH~G~skaM~~A~  424 (441)
T COG4098         378 VLGAEHRVFT---ESALVQIAGRVGRSLERPTGDVLFFHYGKSKAMKQAR  424 (441)
T ss_pred             EecCCccccc---HHHHHHHhhhccCCCcCCCCcEEEEeccchHHHHHHH
Confidence            9999888864   44555666666532     357777776766655433

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

Probab=93.57  E-value=0.47  Score=41.55  Aligned_cols=71  Identities=8%  Similarity=0.159  Sum_probs=53.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|+.-|..+.+.+...    .++++..+.|+.+..++..   ....+..+|+|||.     .+.  .++|+.+++
T Consensus       370 ~iVFv~s~~~a~~l~~~L~~~----~g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTd-----vl~--rGiDip~v~  438 (518)
T PLN00206        370 AVVFVSSRLGADLLANAITVV----TGLKALSIHGEKSMKERREVMKSFLVGEVPVIVATG-----VLG--RGVDLLRVR  438 (518)
T ss_pred             EEEEcCCchhHHHHHHHHhhc----cCcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEec-----Hhh--ccCCcccCC
Confidence            789999999998887766543    2678888999877654433   34456789999995     444  479999999


Q ss_pred             EEEEc
Q 030094           79 ILVLD   83 (183)
Q Consensus        79 ~lVvD   83 (183)
                      ++|.=
T Consensus       439 ~VI~~  443 (518)
T PLN00206        439 QVIIF  443 (518)
T ss_pred             EEEEe
Confidence            98853

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=93.47  E-value=0.45  Score=42.54  Aligned_cols=71  Identities=11%  Similarity=0.178  Sum_probs=53.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|+.-|.++++.+.+.     ++++..+.|+.+.++...   ....+..+|+|||.     .+.  .++|..+++
T Consensus       239 ~IIFc~tr~~~e~la~~L~~~-----g~~v~~~Ha~l~~~~R~~i~~~F~~g~~~VLVaT~-----a~~--~GIDip~V~  306 (607)
T PRK11057        239 GIIYCNSRAKVEDTAARLQSR-----GISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATV-----AFG--MGINKPNVR  306 (607)
T ss_pred             EEEEECcHHHHHHHHHHHHhC-----CCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEec-----hhh--ccCCCCCcC
Confidence            689999999999988877664     677888888876544433   33356789999996     343  578999999


Q ss_pred             EEEEcc
Q 030094           79 ILVLDE   84 (183)
Q Consensus        79 ~lVvDE   84 (183)
                      ++|.-.
T Consensus       307 ~VI~~d  312 (607)
T PRK11057        307 FVVHFD  312 (607)
T ss_pred             EEEEeC
Confidence            887433

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

Probab=93.45  E-value=1.1  Score=30.55  Aligned_cols=74  Identities=16%  Similarity=0.336  Sum_probs=52.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHH---HHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKAD---VKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~---~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      .||.+++++-+.++.+.+.+     +...+..+.|+.+..+.   ...+.+....|+++|.     .+ . .++|+..+.
T Consensus        31 ~lvf~~~~~~~~~~~~~l~~-----~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~-----~~-~-~G~d~~~~~   98 (131)
T cd00079          31 VLIFCPSKKMLDELAELLRK-----PGIKVAALHGDGSQEEREEVLKDFREGEIVVLVATD-----VI-A-RGIDLPNVS   98 (131)
T ss_pred             EEEEeCcHHHHHHHHHHHHh-----cCCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcC-----hh-h-cCcChhhCC
Confidence            68999999999999888876     25667788887653322   2234445678999996     23 2 578888888


Q ss_pred             EEEEcccch
Q 030094           79 ILVLDEADR   87 (183)
Q Consensus        79 ~lVvDEad~   87 (183)
                      .+|+.+.+.
T Consensus        99 ~vi~~~~~~  107 (131)
T cd00079          99 VVINYDLPW  107 (131)
T ss_pred             EEEEeCCCC
Confidence            888777643

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=93.31  E-value=0.5  Score=44.32  Aligned_cols=114  Identities=17%  Similarity=0.213  Sum_probs=62.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHH-hhh-----hCCC--ceEEEEEcCc-------chHHHHHHHHh-c-----CCcEEEeCcH
Q 030094            2 GMIISPTRELSSQIYHVAQP-FIS-----TLPD--VKSVLLVGGV-------EVKADVKKIEE-E-----GANLLIGTPG   60 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~-l~~-----~~~~--~~~~~~~g~~-------~~~~~~~~l~~-~-----~~~IiV~TP~   60 (183)
                      .||+||+...-..+...+.. .++     .+.+  ++.....++.       ....+.+.... .     +.+|+|.|-+
T Consensus        92 fii~vp~~aI~egv~~~l~s~~~k~hF~~~y~~~~~~~~~~~S~k~~k~gr~~~~~~i~~Fa~~~~~~~~~I~Ilv~niq  171 (986)
T PRK15483         92 FIIVVPTPAIKEGTRNFIQSDYAKQHFSQFYENTRIELYVINAGDKKKSGRKNFPAQLSNFVKASRQNSNTIHVLLINAG  171 (986)
T ss_pred             EEEEeCCHHHHHHHHHHhhHHHHHHHHHHHcCCceeEEEEEecCcccccccccChHHHHHHHhccccCCCceEEEEEehH
Confidence            58999999888888766551 111     1222  3333333322       22334333222 2     5899999998


Q ss_pred             HHHHHHH-h-c----------CCc-CCCCce-EEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCCh
Q 030094           61 RLYDIME-R-M----------DVL-DFRNLE-ILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (183)
Q Consensus        61 ~l~~~l~-~-~----------~~~-~l~~l~-~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~  119 (183)
                      .+..-.. + .          ..+ .+...+ ++|+||.|++-..  ....+.| ..+.+.+ ++.||||++.
T Consensus       172 a~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEPh~~~~~--~k~~~~i-~~lnpl~-~lrysAT~~~  240 (986)
T PRK15483        172 MLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEPHRFPRD--NKFYQAI-EALKPQM-IIRFGATFPD  240 (986)
T ss_pred             HhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECCCCCCcc--hHHHHHH-HhcCccc-EEEEeeecCC
Confidence            7755211 0 0          011 133333 6899999998432  1222344 5554433 4669999987

>TIGR00595 priA primosomal protein N'

Probab=93.25  E-value=0.95  Score=39.62  Aligned_cols=97  Identities=15%  Similarity=0.219  Sum_probs=60.4

Q ss_pred             HHHHHHHHHhhhhCCCceEEEEEcCcch-----HHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccch
Q 030094           13 SQIYHVAQPFISTLPDVKSVLLVGGVEV-----KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADR   87 (183)
Q Consensus        13 ~Qi~~~~~~l~~~~~~~~~~~~~g~~~~-----~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~   87 (183)
                      .++.+.+.+   .+|+.++..+.+....     +.....+.++.++|+|||+     ++.  +++|+.++.++++=.+|.
T Consensus       272 e~~~e~l~~---~fp~~~v~~~d~d~~~~~~~~~~~l~~f~~g~~~ILVgT~-----~i~--kG~d~~~v~lV~vl~aD~  341 (505)
T TIGR00595       272 EQVEEELAK---LFPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQ-----MIA--KGHHFPNVTLVGVLDADS  341 (505)
T ss_pred             HHHHHHHHh---hCCCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCc-----ccc--cCCCCCcccEEEEEcCcc
Confidence            444444444   4578888877766432     3445566567899999998     343  579999999999999999


Q ss_pred             hhccc-h---HHHHHHHHH---hCC---CCCeEEEEeecCCh
Q 030094           88 LLDMG-F---QKQISYIIS---RLP---KLRRTGLFSATQTE  119 (183)
Q Consensus        88 ll~~~-~---~~~l~~i~~---~l~---~~~Q~v~~SAT~~~  119 (183)
                      .+... |   +.....+.+   +-+   +..+.++-+.....
T Consensus       342 ~l~~pd~ra~E~~~~ll~q~~GRagR~~~~g~viiqt~~p~~  383 (505)
T TIGR00595       342 GLHSPDFRAAERGFQLLTQVAGRAGRAEDPGQVIIQTYNPNH  383 (505)
T ss_pred             cccCcccchHHHHHHHHHHHHhccCCCCCCCEEEEEeCCCCC
Confidence            77532 2   222333333   322   24466666655543

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).

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=93.13  E-value=0.59  Score=41.55  Aligned_cols=71  Identities=11%  Similarity=0.227  Sum_probs=52.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+||..|.++++.+...     ++.+..+.|+.+.++...   ....+.++|+|||-     .+.  .++|..+++
T Consensus       227 ~IIf~~sr~~~e~la~~L~~~-----g~~~~~~H~~l~~~~R~~i~~~F~~g~~~vlVaT~-----a~~--~GID~p~v~  294 (591)
T TIGR01389       227 GIIYASSRKKVEELAERLESQ-----GISALAYHAGLSNKVRAENQEDFLYDDVKVMVATN-----AFG--MGIDKPNVR  294 (591)
T ss_pred             EEEEECcHHHHHHHHHHHHhC-----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEec-----hhh--ccCcCCCCC
Confidence            689999999999998877653     677888888876544433   33346799999995     343  478888999


Q ss_pred             EEEEcc
Q 030094           79 ILVLDE   84 (183)
Q Consensus        79 ~lVvDE   84 (183)
                      ++|.=.
T Consensus       295 ~VI~~~  300 (591)
T TIGR01389       295 FVIHYD  300 (591)
T ss_pred             EEEEcC
Confidence            887533

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.

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=93.10  E-value=0.32  Score=42.32  Aligned_cols=109  Identities=16%  Similarity=0.152  Sum_probs=68.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhc-------CCcCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM-------DVLDF   74 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~-------~~~~l   74 (183)
                      ||+||.+.--+.|....+...+. ..+-.++-++....      .....++.|+|+|-..+..--++.       .-+.-
T Consensus       348 clvLcts~VSVeQWkqQfk~wst-i~d~~i~rFTsd~K------e~~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~  420 (776)
T KOG1123|consen  348 CLVLCTSAVSVEQWKQQFKQWST-IQDDQICRFTSDAK------ERFPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRG  420 (776)
T ss_pred             EEEEecCccCHHHHHHHHHhhcc-cCccceEEeecccc------ccCCCCCcEEEEeeehhhhcccccHHHHHHHHHHhc
Confidence            78999999999999988888753 32344444443221      123568999999986543321110       00112


Q ss_pred             CCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHH
Q 030094           75 RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE  122 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~  122 (183)
                      ....++++||+|.+=..=|..-+.-+-.+.     .+.++||+-.+=.
T Consensus       421 ~EWGllllDEVHvvPA~MFRRVlsiv~aHc-----KLGLTATLvREDd  463 (776)
T KOG1123|consen  421 REWGLLLLDEVHVVPAKMFRRVLSIVQAHC-----KLGLTATLVREDD  463 (776)
T ss_pred             CeeeeEEeehhccchHHHHHHHHHHHHHHh-----hccceeEEeeccc
Confidence            567899999999985544565555444444     3778999865533

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=93.07  E-value=0.37  Score=44.53  Aligned_cols=84  Identities=12%  Similarity=0.100  Sum_probs=62.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHH-HHHHhcC-----CcCCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-DIMERMD-----VLDFR   75 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~-~~l~~~~-----~~~l~   75 (183)
                      +-|++.+--||..=.+.+..+..++ ++++.+...+....+....   ..|||.-||...+- ++++.+=     ..-.+
T Consensus       122 VhVVTvNdYLA~RDae~mg~vy~fL-GLsvG~i~~~~~~~~rr~a---Y~~DItYgTn~E~gFDYLRDnm~~~~~~~vqR  197 (925)
T PRK12903        122 VIVSTVNEYLAERDAEEMGKVFNFL-GLSVGINKANMDPNLKREA---YACDITYSVHSELGFDYLRDNMVSSKEEKVQR  197 (925)
T ss_pred             eEEEecchhhhhhhHHHHHHHHHHh-CCceeeeCCCCChHHHHHh---ccCCCeeecCcccchhhhhhcccccHHHhcCc
Confidence            4578888899998888888888888 9999988876655544333   46999999998763 3443211     11246


Q ss_pred             CceEEEEcccchhh
Q 030094           76 NLEILVLDEADRLL   89 (183)
Q Consensus        76 ~l~~lVvDEad~ll   89 (183)
                      .+.+.|+||+|.+|
T Consensus       198 ~~~faIVDEVDSIL  211 (925)
T PRK12903        198 GLNFCLIDEVDSIL  211 (925)
T ss_pred             ccceeeeccchhee
Confidence            77899999999987

>PRK13767 ATP-dependent helicase; Provisional

Probab=93.02  E-value=0.85  Score=42.61  Aligned_cols=76  Identities=11%  Similarity=0.153  Sum_probs=54.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhh-CCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            2 GMIISPTRELSSQIYHVAQPFIST-LPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~-~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +||.|+||..|..++..+.+.... +.+..+....|+.+.+++..   .++++..+|+|||.     .+.  .++|+.++
T Consensus       287 ~LVF~nTr~~ae~la~~L~~~~~~~~~~~~i~~hHg~ls~~~R~~ve~~fk~G~i~vLVaTs-----~Le--~GIDip~V  359 (876)
T PRK13767        287 TLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSST-----SLE--LGIDIGYI  359 (876)
T ss_pred             EEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECC-----hHH--hcCCCCCC
Confidence            799999999999998888774331 12456788888877554433   44556789999997     344  36888888


Q ss_pred             eEEEEcc
Q 030094           78 EILVLDE   84 (183)
Q Consensus        78 ~~lVvDE   84 (183)
                      +++|.-.
T Consensus       360 d~VI~~~  366 (876)
T PRK13767        360 DLVVLLG  366 (876)
T ss_pred             cEEEEeC
Confidence            8887533

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

Probab=92.99  E-value=1.5  Score=38.55  Aligned_cols=110  Identities=13%  Similarity=0.320  Sum_probs=81.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHH---HHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKAD---VKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~---~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.+-|+-.|....+-+...     ++++..+.+....-+.   .+.+..+..||+||-     ++++  .++|+-.|.
T Consensus       449 vLVTtLTKkmAEdLT~Yl~e~-----gikv~YlHSdidTlER~eIirdLR~G~~DvLVGI-----NLLR--EGLDiPEVs  516 (663)
T COG0556         449 VLVTTLTKKMAEDLTEYLKEL-----GIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVGI-----NLLR--EGLDLPEVS  516 (663)
T ss_pred             EEEEeehHHHHHHHHHHHHhc-----CceEEeeeccchHHHHHHHHHHHhcCCccEEEee-----hhhh--ccCCCccee
Confidence            577788888888776665554     8999999988765444   445656789999996     5775  489999999


Q ss_pred             EEEEcccchhhccchHHHHHHHHHhCC-----CCCeEEEEeecCChHHHHHHH
Q 030094           79 ILVLDEADRLLDMGFQKQISYIISRLP-----KLRRTGLFSATQTEAVEELSK  126 (183)
Q Consensus        79 ~lVvDEad~ll~~~~~~~l~~i~~~l~-----~~~Q~v~~SAT~~~~v~~~~~  126 (183)
                      ++.+=+||.   .||...-.++++.++     .+-.+++..-.+++.+...+.
T Consensus       517 LVAIlDADK---eGFLRse~SLIQtIGRAARN~~GkvIlYAD~iT~sM~~Ai~  566 (663)
T COG0556         517 LVAILDADK---EGFLRSERSLIQTIGRAARNVNGKVILYADKITDSMQKAID  566 (663)
T ss_pred             EEEEeecCc---cccccccchHHHHHHHHhhccCCeEEEEchhhhHHHHHHHH
Confidence            998888998   466655555555543     245789998889988776554

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

Probab=92.88  E-value=1.8  Score=38.14  Aligned_cols=75  Identities=15%  Similarity=0.310  Sum_probs=59.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcch---HHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEV---KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~---~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.+-+.|-|.|.+..+.    .++++.+..+.|..+.   ++.......+...++|||     +++.+  ++|+..+.
T Consensus       390 ~lIfVQs~eRak~L~~~L~----~~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicT-----dll~R--GiDf~gvn  458 (593)
T KOG0344|consen  390 VLIFVQSKERAKQLFEELE----IYDNINVDVIHGERSQKQRDETMERFRIGKIWVLICT-----DLLAR--GIDFKGVN  458 (593)
T ss_pred             eEEEEecHHHHHHHHHHhh----hccCcceeeEecccchhHHHHHHHHHhccCeeEEEeh-----hhhhc--cccccCcc
Confidence            5788999999999999887    3358999999998653   344455556789999999     57766  69999999


Q ss_pred             EEEEcccch
Q 030094           79 ILVLDEADR   87 (183)
Q Consensus        79 ~lVvDEad~   87 (183)
                      ++|-++.-.
T Consensus       459 ~VInyD~p~  467 (593)
T KOG0344|consen  459 LVINYDFPQ  467 (593)
T ss_pred             eEEecCCCc
Confidence            999876644

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=92.58  E-value=0.15  Score=41.49  Aligned_cols=114  Identities=16%  Similarity=0.109  Sum_probs=67.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhc----CC------
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM----DV------   71 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~----~~------   71 (183)
                      +|++..+.+|-....+-++.+...  .+.+..+..-... ..    ....-.|+.+|-..|..--...    ..      
T Consensus        94 ~vwvS~s~dL~~Da~RDl~DIG~~--~i~v~~l~~~~~~-~~----~~~~~GvlF~TYs~L~~~~~~~~~~~sRl~ql~~  166 (303)
T PF13872_consen   94 AVWVSVSNDLKYDAERDLRDIGAD--NIPVHPLNKFKYG-DI----IRLKEGVLFSTYSTLISESQSGGKYRSRLDQLVD  166 (303)
T ss_pred             eEEEECChhhhhHHHHHHHHhCCC--cccceechhhccC-cC----CCCCCCccchhHHHHHhHHhccCCccchHHHHHH
Confidence            577888888888877777777543  3333333221100 00    0123358888877665553210    01      


Q ss_pred             ---cCCCCceEEEEcccchhhccc--------hHHHHHHHHHhCCCCCeEEEEeecCChHHHHHH
Q 030094           72 ---LDFRNLEILVLDEADRLLDMG--------FQKQISYIISRLPKLRRTGLFSATQTEAVEELS  125 (183)
Q Consensus        72 ---~~l~~l~~lVvDEad~ll~~~--------~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~  125 (183)
                         -+++  .++|+||+|..=+..        ....+..+-+.+|+ .+++++|||--.+.++++
T Consensus       167 W~g~dfd--gvivfDEcH~akn~~~~~~~~sk~g~avl~LQ~~LP~-ARvvY~SATgasep~Nma  228 (303)
T PF13872_consen  167 WCGEDFD--GVIVFDECHKAKNLSSGSKKPSKTGIAVLELQNRLPN-ARVVYASATGASEPRNMA  228 (303)
T ss_pred             HHhcCCC--ceEEeccchhcCCCCccCccccHHHHHHHHHHHhCCC-CcEEEecccccCCCceee
Confidence               1122  389999999985432        23456666777764 559999999987766664

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

Probab=92.26  E-value=1.3  Score=42.09  Aligned_cols=104  Identities=13%  Similarity=0.212  Sum_probs=72.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHH---HHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKA---DVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~---~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      |+-+|.|--|-..++.+.++.+   .|..+++...|...-.+   -+....++..||+|||-     +++.  ++|.-+.
T Consensus       805 QvfYv~NrV~~Ie~~~~~L~~L---VPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TT-----IIEt--GIDIPnA  874 (1139)
T COG1197         805 QVFYVHNRVESIEKKAERLREL---VPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTT-----IIET--GIDIPNA  874 (1139)
T ss_pred             EEEEEecchhhHHHHHHHHHHh---CCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEee-----eeec--CcCCCCC
Confidence            3456667666666666666665   48899999998766433   33344467899999994     6664  7999999


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      -.+|++-||++   | ..++..+-.+.++..+.-++=-+.+
T Consensus       875 NTiIIe~AD~f---G-LsQLyQLRGRVGRS~~~AYAYfl~p  911 (1139)
T COG1197         875 NTIIIERADKF---G-LAQLYQLRGRVGRSNKQAYAYFLYP  911 (1139)
T ss_pred             ceEEEeccccc---c-HHHHHHhccccCCccceEEEEEeec
Confidence            99999999997   3 5566667777776655444433433

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

Probab=92.23  E-value=0.31  Score=43.10  Aligned_cols=147  Identities=12%  Similarity=-0.009  Sum_probs=87.4

Q ss_pred             EEEeCcHHHHHHHHHHHHHhhhhCCCceEEEE--EcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcC----CCC
Q 030094            3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLL--VGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLD----FRN   76 (183)
Q Consensus         3 lIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~--~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~----l~~   76 (183)
                      +...|+.|+++.-.+.+.-.....|..+.+.+  +.|.+ +...+.+...|.+++.+.|......+-. +..+    +-+
T Consensus       335 ~~~~~~~~~~~~~~~~~~V~~~~I~~~K~A~V~~~D~~s-E~~~~A~~R~~~~~~~s~~~~~~s~~L~-~~~~~~~~~~~  412 (1034)
T KOG4150|consen  335 LLPSEMVEHLRNGSKGQVVHVEVIKARKSAYVEMSDKLS-ETTKSALKRIGLNTLYSHQAEAISAALA-KSLCYNVPVFE  412 (1034)
T ss_pred             ecchhHHHHhhccCCceEEEEEehhhhhcceeecccCCC-chhHHHHHhcCcceeecCHHHHHHHHhh-hccccccHHHH
Confidence            45567777776443332222223333333222  23333 3444555577999999999887665433 3332    456


Q ss_pred             ceEEEEcccchhhccchHHHHHHHHHhC---------CCCCeEEEEeecCChHHHHHHHhhCCCCe-EEEEccCCccccc
Q 030094           77 LEILVLDEADRLLDMGFQKQISYIISRL---------PKLRRTGLFSATQTEAVEELSKAGLRNPV-RVEVRAESKSHHV  146 (183)
Q Consensus        77 l~~lVvDEad~ll~~~~~~~l~~i~~~l---------~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~-~i~~~~~~~~~~~  146 (183)
                      .++.++||.|..+.. |...+...++++         ..+-|++-.|||+.+.+.....-+--+-+ .|..+..      
T Consensus       413 ~~~~~~~~~~~Y~~~-~~~~~~~~~R~L~~L~~~F~~~~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~~DGS------  485 (1034)
T KOG4150|consen  413 ELCKDTNSCALYLFP-TKALAQDQLRALSDLIKGFEASINMGVYDGDTPYKDRTRLRSELANLSELELVTIDGS------  485 (1034)
T ss_pred             HHHhcccceeeeecc-hhhHHHHHHHHHHHHHHHHHhhcCcceEeCCCCcCCHHHHHHHhcCCcceEEEEecCC------
Confidence            678899999987642 444444333333         34679999999999998777665543443 4443333      


Q ss_pred             ccchhhcccCCCccCceEEEEEec
Q 030094          147 SASSQQLASSKTPLGLHLEVIWNV  170 (183)
Q Consensus       147 ~~~~~~~~~~~~~~~l~q~~i~~~  170 (183)
                                  |.+-+++++|.+
T Consensus       486 ------------Ps~~K~~V~WNP  497 (1034)
T KOG4150|consen  486 ------------PSSEKLFVLWNP  497 (1034)
T ss_pred             ------------CCccceEEEeCC
Confidence                        667778887765

>PF02463 SMC_N: RecF/RecN/SMC N terminal domain; InterPro: IPR003395 This domain is found at the N terminus of structural maintenance of chromosomes (SMC) proteins, which function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression []

Probab=92.01  E-value=0.21  Score=38.26  Aligned_cols=41  Identities=24%  Similarity=0.331  Sum_probs=33.1

Q ss_pred             CCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEee
Q 030094           75 RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSA  115 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SA  115 (183)
                      ....++++||+|.=+|......+..++..+.+.+|+++.|.
T Consensus       157 ~~~p~~ilDEvd~~LD~~~~~~l~~~l~~~~~~~Q~ii~Th  197 (220)
T PF02463_consen  157 KPSPFLILDEVDAALDEQNRKRLADLLKELSKQSQFIITTH  197 (220)
T ss_dssp             S--SEEEEESTTTTS-HHHHHHHHHHHHHHTTTSEEEEE-S
T ss_pred             ccccccccccccccccccccccccccccccccccccccccc
Confidence            45679999999999998888999999999988999998753

The domain is also found in RecF and RecN proteins, which are involved in DNA metabolism and recombination.; PDB: 3HTK_A 1W1W_C 2WD5_A 3L51_A 1XEW_Y 3KTA_B 3NWC_B 1XEX_A 1GXL_C 1GXK_A ....

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=91.92  E-value=1.1  Score=41.56  Aligned_cols=71  Identities=15%  Similarity=0.260  Sum_probs=55.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHh---cCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEE---EGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~---~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.+|+++-+.++++.+++...  +++.+..++|+.+.+++.+.+..   +...|||+|.     ..+  .++++.+++
T Consensus       212 iLVFlpg~~eI~~l~~~L~~~~~--~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATn-----IAE--rgItIp~V~  282 (819)
T TIGR01970       212 ILVFLPGQAEIRRVQEQLAERLD--SDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATN-----IAE--TSLTIEGIR  282 (819)
T ss_pred             EEEEECCHHHHHHHHHHHHhhcC--CCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecc-----hHh--hcccccCce
Confidence            69999999999988888876322  37889999999988877766543   3468999995     444  579999998


Q ss_pred             EEE
Q 030094           79 ILV   81 (183)
Q Consensus        79 ~lV   81 (183)
                      ++|
T Consensus       283 ~VI  285 (819)
T TIGR01970       283 VVI  285 (819)
T ss_pred             EEE
Confidence            776

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.

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=91.88  E-value=3.8  Score=37.66  Aligned_cols=126  Identities=15%  Similarity=0.127  Sum_probs=75.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcch--HHHHHHHH----hcCCcEEEeCcHHHHHHHHhcCCcCCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEV--KADVKKIE----EEGANLLIGTPGRLYDIMERMDVLDFR   75 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~--~~~~~~l~----~~~~~IiV~TP~~l~~~l~~~~~~~l~   75 (183)
                      +||++|.. |..-..+++.+..... .+....++|+..-  -...+.+.    ...--|++-+-+.+.++++.   +...
T Consensus       301 ~lVV~P~s-Lv~nWkkEF~KWl~~~-~i~~l~~~~~~~~~w~~~~sil~~~~~~~~~~vli~sye~~~~~~~~---il~~  375 (776)
T KOG0390|consen  301 PLVVAPSS-LVNNWKKEFGKWLGNH-RINPLDFYSTKKSSWIKLKSILFLGYKQFTTPVLIISYETASDYCRK---ILLI  375 (776)
T ss_pred             cEEEccHH-HHHHHHHHHHHhcccc-ccceeeeecccchhhhhhHHHHHhhhhheeEEEEeccHHHHHHHHHH---HhcC
Confidence            58888854 4555555555554322 5666666666552  11212111    11234667777777766654   5667


Q ss_pred             CceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecC-ChHHHHHHHhh-CCCCeEE
Q 030094           76 NLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ-TEAVEELSKAG-LRNPVRV  135 (183)
Q Consensus        76 ~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~-~~~v~~~~~~~-~~~~~~i  135 (183)
                      .+.++|+||.|++=+  -...+...+..+ +-+..|++|.|+ .+++.++.+.. +-+|-.+
T Consensus       376 ~~glLVcDEGHrlkN--~~s~~~kaL~~l-~t~rRVLLSGTp~QNdl~EyFnlL~fvrP~~L  434 (776)
T KOG0390|consen  376 RPGLLVCDEGHRLKN--SDSLTLKALSSL-KTPRRVLLTGTPIQNDLKEYFNLLDFVRPGFL  434 (776)
T ss_pred             CCCeEEECCCCCccc--hhhHHHHHHHhc-CCCceEEeeCCcccccHHHHHHHHhhcChhhc
Confidence            889999999999843  344555556666 345667778885 66777766643 4455444

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=91.84  E-value=0.24  Score=46.07  Aligned_cols=106  Identities=18%  Similarity=0.222  Sum_probs=59.7

Q ss_pred             EEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchH-HHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVK-ADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         3 lIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~-~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      ||+||+--|..=..+    +..-.|++......|..... .-...+..++.+|+++|-+.+.+   .+.-+.--+.+++|
T Consensus       448 LvivPlstL~NW~~E----f~kWaPSv~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik---dk~lLsKI~W~yMI  520 (1157)
T KOG0386|consen  448 LIIVPLSTLVNWSSE----FPKWAPSVQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK---DKALLSKISWKYMI  520 (1157)
T ss_pred             EEeccccccCCchhh----ccccccceeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC---CHHHHhccCCccee
Confidence            688888877764433    33334677776666654422 22223445689999999875544   21222334456899


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ  117 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~  117 (183)
                      |||.|+|=  +....+..-+..--.....++.+.|.
T Consensus       521 IDEGHRmK--Na~~KLt~~L~t~y~~q~RLLLTGTP  554 (1157)
T KOG0386|consen  521 IDEGHRMK--NAICKLTDTLNTHYRAQRRLLLTGTP  554 (1157)
T ss_pred             eccccccc--chhhHHHHHhhccccchhhhhhcCCh
Confidence            99999983  23333333333222333445556664

>PHA02653 RNA helicase NPH-II; Provisional

Probab=91.74  E-value=0.83  Score=41.42  Aligned_cols=70  Identities=16%  Similarity=0.309  Sum_probs=52.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHH-HHHH-HhcCCcEEEeCcHHHHHHHHhcCCcCCCCceE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKAD-VKKI-EEEGANLLIGTPGRLYDIMERMDVLDFRNLEI   79 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~-~~~l-~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~   79 (183)
                      +||.+||++-+..+.+.+++..   +++.+..++|+.+..++ .+.. .++...|+|+|.     ..+  .+++..++.+
T Consensus       398 iLVFlpg~~ei~~l~~~L~~~~---~~~~v~~LHG~Lsq~eq~l~~ff~~gk~kILVATd-----IAE--RGIDIp~V~~  467 (675)
T PHA02653        398 GIVFVASVSQCEEYKKYLEKRL---PIYDFYIIHGKVPNIDEILEKVYSSKNPSIIISTP-----YLE--SSVTIRNATH  467 (675)
T ss_pred             EEEEECcHHHHHHHHHHHHhhc---CCceEEeccCCcCHHHHHHHHHhccCceeEEeccC-----hhh--ccccccCeeE
Confidence            7999999998887777666542   46889999998775533 2444 345689999996     444  5899999988


Q ss_pred             EE
Q 030094           80 LV   81 (183)
Q Consensus        80 lV   81 (183)
                      +|
T Consensus       468 VI  469 (675)
T PHA02653        468 VY  469 (675)
T ss_pred             EE
Confidence            76

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=91.69  E-value=0.97  Score=39.41  Aligned_cols=116  Identities=17%  Similarity=0.256  Sum_probs=70.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHh-cCC------cC-
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMER-MDV------LD-   73 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~-~~~------~~-   73 (183)
                      .|+++|+-.|. |..+.+.+.+++  .+++....|. ........+  .+.|++.+|...+-.-.++ ..+      .+ 
T Consensus       234 tLVvaP~VAlm-QW~nEI~~~T~g--slkv~~YhG~-~R~~nikel--~~YDvVLTty~vvEs~yRk~~~GfrrKngv~k  307 (791)
T KOG1002|consen  234 TLVVAPTVALM-QWKNEIERHTSG--SLKVYIYHGA-KRDKNIKEL--MNYDVVLTTYAVVESVYRKQDYGFRRKNGVDK  307 (791)
T ss_pred             eeEEccHHHHH-HHHHHHHHhccC--ceEEEEEecc-cccCCHHHh--hcCcEEEEecHHHHHHHHhccccccccCCccc
Confidence            58999999864 666777777663  5676666654 444444555  4789999999877665543 111      22 


Q ss_pred             ----CCCceE--EEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecC-ChHHHHHHH
Q 030094           74 ----FRNLEI--LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ-TEAVEELSK  126 (183)
Q Consensus        74 ----l~~l~~--lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~-~~~v~~~~~  126 (183)
                          +.++++  +|+||||-+=+..  ..-.+..-.+ +....+++|.|. .+.+-++..
T Consensus       308 e~SlLHsi~~~RiIlDEAH~IK~R~--snTArAV~~L-~tt~rw~LSGTPLQNrigElyS  364 (791)
T KOG1002|consen  308 EKSLLHSIKFYRIILDEAHNIKDRQ--SNTARAVFAL-ETTYRWCLSGTPLQNRIGELYS  364 (791)
T ss_pred             ccchhhhceeeeeehhhhccccccc--ccHHHHHHhh-HhhhhhhccCCcchhhHHHHHH
Confidence                566775  6999999985432  1222222222 234457778885 444544433

>TIGR01054 rgy reverse gyrase

Probab=91.58  E-value=0.72  Score=44.41  Aligned_cols=73  Identities=23%  Similarity=0.329  Sum_probs=52.8

Q ss_pred             CEEEEeCcH---HHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCC-
Q 030094            1 MGMIISPTR---ELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRN-   76 (183)
Q Consensus         1 ~alIl~Ptr---eLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~-   76 (183)
                      .+||.|||+   +-|..+.+.+++.     ++++..+.|+.+ ....+...++..+|+|||.. ..+.+.  .++|+.+ 
T Consensus       328 ~~IVFv~t~~~~~~a~~l~~~L~~~-----g~~a~~lhg~~~-~~~l~~Fr~G~~~vLVata~-~tdv~a--RGIDip~~  398 (1171)
T TIGR01054       328 GGIVYVSIDYGKEKAEEIAEFLENH-----GVKAVAYHATKP-KEDYEKFAEGEIDVLIGVAS-YYGTLV--RGLDLPER  398 (1171)
T ss_pred             CEEEEEeccccHHHHHHHHHHHHhC-----CceEEEEeCCCC-HHHHHHHHcCCCCEEEEecc-ccCccc--ccCCCCcc
Confidence            379999999   8888887766553     688899999875 34556666788999999731 012333  4788877 


Q ss_pred             ceEEEE
Q 030094           77 LEILVL   82 (183)
Q Consensus        77 l~~lVv   82 (183)
                      ++++|.
T Consensus       399 V~~vI~  404 (1171)
T TIGR01054       399 VRYAVF  404 (1171)
T ss_pred             ccEEEE
Confidence            788887

Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=91.56  E-value=1.5  Score=36.49  Aligned_cols=68  Identities=19%  Similarity=0.209  Sum_probs=48.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||+|+|+.-|..+++.+++..  . +..+..+.|..+..++.+.   ...+|+|||.     .+.  .++|+... .+|
T Consensus       275 ~LIf~nt~~~~~~l~~~L~~~~--~-~~~~~~l~g~~~~~~R~~~---~~~~iLVaTd-----v~~--rGiDi~~~-~vi  340 (357)
T TIGR03158       275 GAIILDSLDEVNRLSDLLQQQG--L-GDDIGRITGFAPKKDRERA---MQFDILLGTS-----TVD--VGVDFKRD-WLI  340 (357)
T ss_pred             EEEEECCHHHHHHHHHHHhhhC--C-CceEEeeecCCCHHHHHHh---ccCCEEEEec-----HHh--cccCCCCc-eEE
Confidence            7999999999999999888742  2 4566777776665544322   3689999996     454  47887766 555


Q ss_pred             Ec
Q 030094           82 LD   83 (183)
Q Consensus        82 vD   83 (183)
                      .|
T Consensus       341 ~~  342 (357)
T TIGR03158       341 FS  342 (357)
T ss_pred             EC
Confidence            54

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.

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

Probab=91.56  E-value=1  Score=39.39  Aligned_cols=84  Identities=13%  Similarity=0.234  Sum_probs=61.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHH---hcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIE---EEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~---~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|-|+.-|.++...+++.     +..+..+.|..+..+....|.   ++.+.|+|||-     .. . .++|+.+|+
T Consensus       344 vIIFc~tkr~~~~l~~~l~~~-----~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATd-----VA-a-RGLDi~dV~  411 (519)
T KOG0331|consen  344 VIIFCETKRTCDELARNLRRK-----GWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATD-----VA-A-RGLDVPDVD  411 (519)
T ss_pred             EEEEecchhhHHHHHHHHHhc-----CcceeeecccccHHHHHHHHHhcccCCcceEEEcc-----cc-c-ccCCCcccc
Confidence            799999999999888876664     467889999888766655443   56799999995     32 3 689999999


Q ss_pred             EEEEcccchhhccchHHHHHHHHHhCC
Q 030094           79 ILVLDEADRLLDMGFQKQISYIISRLP  105 (183)
Q Consensus        79 ~lVvDEad~ll~~~~~~~l~~i~~~l~  105 (183)
                      ++|        ..+|...++.-+.+.+
T Consensus       412 lVI--------nydfP~~vEdYVHRiG  430 (519)
T KOG0331|consen  412 LVI--------NYDFPNNVEDYVHRIG  430 (519)
T ss_pred             EEE--------eCCCCCCHHHHHhhcC
Confidence            988        3345555555555554

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

Probab=91.54  E-value=1.1  Score=39.17  Aligned_cols=68  Identities=16%  Similarity=0.282  Sum_probs=53.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHH---HhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l---~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      .+|.+.|++=|.-+.+.+.+.     +.+++.+.||.+.++....|   ..+..+|+|||-     . .. .++|..++.
T Consensus       520 iIIFvN~kk~~d~lAk~LeK~-----g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTD-----v-Ag-RGIDIpnVS  587 (673)
T KOG0333|consen  520 IIIFVNTKKGADALAKILEKA-----GYKVTTLHGGKSQEQRENALADFREGTGDILVATD-----V-AG-RGIDIPNVS  587 (673)
T ss_pred             EEEEEechhhHHHHHHHHhhc-----cceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEec-----c-cc-cCCCCCccc
Confidence            588999999998888877776     67899999998877665543   345689999995     2 23 689999999


Q ss_pred             EEE
Q 030094           79 ILV   81 (183)
Q Consensus        79 ~lV   81 (183)
                      ++|
T Consensus       588 lVi  590 (673)
T KOG0333|consen  588 LVI  590 (673)
T ss_pred             eee
Confidence            887

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=91.37  E-value=2.3  Score=35.22  Aligned_cols=73  Identities=19%  Similarity=0.190  Sum_probs=43.7

Q ss_pred             EEeCcHHHHHHHHhcCCcCCCCceEEEEcccchhhcc-------chHHHHHHHHHhCC------CCCeEEEEeecCChH-
Q 030094           55 LIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDM-------GFQKQISYIISRLP------KLRRTGLFSATQTEA-  120 (183)
Q Consensus        55 iV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~ll~~-------~~~~~l~~i~~~l~------~~~Q~v~~SAT~~~~-  120 (183)
                      .+..|..+...... .........++|+||||++...       .....+..+++.-.      ...|.+--+...+.+ 
T Consensus        63 ~~~~~~~~i~~~~~-~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~~L~~i~~~~kv~v~f~D~~Q~i~~~e~~~~~~  141 (352)
T PF09848_consen   63 DFRKPTSFINNYSE-SDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPNQLDEIIKRAKVVVFFYDENQSIRPSEIGTLEN  141 (352)
T ss_pred             hhhhhHHHHhhccc-ccccCCcCCEEEEehhHhhhhccccccccccHHHHHHHHhcCCEEEEEEccccEeecccCCCHHH
Confidence            34445444433331 2234567789999999999873       12467777777632      245777776666554 


Q ss_pred             HHHHHHhh
Q 030094          121 VEELSKAG  128 (183)
Q Consensus       121 v~~~~~~~  128 (183)
                      +..++..+
T Consensus       142 l~~~~~~~  149 (352)
T PF09848_consen  142 LEEIAENL  149 (352)
T ss_pred             HHHHHHhc
Confidence            55555544

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]

Probab=91.32  E-value=3.1  Score=38.10  Aligned_cols=69  Identities=19%  Similarity=0.284  Sum_probs=49.9

Q ss_pred             HHHHHHHHHhhhhCCCceEEEEEcCcch-----HHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccch
Q 030094           13 SQIYHVAQPFISTLPDVKSVLLVGGVEV-----KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADR   87 (183)
Q Consensus        13 ~Qi~~~~~~l~~~~~~~~~~~~~g~~~~-----~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~   87 (183)
                      +++.+++.+   .+|+.++.-+.++...     +........+.+||+|||+     ++-  ++.++-++.++++=.||.
T Consensus       494 erieeeL~~---~FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQ-----mia--KG~~fp~vtLVgvl~aD~  563 (730)
T COG1198         494 ERIEEELKR---LFPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQ-----MIA--KGHDFPNVTLVGVLDADT  563 (730)
T ss_pred             HHHHHHHHH---HCCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecch-----hhh--cCCCcccceEEEEEechh
Confidence            344455544   5678888877766543     3345556668899999997     454  579999999998888999


Q ss_pred             hhcc
Q 030094           88 LLDM   91 (183)
Q Consensus        88 ll~~   91 (183)
                      ++..
T Consensus       564 ~L~~  567 (730)
T COG1198         564 GLGS  567 (730)
T ss_pred             hhcC
Confidence            9864

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

Probab=91.23  E-value=1.2  Score=40.87  Aligned_cols=78  Identities=12%  Similarity=0.147  Sum_probs=55.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhC-C--CceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTL-P--DVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDF   74 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~-~--~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l   74 (183)
                      ++||.|+||..|..+++.+++..... +  +.++....||...+++..   .++++..+++|+|.     .+..  ++|.
T Consensus       273 ~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVaTd-----~ler--GIDI  345 (742)
T TIGR03817       273 RTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATTN-----ALEL--GVDI  345 (742)
T ss_pred             CEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEECc-----hHhc--cCCc
Confidence            47999999999999999887753321 1  356677788776544433   44566789999995     5544  7888


Q ss_pred             CCceEEEEccc
Q 030094           75 RNLEILVLDEA   85 (183)
Q Consensus        75 ~~l~~lVvDEa   85 (183)
                      .+++++|.-+.
T Consensus       346 ~~vd~VI~~~~  356 (742)
T TIGR03817       346 SGLDAVVIAGF  356 (742)
T ss_pred             ccccEEEEeCC
Confidence            88888876554

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.

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

Probab=91.02  E-value=0.65  Score=40.35  Aligned_cols=78  Identities=15%  Similarity=0.099  Sum_probs=47.8

Q ss_pred             eCcHHHHHHHHh-------cCCcCCCCceEEEEcccchhh-cc-chHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHh
Q 030094           57 GTPGRLYDIMER-------MDVLDFRNLEILVLDEADRLL-DM-GFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (183)
Q Consensus        57 ~TP~~l~~~l~~-------~~~~~l~~l~~lVvDEad~ll-~~-~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~  127 (183)
                      +||..++.++..       +..-.+.+-+.+|+||||.=. .. -....++.+...- ++-.++.+|||+...   -.+.
T Consensus       133 ~~~~T~Lky~tDgmLlrEams~p~l~~y~viiLDeahERtlATDiLmGllk~v~~~r-pdLk~vvmSatl~a~---Kfq~  208 (699)
T KOG0925|consen  133 TSPNTLLKYCTDGMLLREAMSDPLLGRYGVIILDEAHERTLATDILMGLLKEVVRNR-PDLKLVVMSATLDAE---KFQR  208 (699)
T ss_pred             CChhHHHHHhcchHHHHHHhhCcccccccEEEechhhhhhHHHHHHHHHHHHHHhhC-CCceEEEeecccchH---HHHH
Confidence            566666666542       112347888999999999731 11 1233444444444 478899999998733   3455


Q ss_pred             hCCCCeEEEEc
Q 030094          128 GLRNPVRVEVR  138 (183)
Q Consensus       128 ~~~~~~~i~~~  138 (183)
                      |+.|+-.+.+.
T Consensus       209 yf~n~Pll~vp  219 (699)
T KOG0925|consen  209 YFGNAPLLAVP  219 (699)
T ss_pred             HhCCCCeeecC
Confidence            66666555544

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=90.98  E-value=1.6  Score=41.74  Aligned_cols=125  Identities=14%  Similarity=0.193  Sum_probs=71.8

Q ss_pred             EEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHH---Hhc-----CCcEEEeCcHHHHHHHHhcCCcCC
Q 030094            3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKI---EEE-----GANLLIGTPGRLYDIMERMDVLDF   74 (183)
Q Consensus         3 lIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l---~~~-----~~~IiV~TP~~l~~~l~~~~~~~l   74 (183)
                      ||+||-.-++.= .+.+..-   . +..+.+..|.....+-.+..   .+.     .++++++|-+.++.--.   -+.-
T Consensus       424 lvvvplst~~~W-~~ef~~w---~-~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk~---~L~~  495 (1373)
T KOG0384|consen  424 LVVVPLSTITAW-EREFETW---T-DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDKA---ELSK  495 (1373)
T ss_pred             EEEeehhhhHHH-HHHHHHH---h-hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhccHh---hhcc
Confidence            677886654432 2333333   2 56777777766544443322   222     48999999876544221   1222


Q ss_pred             CCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHh-hCCCCeEEEE
Q 030094           75 RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKA-GLRNPVRVEV  137 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~-~~~~~~~i~~  137 (183)
                      -...++++||||+|=+  -...+-..+..+.-+...++.+.-+.+.++++... ++..|-.+..
T Consensus       496 i~w~~~~vDeahrLkN--~~~~l~~~l~~f~~~~rllitgTPlQNsikEL~sLl~Fl~P~kf~~  557 (1373)
T KOG0384|consen  496 IPWRYLLVDEAHRLKN--DESKLYESLNQFKMNHRLLITGTPLQNSLKELWSLLHFLMPGKFDS  557 (1373)
T ss_pred             CCcceeeecHHhhcCc--hHHHHHHHHHHhcccceeeecCCCccccHHHHHHHhcccCCCCCCc
Confidence            3356899999999843  23444444666655555555444467778887753 3556655544

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=90.71  E-value=1.5  Score=40.60  Aligned_cols=71  Identities=17%  Similarity=0.233  Sum_probs=55.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHh---cCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEE---EGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~---~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.+|+++-+.++++.+++...  .++.+..++|+.+.+++...+..   +...|||+|.     ..+  .++++.++.
T Consensus       215 iLVFlpg~~ei~~l~~~L~~~~~--~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATn-----IAE--rsLtIp~V~  285 (812)
T PRK11664        215 LLLFLPGVGEIQRVQEQLASRVA--SDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATN-----IAE--TSLTIEGIR  285 (812)
T ss_pred             EEEEcCCHHHHHHHHHHHHHhcc--CCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecc-----hHH--hcccccCce
Confidence            69999999999999988886321  26888999999888777665532   3468999996     444  579999999


Q ss_pred             EEE
Q 030094           79 ILV   81 (183)
Q Consensus        79 ~lV   81 (183)
                      ++|
T Consensus       286 ~VI  288 (812)
T PRK11664        286 LVV  288 (812)
T ss_pred             EEE
Confidence            776

>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=90.69  E-value=0.19  Score=37.26  Aligned_cols=38  Identities=32%  Similarity=0.548  Sum_probs=25.8

Q ss_pred             CCcEEEeCcHHHHHHHHhcCC---cCCCCceEEEEcccchhhc
Q 030094           51 GANLLIGTPGRLYDIMERMDV---LDFRNLEILVLDEADRLLD   90 (183)
Q Consensus        51 ~~~IiV~TP~~l~~~l~~~~~---~~l~~l~~lVvDEad~ll~   90 (183)
                      .+||+|++-.-|..-... ..   ++++. .++|+||||.+.+
T Consensus       119 ~adivi~~y~yl~~~~~~-~~~~~~~~~~-~ivI~DEAHNL~~  159 (174)
T PF06733_consen  119 NADIVICNYNYLFDPSIR-KSLFGIDLKD-NIVIFDEAHNLED  159 (174)
T ss_dssp             G-SEEEEETHHHHSHHHH-HHHCT--CCC-EEEEETTGGGCGG
T ss_pred             cCCEEEeCHHHHhhHHHH-hhhccccccC-cEEEEecccchHH
Confidence            589999999877665433 22   33444 6899999999865

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.

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

Probab=90.54  E-value=0.68  Score=41.54  Aligned_cols=96  Identities=22%  Similarity=0.375  Sum_probs=67.4

Q ss_pred             CEEEEeCcHHHHH-----HHHHHHHHhhhhCCCceEEEEEcCcchHHH---HHHHHhcCCcEEEeCcHHHHHHHHhcCCc
Q 030094            1 MGMIISPTRELSS-----QIYHVAQPFISTLPDVKSVLLVGGVEVKAD---VKKIEEEGANLLIGTPGRLYDIMERMDVL   72 (183)
Q Consensus         1 ~alIl~PtreLa~-----Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~---~~~l~~~~~~IiV~TP~~l~~~l~~~~~~   72 (183)
                      ||-|+||--|=..     -..+.+..+...+|+.++..+.|....++.   +...+++..||+|+|-     .++  -++
T Consensus       475 QaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTT-----VIE--VGV  547 (677)
T COG1200         475 QAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATT-----VIE--VGV  547 (677)
T ss_pred             EEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEee-----EEE--ecc
Confidence            5778888665332     344455555567788999999998774333   3344456899999995     343  478


Q ss_pred             CCCCceEEEEcccchhhccchHHHHHHHHHhCCCC
Q 030094           73 DFRNLEILVLDEADRLLDMGFQKQISYIISRLPKL  107 (183)
Q Consensus        73 ~l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~  107 (183)
                      |.-+-.+.|+..|+++   | ..++..+-.+.++.
T Consensus       548 dVPnATvMVIe~AERF---G-LaQLHQLRGRVGRG  578 (677)
T COG1200         548 DVPNATVMVIENAERF---G-LAQLHQLRGRVGRG  578 (677)
T ss_pred             cCCCCeEEEEechhhh---h-HHHHHHhccccCCC
Confidence            9999999999999996   2 45666666666643

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=90.52  E-value=0.26  Score=34.15  Aligned_cols=36  Identities=25%  Similarity=0.369  Sum_probs=20.7

Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEee
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSA  115 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SA  115 (183)
                      .++|+||||.+.+..+...+..+.+  ....++++++.
T Consensus        89 ~~lviDe~~~l~~~~~l~~l~~l~~--~~~~~vvl~G~  124 (131)
T PF13401_consen   89 VLLVIDEADHLFSDEFLEFLRSLLN--ESNIKVVLVGT  124 (131)
T ss_dssp             EEEEEETTHHHHTHHHHHHHHHHTC--SCBEEEEEEES
T ss_pred             eEEEEeChHhcCCHHHHHHHHHHHh--CCCCeEEEEEC
Confidence            7999999999643233344433333  33445555443

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=90.43  E-value=1.8  Score=37.78  Aligned_cols=103  Identities=17%  Similarity=0.221  Sum_probs=55.3

Q ss_pred             EEEeCcHHHHHHHHHHHHHhhhhCCCce-EEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            3 MIISPTRELSSQIYHVAQPFISTLPDVK-SVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         3 lIl~PtreLa~Qi~~~~~~l~~~~~~~~-~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      ||+||..-+ .-..+.+.++.   |... +..+.++.+.....    ..-+.|.|-+-+.+..+-+   .+.-...+.+|
T Consensus       245 liVcPAsvr-ftWa~al~r~l---ps~~pi~vv~~~~D~~~~~----~t~~~v~ivSye~ls~l~~---~l~~~~~~vvI  313 (689)
T KOG1000|consen  245 LIVCPASVR-FTWAKALNRFL---PSIHPIFVVDKSSDPLPDV----CTSNTVAIVSYEQLSLLHD---ILKKEKYRVVI  313 (689)
T ss_pred             EEEecHHHh-HHHHHHHHHhc---ccccceEEEecccCCcccc----ccCCeEEEEEHHHHHHHHH---HHhcccceEEE
Confidence            688885332 23344455544   3332 34445544432221    1224567777655444322   23334578999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ  117 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~  117 (183)
                      +||.|.|=+. -....+.++..+.+-.+++++|.|.
T Consensus       314 ~DEsH~Lk~s-ktkr~Ka~~dllk~akhvILLSGTP  348 (689)
T KOG1000|consen  314 FDESHMLKDS-KTKRTKAATDLLKVAKHVILLSGTP  348 (689)
T ss_pred             Eechhhhhcc-chhhhhhhhhHHHHhhheEEecCCc
Confidence            9999998543 2333555555555555667777664

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=90.29  E-value=1.5  Score=36.17  Aligned_cols=72  Identities=17%  Similarity=0.320  Sum_probs=50.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHH-------HHHHHhcCCcEEEeCcHHHHHHHHhcCCcC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKAD-------VKKIEEEGANLLIGTPGRLYDIMERMDVLD   73 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~-------~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~   73 (183)
                      .+||+|+|++-|..+++.+++..   ++..+..+.|+....+.       .+...++.+.|+|||.     .+.  .++|
T Consensus       224 ~~lVf~~t~~~~~~~~~~L~~~~---~~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~-----~~~--~GiD  293 (358)
T TIGR01587       224 KIAIIVNTVDRAQEFYQQLKENA---PEEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQ-----VIE--ASLD  293 (358)
T ss_pred             eEEEEECCHHHHHHHHHHHHhhc---CCCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECc-----chh--ceec
Confidence            37999999999999888777642   24578888888654433       2334456789999996     444  3677


Q ss_pred             CCCceEEEEc
Q 030094           74 FRNLEILVLD   83 (183)
Q Consensus        74 l~~l~~lVvD   83 (183)
                      +. +.++|.+
T Consensus       294 i~-~~~vi~~  302 (358)
T TIGR01587       294 IS-ADVMITE  302 (358)
T ss_pred             cC-CCEEEEc
Confidence            73 5666654

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.

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

Probab=89.47  E-value=1.7  Score=41.55  Aligned_cols=69  Identities=13%  Similarity=0.205  Sum_probs=52.3

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|.||.-+.++++.+.+.     ++++....||.+..+...   ....+..+|||||-     .+.  -++|..+++
T Consensus       683 gIIYC~SRke~E~LAe~L~~~-----Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATd-----AFG--MGIDkPDVR  750 (1195)
T PLN03137        683 GIIYCLSRMDCEKVAERLQEF-----GHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATV-----AFG--MGINKPDVR  750 (1195)
T ss_pred             ceeEeCchhHHHHHHHHHHHC-----CCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEec-----hhh--cCCCccCCc
Confidence            689999999999888876653     678888899877554433   34456789999995     333  479999999


Q ss_pred             EEEE
Q 030094           79 ILVL   82 (183)
Q Consensus        79 ~lVv   82 (183)
                      ++|-
T Consensus       751 ~VIH  754 (1195)
T PLN03137        751 FVIH  754 (1195)
T ss_pred             EEEE
Confidence            9884

>PRK09694 helicase Cas3; Provisional

Probab=89.47  E-value=2.4  Score=39.69  Aligned_cols=74  Identities=14%  Similarity=0.268  Sum_probs=49.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH-------HHH-HhcC---CcEEEeCcHHHHHHHHhcC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV-------KKI-EEEG---ANLLIGTPGRLYDIMERMD   70 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~-------~~l-~~~~---~~IiV~TP~~l~~~l~~~~   70 (183)
                      ++|+++|.+-|.++++.+++...  ++..+..+.++....+..       +.. +++.   ..|+|+|.     .++.  
T Consensus       563 vLVf~NTV~~Aq~ly~~L~~~~~--~~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQ-----ViE~--  633 (878)
T PRK09694        563 VCLICNLVDDAQKLYQRLKELNN--TQVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQ-----VVEQ--  633 (878)
T ss_pred             EEEEECCHHHHHHHHHHHHhhCC--CCceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECc-----chhh--
Confidence            78999999999999998886421  246788888886543331       112 1112   36999994     5554  


Q ss_pred             CcCCCCceEEEEccc
Q 030094           71 VLDFRNLEILVLDEA   85 (183)
Q Consensus        71 ~~~l~~l~~lVvDEa   85 (183)
                      ++|+ ++.++|.|-+
T Consensus       634 GLDI-d~DvlItdla  647 (878)
T PRK09694        634 SLDL-DFDWLITQLC  647 (878)
T ss_pred             eeec-CCCeEEECCC
Confidence            6676 4677887754

>COG4889 Predicted helicase [General function prediction only]

Probab=89.18  E-value=2.3  Score=39.75  Aligned_cols=86  Identities=19%  Similarity=0.272  Sum_probs=56.9

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcch-----------------------HHHHH-HHHhcCCcEEEe
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEV-----------------------KADVK-KIEEEGANLLIG   57 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~-----------------------~~~~~-~l~~~~~~IiV~   57 (183)
                      .|+|||+-.|-.|..+.-..- +.. +++...+++....                       -+... .-+..+--|+.+
T Consensus       209 iL~LvPSIsLLsQTlrew~~~-~~l-~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFs  286 (1518)
T COG4889         209 ILFLVPSISLLSQTLREWTAQ-KEL-DFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFS  286 (1518)
T ss_pred             eEeecchHHHHHHHHHHHhhc-cCc-cceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEE
Confidence            589999999999998866654 223 4555555443211                       01111 111245679999


Q ss_pred             CcHHHHHHHHhcCCcCCCCceEEEEcccchhhc
Q 030094           58 TPGRLYDIMERMDVLDFRNLEILVLDEADRLLD   90 (183)
Q Consensus        58 TP~~l~~~l~~~~~~~l~~l~~lVvDEad~ll~   90 (183)
                      |-+.+-..-+. ...-+....++|.||||+-.+
T Consensus       287 TYQSl~~i~eA-Qe~G~~~fDliicDEAHRTtG  318 (1518)
T COG4889         287 TYQSLPRIKEA-QEAGLDEFDLIICDEAHRTTG  318 (1518)
T ss_pred             cccchHHHHHH-HHcCCCCccEEEecchhcccc
Confidence            99988776654 455577788999999999764

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=89.05  E-value=0.37  Score=38.96  Aligned_cols=39  Identities=26%  Similarity=0.237  Sum_probs=28.0

Q ss_pred             CCcEEEeCcHHHHHHHHh-cCCcCCCCceEEEEcccchhhc
Q 030094           51 GANLLIGTPGRLYDIMER-MDVLDFRNLEILVLDEADRLLD   90 (183)
Q Consensus        51 ~~~IiV~TP~~l~~~l~~-~~~~~l~~l~~lVvDEad~ll~   90 (183)
                      .+||||++..-|.+-..+ .-+.++ .-.++|+||||.+-+
T Consensus       211 ~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00489      211 FANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             cCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            589999999888766533 112344 357999999999864

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=89.05  E-value=0.37  Score=38.96  Aligned_cols=39  Identities=26%  Similarity=0.237  Sum_probs=28.0

Q ss_pred             CCcEEEeCcHHHHHHHHh-cCCcCCCCceEEEEcccchhhc
Q 030094           51 GANLLIGTPGRLYDIMER-MDVLDFRNLEILVLDEADRLLD   90 (183)
Q Consensus        51 ~~~IiV~TP~~l~~~l~~-~~~~~l~~l~~lVvDEad~ll~   90 (183)
                      .+||||++..-|.+-..+ .-+.++ .-.++|+||||.+-+
T Consensus       211 ~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00488      211 FANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             cCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            589999999888766533 112344 357999999999864

>PRK09401 reverse gyrase; Reviewed

Probab=89.04  E-value=1.1  Score=43.18  Aligned_cols=72  Identities=17%  Similarity=0.415  Sum_probs=50.7

Q ss_pred             CEEEEeCcHHH---HHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCC-
Q 030094            1 MGMIISPTREL---SSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRN-   76 (183)
Q Consensus         1 ~alIl~PtreL---a~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~-   76 (183)
                      .+||.|||++-   |..+.+.++..     ++++..++|+.  +.......++..+|+|||... .+.+.  .++|+.+ 
T Consensus       330 ~~LIFv~t~~~~~~ae~l~~~L~~~-----gi~v~~~hg~l--~~~l~~F~~G~~~VLVatas~-tdv~a--RGIDiP~~  399 (1176)
T PRK09401        330 GGLIFVPSDKGKEYAEELAEYLEDL-----GINAELAISGF--ERKFEKFEEGEVDVLVGVASY-YGVLV--RGIDLPER  399 (1176)
T ss_pred             CEEEEEecccChHHHHHHHHHHHHC-----CCcEEEEeCcH--HHHHHHHHCCCCCEEEEecCC-CCcee--ecCCCCcc
Confidence            47999999655   77776665553     78899999987  344566667889999997410 12232  4788877 


Q ss_pred             ceEEEE
Q 030094           77 LEILVL   82 (183)
Q Consensus        77 l~~lVv   82 (183)
                      ++++|.
T Consensus       400 IryVI~  405 (1176)
T PRK09401        400 IRYAIF  405 (1176)
T ss_pred             eeEEEE
Confidence            788876

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=88.45  E-value=0.94  Score=42.55  Aligned_cols=84  Identities=12%  Similarity=0.211  Sum_probs=59.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhc-----CCcCCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERM-----DVLDFR   75 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~-----~~~~l~   75 (183)
                      +-|++.+--||..=.+.+..+..++ +++|.++..+.+..+...   ..+|||.-||...+ .++++.+     ...-.+
T Consensus       182 VHvVTvNDYLA~RDaewm~p~y~fl-GLtVg~i~~~~~~~~Rr~---aY~~DItYgTn~EfGFDYLRDnma~~~~~~vqR  257 (1025)
T PRK12900        182 VHVVTVNDYLAQRDKEWMNPVFEFH-GLSVGVILNTMRPEERRE---QYLCDITYGTNNEFGFDYLRDNMAGTPEEMVQR  257 (1025)
T ss_pred             cEEEeechHhhhhhHHHHHHHHHHh-CCeeeeeCCCCCHHHHHH---hCCCcceecCCCccccccchhccccchhhhhcc
Confidence            3467778888988888888888888 999998866555444332   35899999999775 2333321     111236


Q ss_pred             CceEEEEcccchhh
Q 030094           76 NLEILVLDEADRLL   89 (183)
Q Consensus        76 ~l~~lVvDEad~ll   89 (183)
                      ..-+.|+||+|.+|
T Consensus       258 ~~~faIVDEvDSvL  271 (1025)
T PRK12900        258 DFYFAIVDEVDSVL  271 (1025)
T ss_pred             CCceEEEechhhhh
Confidence            67799999999986

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

Probab=88.36  E-value=2.9  Score=35.23  Aligned_cols=122  Identities=13%  Similarity=0.157  Sum_probs=74.8

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +++|.|.||.-|.-++..+..-     +-.+.++.|.....+...   ..+.+...|+|+|.     .+.  +++|...+
T Consensus       332 qsiIFc~tk~ta~~l~~~m~~~-----Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTn-----V~A--RGiDv~qV  399 (477)
T KOG0332|consen  332 QSIIFCHTKATAMWLYEEMRAE-----GHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTN-----VCA--RGIDVAQV  399 (477)
T ss_pred             heEEEEeehhhHHHHHHHHHhc-----CceeEEeeccchhHHHHHHHHHHhcCcceEEEEec-----hhh--cccccceE
Confidence            5899999999999998877775     456788888766554433   33345678999995     343  57999999


Q ss_pred             eEEEEcccchhhcc----chHHHHHHHHHhCCCCCeEEE---EeecCChHHHHHHHhhCC-CCeEEE
Q 030094           78 EILVLDEADRLLDM----GFQKQISYIISRLPKLRRTGL---FSATQTEAVEELSKAGLR-NPVRVE  136 (183)
Q Consensus        78 ~~lVvDEad~ll~~----~~~~~l~~i~~~l~~~~Q~v~---~SAT~~~~v~~~~~~~~~-~~~~i~  136 (183)
                      .++|=  .|.=.+.    ++..-+.+|-+.=.-.+.-+.   .-...+.++.+-+.+|+. ++..+.
T Consensus       400 s~VvN--ydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~~mn~iq~~F~~~i~~~~  464 (477)
T KOG0332|consen  400 SVVVN--YDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMNIMNKIQKHFNMKIKRLD  464 (477)
T ss_pred             EEEEe--cCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHHHHHHHHHHHhhcceecC
Confidence            98872  2222221    244444444332111233333   334456666666777774 444443

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=88.33  E-value=0.58  Score=42.56  Aligned_cols=41  Identities=22%  Similarity=0.230  Sum_probs=29.3

Q ss_pred             cCCcEEEeCcHHHHHHHHh-cCCcCCC-CceEEEEcccchhhc
Q 030094           50 EGANLLIGTPGRLYDIMER-MDVLDFR-NLEILVLDEADRLLD   90 (183)
Q Consensus        50 ~~~~IiV~TP~~l~~~l~~-~~~~~l~-~l~~lVvDEad~ll~   90 (183)
                      ..+||||+...-|...+.. .+.+.+. .-..+|+||||++-+
T Consensus       218 ~~AdivVtNH~LLladl~~~~~~iLp~~~~~~lViDEAH~L~d  260 (697)
T PRK11747        218 DEADVVVANHDLVLADLELGGGVVLPDPENLLYVLDEGHHLPD  260 (697)
T ss_pred             hhCCEEEECcHHHHhhhhccCCcccCCCCCCEEEEECccchHH
Confidence            4689999999987766642 1233332 457899999999964

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=88.24  E-value=12  Score=32.30  Aligned_cols=120  Identities=13%  Similarity=0.221  Sum_probs=63.6

Q ss_pred             EeCcHHHHHHHHHHHHHhhhhCC--CceEEEEEcCcchHH------HHHHHHhcCCcEEEeCcHHHHHHHHh---cCCc-
Q 030094            5 ISPTRELSSQIYHVAQPFISTLP--DVKSVLLVGGVEVKA------DVKKIEEEGANLLIGTPGRLYDIMER---MDVL-   72 (183)
Q Consensus         5 l~PtreLa~Qi~~~~~~l~~~~~--~~~~~~~~g~~~~~~------~~~~l~~~~~~IiV~TP~~l~~~l~~---~~~~-   72 (183)
                      +-|..++|......+.+-....+  ......++|+.....      -...+...+..++..+...+...+..   .+.. 
T Consensus       115 ~g~~N~~a~~~a~~~a~~~~~~~~~~~npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f~~~~~~~l~~~~~~  194 (445)
T PRK12422        115 VTPENDLPHRILQEFTKVSEQGKGFPFNPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEHLVSAIRSGEMQ  194 (445)
T ss_pred             eCCcHHHHHHHHHHHHhccccccCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHHHHHHHHHHhcchHH
Confidence            35666666544443332111111  235567887654321      12223334678888887765443321   0111 


Q ss_pred             ----CCCCceEEEEcccchhhccc-hHHHHHHHHHhC-CCCCeEEEEeecCChHHHHH
Q 030094           73 ----DFRNLEILVLDEADRLLDMG-FQKQISYIISRL-PKLRRTGLFSATQTEAVEEL  124 (183)
Q Consensus        73 ----~l~~l~~lVvDEad~ll~~~-~~~~l~~i~~~l-~~~~Q~v~~SAT~~~~v~~~  124 (183)
                          ...++.++++||+|.+-+.. ....+-.++..+ ....|+++.|.+.+.++..+
T Consensus       195 ~f~~~~~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l  252 (445)
T PRK12422        195 RFRQFYRNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAM  252 (445)
T ss_pred             HHHHHcccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhh
Confidence                15678899999999985432 344555555543 24567777665556555433

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

Probab=88.05  E-value=2.7  Score=38.37  Aligned_cols=75  Identities=17%  Similarity=0.250  Sum_probs=55.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCc--------chHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGV--------EVKADVK---KIEEEGANLLIGTPGRLYDIMERMD   70 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~--------~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~   70 (183)
                      ++|.|-||+.|..+...+..+.  .++++...+.|-.        +.++|..   ....+..+|+|||.      +.. .
T Consensus       416 ~IIFve~R~sa~~l~~~l~~~~--~~~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATS------V~E-E  486 (746)
T KOG0354|consen  416 TIIFVETRESALALKKWLLQLH--ELGIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATS------VAE-E  486 (746)
T ss_pred             EEEEEehHHHHHHHHHHHHhhh--hcccccceeeeccccccccccCHHHHHHHHHHHhCCCccEEEEec------chh-c
Confidence            7899999999999999998853  2478888888733        3344444   33457799999996      344 6


Q ss_pred             CcCCCCceEEEEccc
Q 030094           71 VLDFRNLEILVLDEA   85 (183)
Q Consensus        71 ~~~l~~l~~lVvDEa   85 (183)
                      ++|...|.++|-=++
T Consensus       487 GLDI~ec~lVIcYd~  501 (746)
T KOG0354|consen  487 GLDIGECNLVICYDY  501 (746)
T ss_pred             cCCcccccEEEEecC
Confidence            899999999885443

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

Probab=87.82  E-value=3.3  Score=33.74  Aligned_cols=69  Identities=14%  Similarity=0.211  Sum_probs=50.8

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      ||+|.|.||.-+.-..+-++.    . ++.+.+..|....++...   ....+...|+|+|-     . +. +++|...+
T Consensus       268 QavIFcnTk~kVdwLtekm~~----~-nftVssmHGDm~qkERd~im~dFRsg~SrvLitTD-----V-wa-RGiDv~qV  335 (400)
T KOG0328|consen  268 QAVIFCNTKRKVDWLTEKMRE----A-NFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTD-----V-WA-RGIDVQQV  335 (400)
T ss_pred             eEEEEecccchhhHHHHHHHh----h-CceeeeccCCcchhHHHHHHHHhhcCCceEEEEec-----h-hh-ccCCccee
Confidence            689999999887765554433    2 688899999877655533   44556789999995     3 34 68999999


Q ss_pred             eEEE
Q 030094           78 EILV   81 (183)
Q Consensus        78 ~~lV   81 (183)
                      .++|
T Consensus       336 slvi  339 (400)
T KOG0328|consen  336 SLVI  339 (400)
T ss_pred             EEEE
Confidence            8887

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=87.36  E-value=2  Score=39.15  Aligned_cols=106  Identities=19%  Similarity=0.236  Sum_probs=64.0

Q ss_pred             EEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHH--------HhcCCcEEEeCcHHHHHHHHhcCCcCC
Q 030094            3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKI--------EEEGANLLIGTPGRLYDIMERMDVLDF   74 (183)
Q Consensus         3 lIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l--------~~~~~~IiV~TP~~l~~~l~~~~~~~l   74 (183)
                      ||++|.    .-.......+++++|++++.-.-|+..-....+..        ...+.||+|+|-+.+..--   +.+.-
T Consensus       621 LVVtpa----StL~NWaqEisrFlP~~k~lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtDe---ky~qk  693 (1185)
T KOG0388|consen  621 LVVTPA----STLHNWAQEISRFLPSFKVLPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTDE---KYLQK  693 (1185)
T ss_pred             EEeehH----HHHhHHHHHHHHhCccceeecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeechH---HHHHh
Confidence            677774    44566777788888999999888876644333321        2357899999987653211   11212


Q ss_pred             CCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC
Q 030094           75 RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      -..++.|+|||..+=+.. ....+.++.-  +-+-.++++.|.-
T Consensus       694 vKWQYMILDEAQAIKSSs-S~RWKtLLsF--~cRNRLLLTGTPI  734 (1185)
T KOG0388|consen  694 VKWQYMILDEAQAIKSSS-SSRWKTLLSF--KCRNRLLLTGTPI  734 (1185)
T ss_pred             hhhhheehhHHHHhhhhh-hhHHHHHhhh--hccceeeecCCcc
Confidence            235689999998875432 3333333332  2233566677753

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=87.05  E-value=2.5  Score=31.90  Aligned_cols=35  Identities=20%  Similarity=0.456  Sum_probs=21.5

Q ss_pred             cCCcEEEeCcHHHHHHHHhcCCcC-C-CCceEEEEcccchhh
Q 030094           50 EGANLLIGTPGRLYDIMERMDVLD-F-RNLEILVLDEADRLL   89 (183)
Q Consensus        50 ~~~~IiV~TP~~l~~~l~~~~~~~-l-~~l~~lVvDEad~ll   89 (183)
                      ..++|+++|+.....     ..+. . ...+++|+|||-++.
T Consensus       169 ~~~~vi~~T~~~~~~-----~~~~~~~~~~d~vIvDEAsq~~  205 (236)
T PF13086_consen  169 KEADVIFTTLSSAAS-----PFLSNFKEKFDVVIVDEASQIT  205 (236)
T ss_dssp             HT-SEEEEETCGGG------CCGTT-----SEEEETTGGGS-
T ss_pred             ccccccccccccchh-----hHhhhhcccCCEEEEeCCCCcc
Confidence            469999999976622     2222 2 278899999998874

>KOG0964 consensus Structural maintenance of chromosome protein 3 (sister chromatid cohesion complex Cohesin, subunit SMC3) [Cell cycle control, cell division, chromosome partitioning]

Probab=86.83  E-value=0.91  Score=42.28  Aligned_cols=51  Identities=16%  Similarity=0.188  Sum_probs=46.1

Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCC
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLR  130 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~  130 (183)
                      .+.++||+|.-|+..+...+..+++.+....|+|.  .||-|++...+.+|+.
T Consensus      1121 PFYlfDEIDAaLDaQyR~aVa~lIkelS~~aQFI~--TTFRpEll~vAdKfyg 1171 (1200)
T KOG0964|consen 1121 PFYLFDEIDAALDAQYRTAVADLIKELSDSAQFIT--TTFRPELLSVADKFYG 1171 (1200)
T ss_pred             chhhHhHHhhhccHHHHHHHHHHHHHHhhccceEe--ecccHHHHHHHHhhhc
Confidence            38899999999999999999999999998888775  6899999999999865

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=86.58  E-value=1.1  Score=36.62  Aligned_cols=53  Identities=15%  Similarity=0.184  Sum_probs=38.2

Q ss_pred             CCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC---hHHHHHHHhh
Q 030094           75 RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT---EAVEELSKAG  128 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~---~~v~~~~~~~  128 (183)
                      ..-+.+|+||||.|... -+..+.+.++..++...+++...-++   ..+..-+.+|
T Consensus       128 ~~fKiiIlDEcdsmtsd-aq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~Kf  183 (346)
T KOG0989|consen  128 PPFKIIILDECDSMTSD-AQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKF  183 (346)
T ss_pred             CcceEEEEechhhhhHH-HHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHh
Confidence            34489999999999754 57788888888888888888766543   3444444444

>PRK05642 DNA replication initiation factor; Validated

Probab=86.12  E-value=9.6  Score=29.68  Aligned_cols=69  Identities=17%  Similarity=0.249  Sum_probs=41.5

Q ss_pred             cCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccchhhcc-chHHHHHHHHHhCCCCCeEEEEeecCCh
Q 030094           50 EGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDM-GFQKQISYIISRLPKLRRTGLFSATQTE  119 (183)
Q Consensus        50 ~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~ll~~-~~~~~l~~i~~~l~~~~Q~v~~SAT~~~  119 (183)
                      .+..++.-+...+...... -.-.+.++.++++|++|.+-.. .....+-++++.+......++++++.++
T Consensus        72 ~~~~v~y~~~~~~~~~~~~-~~~~~~~~d~LiiDDi~~~~~~~~~~~~Lf~l~n~~~~~g~~ilits~~~p  141 (234)
T PRK05642         72 RGEPAVYLPLAELLDRGPE-LLDNLEQYELVCLDDLDVIAGKADWEEALFHLFNRLRDSGRRLLLAASKSP  141 (234)
T ss_pred             CCCcEEEeeHHHHHhhhHH-HHHhhhhCCEEEEechhhhcCChHHHHHHHHHHHHHHhcCCEEEEeCCCCH
Confidence            4677887777776643221 0012556789999999987543 3456677777766543333455555544

>PRK01172 ski2-like helicase; Provisional

Probab=86.02  E-value=6.4  Score=35.62  Aligned_cols=77  Identities=6%  Similarity=0.157  Sum_probs=49.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCC--------------------ceEEEEEcCcchHHHHH---HHHhcCCcEEEe
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPD--------------------VKSVLLVGGVEVKADVK---KIEEEGANLLIG   57 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~--------------------~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~   57 (183)
                      ++||.||||.-|..+.+.+.+.....+.                    ..+...+||.+..++..   ...++...|+||
T Consensus       238 ~vLVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~gv~~~hagl~~~eR~~ve~~f~~g~i~VLva  317 (674)
T PRK01172        238 QVLVFVSSRKNAEDYAEMLIQHFPEFNDFKVSSENNNVYDDSLNEMLPHGVAFHHAGLSNEQRRFIEEMFRNRYIKVIVA  317 (674)
T ss_pred             cEEEEeccHHHHHHHHHHHHHhhhhcccccccccccccccHHHHHHHhcCEEEecCCCCHHHHHHHHHHHHcCCCeEEEe
Confidence            4799999999999888877665332111                    13566777776554433   233467899999


Q ss_pred             CcHHHHHHHHhcCCcCCCCceEEEEccc
Q 030094           58 TPGRLYDIMERMDVLDFRNLEILVLDEA   85 (183)
Q Consensus        58 TP~~l~~~l~~~~~~~l~~l~~lVvDEa   85 (183)
                      |.     .+.  .++|+... .+|++..
T Consensus       318 T~-----~la--~Gvnipa~-~VII~~~  337 (674)
T PRK01172        318 TP-----TLA--AGVNLPAR-LVIVRDI  337 (674)
T ss_pred             cc-----hhh--ccCCCcce-EEEEcCc
Confidence            96     333  35776554 5566544

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=85.97  E-value=1.7  Score=32.49  Aligned_cols=54  Identities=17%  Similarity=0.258  Sum_probs=45.7

Q ss_pred             CCCceEEEEcccchhhccch--HHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHh
Q 030094           74 FRNLEILVLDEADRLLDMGF--QKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~~~--~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~  127 (183)
                      -...+++|+||+-..++.++  .+.+..+++..|...-+|+.+-..|+++.+.++.
T Consensus        95 ~~~~DlvVLDEi~~A~~~gli~~~~v~~lL~~rp~~~evVlTGR~~p~~l~e~AD~  150 (173)
T TIGR00708        95 DPELDLVLLDELTYALKYGYLDVEEVVEALQERPGHQHVIITGRGCPQDLLELADL  150 (173)
T ss_pred             cCCCCEEEehhhHHHHHCCCcCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCce
Confidence            35678999999999888774  5688888998888889999999999988888775

Alternate name: corrinoid adenosyltransferase.

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=85.94  E-value=1.2  Score=36.33  Aligned_cols=58  Identities=16%  Similarity=0.252  Sum_probs=43.9

Q ss_pred             CCCceEEEEcccchhhccchHHHHHHHHHhCC-------CCCeEEEEeecCChHHHHHHHhhCCCC
Q 030094           74 FRNLEILVLDEADRLLDMGFQKQISYIISRLP-------KLRRTGLFSATQTEAVEELSKAGLRNP  132 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~-------~~~Q~v~~SAT~~~~v~~~~~~~~~~~  132 (183)
                      ...=.++|+||+|.| ..+..+.+.-.++..|       ++.-.|+.|.+-..++.+++-.++++.
T Consensus       176 ~C~rslFIFDE~DKm-p~gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg~eI~~~aL~~~~~g  240 (344)
T KOG2170|consen  176 ACQRSLFIFDEVDKL-PPGLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGGSEIARIALENARNG  240 (344)
T ss_pred             hcCCceEEechhhhc-CHhHHHHHhhhhccccccccccccceEEEEEcCCcchHHHHHHHHHHHcC
Confidence            334468999999998 3466777777777654       356789999999999998888776643

>KOG0991 consensus Replication factor C, subunit RFC2 [Replication, recombination and repair]

Probab=85.68  E-value=1.9  Score=34.18  Aligned_cols=44  Identities=23%  Similarity=0.291  Sum_probs=33.3

Q ss_pred             CCCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC
Q 030094           74 FRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      ..+-+.+|+||||.|.+ |-.+.+++-++...+.+++.+...+..
T Consensus       111 ~grhKIiILDEADSMT~-gAQQAlRRtMEiyS~ttRFalaCN~s~  154 (333)
T KOG0991|consen  111 PGRHKIIILDEADSMTA-GAQQALRRTMEIYSNTTRFALACNQSE  154 (333)
T ss_pred             CCceeEEEeeccchhhh-HHHHHHHHHHHHHcccchhhhhhcchh
Confidence            46678999999999975 567788888888877777666555444

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=85.44  E-value=4.8  Score=37.01  Aligned_cols=85  Identities=21%  Similarity=0.292  Sum_probs=52.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCce-EEEEEcCcch----HHHHHHHHhcC----CcEEEeCcHHHHHHHHhcCCc
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVK-SVLLVGGVEV----KADVKKIEEEG----ANLLIGTPGRLYDIMERMDVL   72 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~-~~~~~g~~~~----~~~~~~l~~~~----~~IiV~TP~~l~~~l~~~~~~   72 (183)
                      ++|+||+.-+ .+..+.+.++   .|.++ +....|....    .+....+....    .+++++|-+.+.........+
T Consensus       393 ~liv~p~s~~-~nw~~e~~k~---~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l  468 (866)
T COG0553         393 ALIVVPASLL-SNWKREFEKF---APDLRLVLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGL  468 (866)
T ss_pred             eEEEecHHHH-HHHHHHHhhh---CccccceeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHH
Confidence            5788886554 4444555444   45666 6666765541    33444443322    799999998887732111234


Q ss_pred             CCCCceEEEEcccchhhc
Q 030094           73 DFRNLEILVLDEADRLLD   90 (183)
Q Consensus        73 ~l~~l~~lVvDEad~ll~   90 (183)
                      .-.....+|+||||.+-+
T Consensus       469 ~~~~~~~~v~DEa~~ikn  486 (866)
T COG0553         469 KKIEWDRVVLDEAHRIKN  486 (866)
T ss_pred             hhceeeeeehhhHHHHhh
Confidence            445567899999999644

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=85.39  E-value=4.8  Score=39.23  Aligned_cols=71  Identities=10%  Similarity=0.177  Sum_probs=54.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHh-cCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEE-EGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~-~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +||.+|+++-+..+.+.+++.  ..+...+..++|+.+..++.+.... ++..|||+|.     ..+  .++++.+++++
T Consensus       289 ILVFLpg~~EIe~lae~L~~~--~~~~~~VlpLhg~Ls~~eQ~~Vf~~~g~rkIIVATN-----IAE--tSITIpgI~yV  359 (1294)
T PRK11131        289 ILIFMSGEREIRDTADALNKL--NLRHTEILPLYARLSNSEQNRVFQSHSGRRIVLATN-----VAE--TSLTVPGIKYV  359 (1294)
T ss_pred             EEEEcCCHHHHHHHHHHHHhc--CCCcceEeecccCCCHHHHHHHhcccCCeeEEEecc-----HHh--hccccCcceEE
Confidence            689999999999888877764  3345667788998887777665542 3568999996     444  57999999988


Q ss_pred             E
Q 030094           81 V   81 (183)
Q Consensus        81 V   81 (183)
                      |
T Consensus       360 I  360 (1294)
T PRK11131        360 I  360 (1294)
T ss_pred             E
Confidence            7

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=85.14  E-value=2.2  Score=31.46  Aligned_cols=54  Identities=15%  Similarity=0.236  Sum_probs=45.2

Q ss_pred             CCCceEEEEcccchhhccch--HHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHh
Q 030094           74 FRNLEILVLDEADRLLDMGF--QKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~~~--~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~  127 (183)
                      ....+++|+||+-..++.++  .+.+..+++..|...-+|+.+-..|+++.+.++.
T Consensus        93 ~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e~AD~  148 (159)
T cd00561          93 SGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIEAADL  148 (159)
T ss_pred             cCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCce
Confidence            46778999999998877664  6788888998888888999999999888887764

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.

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=85.06  E-value=5.9  Score=36.80  Aligned_cols=65  Identities=23%  Similarity=0.226  Sum_probs=44.9

Q ss_pred             cCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccchhhccchHHHHHHHHHh-------CCC------CCeEEEEeec
Q 030094           50 EGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISR-------LPK------LRRTGLFSAT  116 (183)
Q Consensus        50 ~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~ll~~~~~~~l~~i~~~-------l~~------~~Q~v~~SAT  116 (183)
                      ....|-+-|-|.|++=|.+  .+-++.-+.+|+||||.=- . +-+-+-.++.+       ..+      .-..|++|||
T Consensus       348 e~T~IkFMTDGVLLrEi~~--DflL~kYSvIIlDEAHERS-v-nTDILiGmLSRiV~LR~k~~ke~~~~kpLKLIIMSAT  423 (1172)
T KOG0926|consen  348 EDTSIKFMTDGVLLREIEN--DFLLTKYSVIILDEAHERS-V-NTDILIGMLSRIVPLRQKYYKEQCQIKPLKLIIMSAT  423 (1172)
T ss_pred             CCceeEEecchHHHHHHHH--hHhhhhceeEEechhhhcc-c-hHHHHHHHHHHHHHHHHHHhhhhcccCceeEEEEeee
Confidence            3567999999999998876  6889999999999999731 1 12222222222       222      2358999999


Q ss_pred             CC
Q 030094          117 QT  118 (183)
Q Consensus       117 ~~  118 (183)
                      +-
T Consensus       424 LR  425 (1172)
T KOG0926|consen  424 LR  425 (1172)
T ss_pred             EE
Confidence            84

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=84.86  E-value=6.5  Score=38.97  Aligned_cols=75  Identities=9%  Similarity=0.160  Sum_probs=49.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhh----------------------------CCCceEEEEEcCcchHHHHH---HHHh
Q 030094            1 MGMIISPTRELSSQIYHVAQPFIST----------------------------LPDVKSVLLVGGVEVKADVK---KIEE   49 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~----------------------------~~~~~~~~~~g~~~~~~~~~---~l~~   49 (183)
                      .+||.|+||..|..+...++++...                            .+...+....|+.+.++...   .+++
T Consensus       246 stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE~~fK~  325 (1490)
T PRK09751        246 STIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITEQALKS  325 (1490)
T ss_pred             CEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHHHHHHHHHHh
Confidence            3699999999999999888776320                            00112445567766544433   4455


Q ss_pred             cCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEE
Q 030094           50 EGANLLIGTPGRLYDIMERMDVLDFRNLEILVL   82 (183)
Q Consensus        50 ~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVv   82 (183)
                      +...++|||.     .+..  ++|+..++++|.
T Consensus       326 G~LrvLVATs-----sLEL--GIDIg~VDlVIq  351 (1490)
T PRK09751        326 GELRCVVATS-----SLEL--GIDMGAVDLVIQ  351 (1490)
T ss_pred             CCceEEEeCc-----HHHc--cCCcccCCEEEE
Confidence            6678888886     3433  677777777775

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=84.84  E-value=5.4  Score=38.89  Aligned_cols=71  Identities=13%  Similarity=0.196  Sum_probs=55.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhc-CCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEE-GANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~-~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +||.+|+++-+.++.+.+.+..  .+++.+..++|+.+..++.+..... +-.|||+|.     ..+  .++++.+++++
T Consensus       282 ILVFLpg~~EI~~l~~~L~~~~--~~~~~VlpLhg~Ls~~eQ~~vf~~~~~rkIVLATN-----IAE--tSLTIpgV~yV  352 (1283)
T TIGR01967       282 ILIFLPGEREIRDAAEILRKRN--LRHTEILPLYARLSNKEQQRVFQPHSGRRIVLATN-----VAE--TSLTVPGIHYV  352 (1283)
T ss_pred             EEEeCCCHHHHHHHHHHHHhcC--CCCcEEEeccCCCCHHHHHHHhCCCCCceEEEecc-----HHH--hccccCCeeEE
Confidence            6899999999998888887642  3467888899998888877766433 358999996     443  57899999987


Q ss_pred             E
Q 030094           81 V   81 (183)
Q Consensus        81 V   81 (183)
                      |
T Consensus       353 I  353 (1283)
T TIGR01967       353 I  353 (1283)
T ss_pred             E
Confidence            6

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.

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=84.75  E-value=2.2  Score=36.95  Aligned_cols=104  Identities=14%  Similarity=0.185  Sum_probs=55.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHh-cCCcCCCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMER-MDVLDFRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~-~~~~~l~~l~~l   80 (183)
                      .++.+++++-|..+++.+.++....|.++...-.       ..  .....-.|.....+.....+.. .+..+=.+..++
T Consensus        57 i~~~A~~~~QA~~~f~~~~~~i~~~~~l~~~~~~-------~~--~~~~~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~  127 (477)
T PF03354_consen   57 IYCAANTRDQAKIVFDEAKKMIEASPELRKRKKP-------KI--IKSNKKEIEFPKTGSFFKALSSDADSLDGLNPSLA  127 (477)
T ss_pred             EEEEeCCHHHHHHHHHHHHHHHHhChhhccchhh-------hh--hhhhceEEEEcCCCcEEEEEecCCCCccCCCCceE
Confidence            5688999999999999999998876544421100       00  0001112222221222222211 123332346899


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEee
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSA  115 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SA  115 (183)
                      |+||+|..-+....+.+..-... .+++|++..|.
T Consensus       128 i~DE~h~~~~~~~~~~l~~g~~~-r~~pl~~~IST  161 (477)
T PF03354_consen  128 IFDELHAHKDDELYDALESGMGA-RPNPLIIIIST  161 (477)
T ss_pred             EEeCCCCCCCHHHHHHHHhhhcc-CCCceEEEEeC
Confidence            99999998553334444433333 24677777654

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A

Probab=84.71  E-value=15  Score=27.74  Aligned_cols=39  Identities=18%  Similarity=0.261  Sum_probs=24.9

Q ss_pred             CCCceEEEEcccchhhccchHHHHHHHHHhCCC-CCeEEEEeec
Q 030094           74 FRNLEILVLDEADRLLDMGFQKQISYIISRLPK-LRRTGLFSAT  116 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~-~~Q~v~~SAT  116 (183)
                      +....++|+|||..+-    ...+..+++..+. ..++++++=.
T Consensus        91 ~~~~~vliVDEasmv~----~~~~~~ll~~~~~~~~klilvGD~  130 (196)
T PF13604_consen   91 LPKKDVLIVDEASMVD----SRQLARLLRLAKKSGAKLILVGDP  130 (196)
T ss_dssp             -TSTSEEEESSGGG-B----HHHHHHHHHHS-T-T-EEEEEE-T
T ss_pred             CCcccEEEEecccccC----HHHHHHHHHHHHhcCCEEEEECCc
Confidence            4455799999998862    4567777777765 6677776543

>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=84.41  E-value=0.74  Score=34.60  Aligned_cols=96  Identities=18%  Similarity=0.273  Sum_probs=36.9

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      ++|-+|+.+=+..+++.+..-.+.. +.+.    ...........+...+..|-.-.|..+...-        ...+++|
T Consensus        29 I~vtAP~~~~~~~lf~~~~~~l~~~-~~~~----~~~~~~~~~~~~~~~~~~i~f~~Pd~l~~~~--------~~~Dlli   95 (177)
T PF05127_consen   29 ILVTAPSPENVQTLFEFAEKGLKAL-GYKE----EKKKRIGQIIKLRFNKQRIEFVAPDELLAEK--------PQADLLI   95 (177)
T ss_dssp             EEEE-SS--S-HHHHHCC-------------------------------CCC--B--HHHHCCT------------SCEE
T ss_pred             EEEecCCHHHHHHHHHHHHhhcccc-cccc----ccccccccccccccccceEEEECCHHHHhCc--------CCCCEEE
Confidence            4677788888877777555443322 2221    0000000111111224455555664433221        1247999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      ||||=.+    -.+.+..+++..+    .++||.|..
T Consensus        96 VDEAAaI----p~p~L~~ll~~~~----~vv~stTi~  124 (177)
T PF05127_consen   96 VDEAAAI----PLPLLKQLLRRFP----RVVFSTTIH  124 (177)
T ss_dssp             ECTGGGS-----HHHHHHHHCCSS----EEEEEEEBS
T ss_pred             EechhcC----CHHHHHHHHhhCC----EEEEEeecc
Confidence            9999665    2556666654333    467788874

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.

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=84.29  E-value=1.4  Score=36.01  Aligned_cols=42  Identities=17%  Similarity=0.243  Sum_probs=28.7

Q ss_pred             CCCceEEEEcccchhhccch--HHHHHHHHHhCCCCCeEEEEee
Q 030094           74 FRNLEILVLDEADRLLDMGF--QKQISYIISRLPKLRRTGLFSA  115 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~~~--~~~l~~i~~~l~~~~Q~v~~SA  115 (183)
                      --.++++|+||.|.++..+.  ...+...++.+.+.-|+-++.+
T Consensus       143 ~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV~v  186 (302)
T PF05621_consen  143 RLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIVGV  186 (302)
T ss_pred             HcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeEEe
Confidence            35679999999999987553  3455566777766666444433

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=84.15  E-value=2.4  Score=32.25  Aligned_cols=55  Identities=15%  Similarity=0.230  Sum_probs=46.4

Q ss_pred             CCCceEEEEcccchhhccch--HHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhh
Q 030094           74 FRNLEILVLDEADRLLDMGF--QKQISYIISRLPKLRRTGLFSATQTEAVEELSKAG  128 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~~~--~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~  128 (183)
                      -...+++|+||+-..++.++  .+++..+++..|...-+|+.+-..|+++.+.++..
T Consensus       113 ~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~~Lie~ADlV  169 (191)
T PRK05986        113 DESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPRELIEAADLV  169 (191)
T ss_pred             CCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCchh
Confidence            45678999999999988875  67888888988888899999998999988887753

>PRK13766 Hef nuclease; Provisional

Probab=83.81  E-value=8.1  Score=35.52  Aligned_cols=83  Identities=18%  Similarity=0.306  Sum_probs=55.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcC--------cchHHH---HHHHHhcCCcEEEeCcHHHHHHHHhcC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGG--------VEVKAD---VKKIEEEGANLLIGTPGRLYDIMERMD   70 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~--------~~~~~~---~~~l~~~~~~IiV~TP~~l~~~l~~~~   70 (183)
                      +||.|+++.-|.++++.+...     ++++..+.|.        .+..++   ......+..+++|+|.     .. . .
T Consensus       368 vlIF~~~~~t~~~L~~~L~~~-----~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~g~~~vLvaT~-----~~-~-e  435 (773)
T PRK13766        368 IIVFTQYRDTAEKIVDLLEKE-----GIKAVRFVGQASKDGDKGMSQKEQIEILDKFRAGEFNVLVSTS-----VA-E-E  435 (773)
T ss_pred             EEEEeCcHHHHHHHHHHHHhC-----CCceEEEEccccccccCCCCHHHHHHHHHHHHcCCCCEEEECC-----hh-h-c
Confidence            699999999999999988553     4556666664        222222   2233345689999997     22 3 5


Q ss_pred             CcCCCCceEEEEcccchhhccchHHHHHHH
Q 030094           71 VLDFRNLEILVLDEADRLLDMGFQKQISYI  100 (183)
Q Consensus        71 ~~~l~~l~~lVvDEad~ll~~~~~~~l~~i  100 (183)
                      ++|+.++.++|+=+.+.    ++...++.+
T Consensus       436 Gldi~~~~~VI~yd~~~----s~~r~iQR~  461 (773)
T PRK13766        436 GLDIPSVDLVIFYEPVP----SEIRSIQRK  461 (773)
T ss_pred             CCCcccCCEEEEeCCCC----CHHHHHHHh
Confidence            78999999999866543    344444433

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=83.77  E-value=1.8  Score=40.95  Aligned_cols=85  Identities=15%  Similarity=0.170  Sum_probs=58.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhc-----CCcCCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERM-----DVLDFR   75 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~-----~~~~l~   75 (183)
                      +-|++.+--||..=.+.+..+..++ ++++.++.......++.+.  ...|||.=||...+ .++++.+     ...-.+
T Consensus       213 VHvVTVNDYLA~RDaewmgply~fL-GLsvg~i~~~~~~~~~rr~--aY~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR  289 (1112)
T PRK12901        213 VHVVTVNDYLAKRDSEWMGPLYEFH-GLSVDCIDKHQPNSEARRK--AYNADITYGTNNEFGFDYLRDNMAHSPEDLVQR  289 (1112)
T ss_pred             cEEEEechhhhhccHHHHHHHHHHh-CCceeecCCCCCCHHHHHH--hCCCcceecCCCccccccchhccccchHhhhCc
Confidence            3467778888988888888888888 9999987663333333333  25799999998765 2333321     112246


Q ss_pred             CceEEEEcccchhh
Q 030094           76 NLEILVLDEADRLL   89 (183)
Q Consensus        76 ~l~~lVvDEad~ll   89 (183)
                      ...+.|+||+|.+|
T Consensus       290 ~~~fAIVDEvDSIL  303 (1112)
T PRK12901        290 KHNYAIVDEVDSVL  303 (1112)
T ss_pred             CCceeEeechhhhh
Confidence            67899999999986

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

Probab=83.77  E-value=7.3  Score=35.36  Aligned_cols=76  Identities=21%  Similarity=0.125  Sum_probs=48.3

Q ss_pred             EEEeCcHHHHHHHHhcCCcCCCCceEEEEcccchh-hccc-hHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCC
Q 030094           54 LLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRL-LDMG-FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRN  131 (183)
Q Consensus        54 IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~l-l~~~-~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~  131 (183)
                      |=.-|-|.|++=+-  ...++.+-+.+++||||.= ++.+ .-..+..|++. .++-..++.|||+..  +.|...|-.-
T Consensus       358 lKYMTDGmLlREfL--~epdLasYSViiiDEAHERTL~TDILfgLvKDIar~-RpdLKllIsSAT~DA--ekFS~fFDda  432 (902)
T KOG0923|consen  358 LKYMTDGMLLREFL--SEPDLASYSVIIVDEAHERTLHTDILFGLVKDIARF-RPDLKLLISSATMDA--EKFSAFFDDA  432 (902)
T ss_pred             eeeecchhHHHHHh--ccccccceeEEEeehhhhhhhhhhHHHHHHHHHHhh-CCcceEEeeccccCH--HHHHHhccCC
Confidence            44678888776654  4678999999999999973 1111 22334444433 357789999999983  3444444334


Q ss_pred             CeE
Q 030094          132 PVR  134 (183)
Q Consensus       132 ~~~  134 (183)
                      |++
T Consensus       433 pIF  435 (902)
T KOG0923|consen  433 PIF  435 (902)
T ss_pred             cEE
Confidence            443

>TIGR01447 recD exodeoxyribonuclease V, alpha subunit

Probab=83.62  E-value=6  Score=35.39  Aligned_cols=37  Identities=27%  Similarity=0.380  Sum_probs=29.2

Q ss_pred             CCCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEe
Q 030094           74 FRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFS  114 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~S  114 (183)
                      ...++++|+|||.++ +   ...+..+++.++..+++|+++
T Consensus       257 ~l~~dvlIiDEaSMv-d---~~l~~~ll~al~~~~rlIlvG  293 (586)
T TIGR01447       257 PLPLDVLVVDEASMV-D---LPLMAKLLKALPPNTKLILLG  293 (586)
T ss_pred             CCcccEEEEcccccC-C---HHHHHHHHHhcCCCCEEEEEC
Confidence            446789999999775 3   457778889998888888865

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.

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=83.56  E-value=2.5  Score=31.78  Aligned_cols=54  Identities=15%  Similarity=0.251  Sum_probs=45.6

Q ss_pred             CCCceEEEEcccchhhccch--HHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHh
Q 030094           74 FRNLEILVLDEADRLLDMGF--QKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~~~--~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~  127 (183)
                      -....++|+||+-..++.++  .+.+..+++..|...-+|+.+-..|+++.+.++.
T Consensus       113 ~~~~dlvVLDEi~~Al~~gli~~eeVl~~L~~rp~~~evILTGR~~p~~Lie~AD~  168 (178)
T PRK07414        113 EGRYSLVVLDELSLAIQFGLIPETEVLEFLEKRPSHVDVILTGPEMPESLLAIADQ  168 (178)
T ss_pred             CCCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCCe
Confidence            35678999999999988875  6788889999888889999999999888877764

>PRK10875 recD exonuclease V subunit alpha; Provisional

Probab=83.23  E-value=6.9  Score=35.21  Aligned_cols=37  Identities=30%  Similarity=0.439  Sum_probs=29.2

Q ss_pred             CCCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEe
Q 030094           74 FRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFS  114 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~S  114 (183)
                      +-..+++|+|||.++ +   ...+..+++.+++.+++|+++
T Consensus       263 ~l~~dvlIvDEaSMv-d---~~lm~~ll~al~~~~rlIlvG  299 (615)
T PRK10875        263 PLHLDVLVVDEASMV-D---LPMMARLIDALPPHARVIFLG  299 (615)
T ss_pred             CCCCCeEEEChHhcc-c---HHHHHHHHHhcccCCEEEEec
Confidence            445689999999775 3   567778889999888888865

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=82.84  E-value=2.4  Score=31.69  Aligned_cols=55  Identities=16%  Similarity=0.301  Sum_probs=40.0

Q ss_pred             CCCCceEEEEcccchhhccch--HHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHh
Q 030094           73 DFRNLEILVLDEADRLLDMGF--QKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (183)
Q Consensus        73 ~l~~l~~lVvDEad~ll~~~~--~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~  127 (183)
                      .-....++|+||+-..++.++  .+++..+++.-|...-+|+..-..|+++.+.++.
T Consensus        93 ~~~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~~~evVlTGR~~~~~l~e~ADl  149 (172)
T PF02572_consen   93 SSGEYDLVILDEINYAVDYGLLSEEEVLDLLENRPESLEVVLTGRNAPEELIEAADL  149 (172)
T ss_dssp             T-TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-TT-EEEEE-SS--HHHHHH-SE
T ss_pred             hCCCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCCCeEEEEECCCCCHHHHHhCCe
Confidence            346788999999999988775  6788889998888899999999999998888774

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.

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=82.63  E-value=8.9  Score=36.36  Aligned_cols=73  Identities=15%  Similarity=0.247  Sum_probs=53.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHH---Hh--cCCcEEEeCcHHHHHHHHhcCCcCCCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKI---EE--EGANLLIGTPGRLYDIMERMDVLDFRN   76 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l---~~--~~~~IiV~TP~~l~~~l~~~~~~~l~~   76 (183)
                      +||+|.+++-+..+.+.++...    ++++..+.|+.+..+..+.+   ..  +++.|+|+|-     . -. .++|+..
T Consensus       496 vLVF~~~~~t~~~L~~~L~~~~----Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTd-----v-gs-eGlNlq~  564 (956)
T PRK04914        496 VLVICAKAATALQLEQALRERE----GIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSE-----I-GS-EGRNFQF  564 (956)
T ss_pred             EEEEeCcHHHHHHHHHHHhhcc----CeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEech-----h-hc-cCCCccc
Confidence            6899999999999998775431    67889999998766554433   22  3689999993     2 23 5789988


Q ss_pred             ceEEEEccc
Q 030094           77 LEILVLDEA   85 (183)
Q Consensus        77 l~~lVvDEa   85 (183)
                      +..+|.=+.
T Consensus       565 a~~VInfDl  573 (956)
T PRK04914        565 ASHLVLFDL  573 (956)
T ss_pred             ccEEEEecC
Confidence            888875444

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

Probab=81.71  E-value=5.8  Score=33.36  Aligned_cols=70  Identities=14%  Similarity=0.256  Sum_probs=51.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcc---hHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVE---VKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~---~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      |++|++.||+-+.++...+.+.     +.++.++.|...   .+...+..+.+...++|.|-     ++.  .++|+.++
T Consensus       265 q~~if~nt~r~v~~l~~~L~~~-----~~~~s~~~~d~~q~~R~~~~~ef~~gssrvlIttd-----l~a--rgidv~~~  332 (397)
T KOG0327|consen  265 QAVIFCNTRRKVDNLTDKLRAH-----GFTVSAIHGDMEQNERDTLMREFRSGSSRVLITTD-----LLA--RGIDVQQV  332 (397)
T ss_pred             cceEEecchhhHHHHHHHHhhC-----CceEEEeecccchhhhhHHHHHhhcCCceEEeecc-----ccc--cccchhhc
Confidence            6899999999999888876433     677777777654   33444555567788999983     443  57899998


Q ss_pred             eEEEE
Q 030094           78 EILVL   82 (183)
Q Consensus        78 ~~lVv   82 (183)
                      ..+|-
T Consensus       333 slvin  337 (397)
T KOG0327|consen  333 SLVVN  337 (397)
T ss_pred             ceeee
Confidence            88873

>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]

Probab=81.62  E-value=2  Score=41.51  Aligned_cols=67  Identities=19%  Similarity=0.339  Sum_probs=51.0

Q ss_pred             hcCCcEEEeCcHHHHHHHHhc--C------------CcCCCCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEe
Q 030094           49 EEGANLLIGTPGRLYDIMERM--D------------VLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFS  114 (183)
Q Consensus        49 ~~~~~IiV~TP~~l~~~l~~~--~------------~~~l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~S  114 (183)
                      ..|..|.+..|+.=..-+...  |            -+.++...|.|+||+|.-+|......+..++..+.++.|+|+.|
T Consensus      1047 ~~Giei~a~ppgK~~~~l~~LSGGEKsLtAlAllFAi~~~~PaPf~vLDEVDAaLD~~Nv~r~~~~i~e~s~~sQFIvIT 1126 (1163)
T COG1196        1047 TAGIEISARPPGKKLQSLSLLSGGEKSLTALALLFAIQKYRPAPFYVLDEVDAALDDANVERVARLIKEMSKETQFIVIT 1126 (1163)
T ss_pred             hcCcEEEEECCCCCccchhhcCCcHHHHHHHHHHHHHHhhCCCCeeeeccchhhccHHHHHHHHHHHHHhCcCCeEEEEE
Confidence            468899999998744322210  1            11246677999999999999888899999999999999999986


Q ss_pred             e
Q 030094          115 A  115 (183)
Q Consensus       115 A  115 (183)
                      -
T Consensus      1127 h 1127 (1163)
T COG1196        1127 H 1127 (1163)
T ss_pred             c
Confidence            4

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=80.80  E-value=22  Score=26.92  Aligned_cols=45  Identities=11%  Similarity=0.254  Sum_probs=26.6

Q ss_pred             CCceEEEEcccchhhcc-chHHHHHHHHHhCCCCCeEEEEeecCCh
Q 030094           75 RNLEILVLDEADRLLDM-GFQKQISYIISRLPKLRRTGLFSATQTE  119 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~~-~~~~~l~~i~~~l~~~~Q~v~~SAT~~~  119 (183)
                      ...+++++||+|.+-.. +....+..+++........++++++.++
T Consensus        89 ~~~~lLvIDdi~~l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~~  134 (226)
T TIGR03420        89 EQADLVCLDDVEAIAGQPEWQEALFHLYNRVREAGGRLLIAGRAAP  134 (226)
T ss_pred             ccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCeEEEECCCCh
Confidence            44578999999997532 2355666666554322224555665443

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.

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

Probab=80.72  E-value=13  Score=32.60  Aligned_cols=73  Identities=16%  Similarity=0.341  Sum_probs=53.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEc--------CcchHHHHHH---HHhcCCcEEEeCcHHHHHHHHhcC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVG--------GVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMD   70 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g--------~~~~~~~~~~---l~~~~~~IiV~TP~~l~~~l~~~~   70 (183)
                      ++|.+..|+-|..+.+.+.+.+   +..+ ..++|        |.+-++|...   .+.+.++++|+|.      +.. .
T Consensus       369 vIVFT~yRdTae~i~~~L~~~~---~~~~-~rFiGQa~r~~~~GMsQkeQ~eiI~~Fr~Ge~nVLVaTS------VgE-E  437 (542)
T COG1111         369 VIVFTEYRDTAEEIVNFLKKIG---IKAR-VRFIGQASREGDKGMSQKEQKEIIDQFRKGEYNVLVATS------VGE-E  437 (542)
T ss_pred             EEEEehhHhHHHHHHHHHHhcC---Ccce-eEEeeccccccccccCHHHHHHHHHHHhcCCceEEEEcc------ccc-c
Confidence            6889999999999888877764   2444 34555        2334455443   3346799999996      445 7


Q ss_pred             CcCCCCceEEEEccc
Q 030094           71 VLDFRNLEILVLDEA   85 (183)
Q Consensus        71 ~~~l~~l~~lVvDEa   85 (183)
                      ++|.-.++++|+=|+
T Consensus       438 GLDIp~vDlVifYEp  452 (542)
T COG1111         438 GLDIPEVDLVIFYEP  452 (542)
T ss_pred             cCCCCcccEEEEecC
Confidence            899999999998877

>PRK06893 DNA replication initiation factor; Validated

Probab=80.67  E-value=4.2  Score=31.55  Aligned_cols=47  Identities=15%  Similarity=0.250  Sum_probs=31.6

Q ss_pred             CCCceEEEEcccchhhcc-chHHHHHHHHHhCCC-CCeEEEEeecCChH
Q 030094           74 FRNLEILVLDEADRLLDM-GFQKQISYIISRLPK-LRRTGLFSATQTEA  120 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~-~~~~~l~~i~~~l~~-~~Q~v~~SAT~~~~  120 (183)
                      +.+.+++++||+|.+... .+...+.++++.... +.+++++|++.++.
T Consensus        89 ~~~~dlLilDDi~~~~~~~~~~~~l~~l~n~~~~~~~~illits~~~p~  137 (229)
T PRK06893         89 LEQQDLVCLDDLQAVIGNEEWELAIFDLFNRIKEQGKTLLLISADCSPH  137 (229)
T ss_pred             cccCCEEEEeChhhhcCChHHHHHHHHHHHHHHHcCCcEEEEeCCCChH
Confidence            567789999999998643 234456666665543 45667788877555

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

Probab=80.65  E-value=10  Score=35.44  Aligned_cols=70  Identities=17%  Similarity=0.150  Sum_probs=47.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH--------HHHHh----c-------CCcEEEeCcHH
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV--------KKIEE----E-------GANLLIGTPGR   61 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~--------~~l~~----~-------~~~IiV~TP~~   61 (183)
                      .+||+|+|++-|..+++.+++.     ++  ..+.|+....+..        +...+    +       ++.|+|||   
T Consensus       274 ~vLVF~NTv~~Aq~L~~~L~~~-----g~--~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVAT---  343 (844)
T TIGR02621       274 AILVFCRTVKHVRKVFAKLPKE-----KF--ELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCT---  343 (844)
T ss_pred             cEEEEECCHHHHHHHHHHHHhc-----CC--eEeeCCCCHHHHhhHHHHHHHHHHhccccccccccccccceEEecc---
Confidence            3799999999999999988764     33  6777776654433        11211    1       26899999   


Q ss_pred             HHHHHHhcCCcCCCCceEEEEccc
Q 030094           62 LYDIMERMDVLDFRNLEILVLDEA   85 (183)
Q Consensus        62 l~~~l~~~~~~~l~~l~~lVvDEa   85 (183)
                        +.+..  ++|++. ..+|.|.+
T Consensus       344 --dVaer--GLDId~-d~VI~d~a  362 (844)
T TIGR02621       344 --SAGEV--GVNISA-DHLVCDLA  362 (844)
T ss_pred             --chhhh--cccCCc-ceEEECCC
Confidence              45554  677765 67777644

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.

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=80.01  E-value=3.7  Score=33.21  Aligned_cols=41  Identities=17%  Similarity=0.160  Sum_probs=29.4

Q ss_pred             CCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEee
Q 030094           75 RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSA  115 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SA  115 (183)
                      ..-+++++||+|.+-.......+..+++..+..+++++.+.
T Consensus        99 ~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n  139 (316)
T PHA02544         99 GGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITAN  139 (316)
T ss_pred             CCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcC
Confidence            35689999999998333345677777887777777776554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	183
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		1e-23
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		9e-22
3ly5_A	262	Ddx18 Dead-Domain Length = 262		9e-22
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		2e-19
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		6e-19
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		8e-19
4a4d_A	253	Crystal Structure Of The N-Terminal Domain Of The H		5e-18
3fe2_A	242	Human Dead-Box Rna Helicase Ddx5 (P68), Conserved D		5e-18
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		5e-18
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		1e-17
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		4e-17
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		4e-17
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		3e-16
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		5e-16
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		8e-16
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		8e-16
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		8e-16
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		8e-16
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		8e-16
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		9e-16
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-15
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		1e-15
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		2e-15
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		2e-15
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		1e-14
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		2e-14
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		9e-14
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		2e-13
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		2e-13
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		2e-13
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		3e-13
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		3e-13
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		3e-13
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		3e-13
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		4e-13
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		6e-13
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		8e-13
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		1e-12
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		3e-11
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		8e-10
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		9e-10
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		9e-10
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		2e-09
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		2e-09
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		2e-09
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		2e-09
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		4e-09
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		6e-09
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		2e-07

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score =  105 bits (263), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 58/139 (41%), Positives = 91/139 (65%), Gaps = 3/139 (2%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +IISPTREL+ Q + V +  +    D  + L++GG ++K + ++I     N+L+ TPGRL
Sbjct: 101 LIISPTRELAYQTFEVLRK-VGKNHDFSAGLIIGGKDLKHEAERIN--NINILVCTPGRL 157
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
              M+        +L++LVLDEADR+LDMGF   ++ +I  LPK R+T LFSATQT++V+
Sbjct: 158 LQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVK 217
Query: 123 ELSKAGLRNPVRVEVRAES 141
           +L++  L+NP  V V  ++
Sbjct: 218 DLARLSLKNPEYVWVHEKA 236

>pdb|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 99.8 bits (247), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 51/139 (36%), Positives = 91/139 (65%), Gaps = 2/139 (1%)
Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             ++++PTREL+ QI    +   S++  V+S ++VGG++  +    + ++  +++I TPG
Sbjct: 113 FALVLTPTRELAFQISEQFEALGSSI-GVQSAVIVGGIDSMSQSLALAKK-PHIIIATPG 170
Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL D +E     + R L+ LV+DEADR+L+M F+ ++  I+  +P+ R+T LFSAT T+ 
Sbjct: 171 RLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKK 230
Query: 121 VEELSKAGLRNPVRVEVRA 139
           V++L +A L+NPV+  V +
Sbjct: 231 VQKLQRAALKNPVKCAVSS 249

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 99.4 bits (246), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 53/128 (41%), Positives = 84/128 (65%), Gaps = 2/128 (1%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I+SPTREL+ Q + V +  ++        L++GG    A+ +K+   G N+++ TPGRL
Sbjct: 130 LILSPTRELAMQTFGVLKELMTHHVHTYG-LIMGGSNRSAEAQKLGN-GINIIVATPGRL 187
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D M+      ++NL+ LV+DEADR+LD+GF++++  II  LP  R+T LFSATQT  VE
Sbjct: 188 LDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVE 247
Query: 123 ELSKAGLR 130
           +L++  L+
Sbjct: 248 DLARISLK 255

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 92.0 bits (227), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 60/153 (39%), Positives = 96/153 (62%), Gaps = 10/153 (6%)
Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           + ++++PTREL+ QIY  A+ F S    V+  ++ GG ++   ++ +E  G +LL+ TPG
Sbjct: 103 ISLVLAPTRELAVQIYEEARKF-SYRSRVRPCVVYGGADIGQQIRDLER-GCHLLVATPG 160
Query: 61  RLYDIMERMDV-LDFRNLEILVLDEADRLLDMGFQKQISYIISR---LPK-LRRTGLFSA 115
           RL D+MER  + LDF   + LVLDEADR+LDMGF+ QI  I+ +    PK +R T +FSA
Sbjct: 161 RLVDMMERGKIGLDF--CKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSA 218
Query: 116 TQTEAVEELSKAGLRNPVRVEV-RAESKSHHVS 147
           T  + ++ L++  L   + + V R  S S +++
Sbjct: 219 TFPKEIQMLARDFLDEYIFLAVGRVGSTSENIT 251

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 90.1 bits (222), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 50/142 (35%), Positives = 85/142 (59%), Gaps = 8/142 (5%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSV---LLVGGVEVKADVKKIEEEGANLLIGT 58
            ++++PTREL+ QI    Q  +  L D         +GG  V+A+V+K++ E  ++++GT
Sbjct: 85  ALVLAPTRELAQQI----QKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGT 140
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  + +++ VLDEAD +L  GF+ QI  I  +L    +  L SAT  
Sbjct: 141 PGRVFDMLNRR-YLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMP 199
Query: 119 EAVEELSKAGLRNPVRVEVRAE 140
             V E++K  +R+P+R+ V+ E
Sbjct: 200 SDVLEVTKKFMRDPIRILVKKE 221

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 89.7 bits (221), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 50/142 (35%), Positives = 85/142 (59%), Gaps = 8/142 (5%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSV---LLVGGVEVKADVKKIEEEGANLLIGT 58
            ++++PTREL+ QI    Q  +  L D         +GG  V+A+V+K++ E  ++++GT
Sbjct: 111 ALVLAPTRELAQQI----QKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGT 166
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  + +++ VLDEAD +L  GF+ QI  I  +L    +  L SAT  
Sbjct: 167 PGRVFDMLNRR-YLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMP 225
Query: 119 EAVEELSKAGLRNPVRVEVRAE 140
             V E++K  +R+P+R+ V+ E
Sbjct: 226 SDVLEVTKKFMRDPIRILVKKE 247

>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 = 87.0 bits (214), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 48/137 (35%), Positives = 80/137 (58%), Gaps = 3/137 (2%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           ++++PTREL+ Q+  VA  +      +KS  + GG      ++ +E  G  + I TPGRL
Sbjct: 120 LVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLER-GVEICIATPGRL 177
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D +E     + R    LVLDEADR+LDMGF+ QI  I+ ++   R+T ++SAT  + V 
Sbjct: 178 IDFLE-CGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVR 236
Query: 123 ELSKAGLRNPVRVEVRA 139
           +L++  L++ + + + A
Sbjct: 237 QLAEDFLKDYIHINIGA 253

>pdb|3FE2|A Chain A, Human Dead-Box Rna Helicase Ddx5 (P68), Conserved Domain I In Complex With Adp Length = 242

Iteration: 1
 Score = 87.0 bits (214), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 48/137 (35%), Positives = 80/137 (58%), Gaps = 3/137 (2%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           ++++PTREL+ Q+  VA  +      +KS  + GG      ++ +E  G  + I TPGRL
Sbjct: 106 LVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLER-GVEICIATPGRL 163
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D +E     + R    LVLDEADR+LDMGF+ QI  I+ ++   R+T ++SAT  + V 
Sbjct: 164 IDFLE-CGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVR 222
Query: 123 ELSKAGLRNPVRVEVRA 139
           +L++  L++ + + + A
Sbjct: 223 QLAEDFLKDYIHINIGA 239

>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 = 87.0 bits (214), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 54/140 (38%), Positives = 90/140 (64%), Gaps = 9/140 (6%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTREL+ QI   +Q F    P ++S ++ GG +  + +++++  G +LL+ TPGRL
Sbjct: 104 LILAPTRELAIQILSESQKFSLNTP-LRSCVVYGGADTHSQIREVQM-GCHLLVATPGRL 161
Query: 63  YDIMERMDV-LDFRNLEILVLDEADRLLDMGFQKQISYII--SRLPK--LRRTGLFSATQ 117
            D +E+  + L+F   + +VLDEADR+LDMGF+ QI  II  S +P    R+T +FSAT 
Sbjct: 162 VDFIEKNKISLEF--CKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATF 219
Query: 118 TEAVEELSKAGLRNPVRVEV 137
            + +++L+   L N + + V
Sbjct: 220 PKEIQKLAADFLYNYIFMTV 239

>pdb|3BOR|A Chain A, Crystal Structure Of The Deadc Domain Of Human Translation Initiation Factor 4a-2 Length = 237

Iteration: 1
 Score = 85.9 bits (211), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 49/142 (34%), Positives = 84/142 (59%), Gaps = 8/142 (5%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLL---VGGVEVKADVKKIEEEGANLLIGT 58
            ++++PTREL+ QI    Q  I  L D         +GG  V+ +++K++ E  ++++GT
Sbjct: 101 ALVLAPTRELAQQI----QKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGT 156
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  + +++ VLDEAD +L  GF+ QI  I  +L    +  L SAT  
Sbjct: 157 PGRVFDMLNRR-YLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMP 215
Query: 119 EAVEELSKAGLRNPVRVEVRAE 140
             V E++K  +R+P+R+ V+ E
Sbjct: 216 TDVLEVTKKFMRDPIRILVKKE 237

>pdb|2GXQ|A Chain A, Hera N-Terminal Domain In Complex With Amp, Crystal Form 1 Length = 207

Iteration: 1
 Score = 84.0 bits (206), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 50/136 (36%), Positives = 79/136 (58%), Gaps = 5/136 (3%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ Q   VA    +  P +K V + GG       K+    GA+ ++ TPGR
Sbjct: 75  ALVLTPTRELALQ---VASELTAVAPHLKVVAVYGGTGYGKQ-KEALLRGADAVVATPGR 130
Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
             D + R  VLD   +E+ VLDEAD +L MGF++++  ++S  P  R+T LFSAT     
Sbjct: 131 ALDYL-RQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWA 189
Query: 122 EELSKAGLRNPVRVEV 137
           + L++  ++NPV + V
Sbjct: 190 KRLAERYMKNPVLINV 205

>pdb|3MWJ|A Chain A, Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Apo Form Length = 207

Iteration: 1
 Score = 84.0 bits (206), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 50/136 (36%), Positives = 79/136 (58%), Gaps = 5/136 (3%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ Q   VA    +  P +K V + GG       K+    GA+ ++ TPGR
Sbjct: 75  ALVLTPTRELALQ---VASELTAVAPHLKVVAVYGGTGY-GKQKEALLRGADAVVATPGR 130
Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
             D + R  VLD   +E+ VLDEAD +L MGF++++  ++S  P  R+T LFSAT     
Sbjct: 131 ALDYL-RQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWA 189
Query: 122 EELSKAGLRNPVRVEV 137
           + L++  ++NPV + V
Sbjct: 190 KRLAERYMKNPVLINV 205

>pdb|2J0U|B Chain B, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 80.9 bits (198), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 50/142 (35%), Positives = 86/142 (60%), Gaps = 9/142 (6%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPD---VKSVLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTREL+ Q+    Q  +  L D   V+S   +GG  V  D++K++  G +++ GT
Sbjct: 72  ALILAPTRELAVQV----QKGLLALGDYMNVQSHACIGGTNVGEDIRKLDY-GQHVVAGT 126
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  R +++LVLDEAD +L+ GF++QI  +   LP   +  L SAT  
Sbjct: 127 PGRVFDMIRRRS-LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 185
Query: 119 EAVEELSKAGLRNPVRVEVRAE 140
             V E++   + +P+R+ V+ +
Sbjct: 186 HEVLEMTNKFMTDPIRILVKRD 207

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 80.5 bits (197), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 50/139 (35%), Positives = 76/139 (54%), Gaps = 5/139 (3%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVL---LVGGVEVKADVKKIEEEGANLLIGT 58
            +I +PTREL++QIYH         P  + ++   L+GG + +  ++K+  +  +++IGT
Sbjct: 75  AVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKLNVQ-PHIVIGT 133
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR+ D + R   LD     ILV+DEAD  LD GF   +  I +R PK  +  +FSAT  
Sbjct: 134 PGRINDFI-REQALDVHTAHILVVDEADLXLDXGFITDVDQIAARXPKDLQXLVFSATIP 192
Query: 119 EAVEELSKAGLRNPVRVEV 137
           E ++   K    NP  V V
Sbjct: 193 EKLKPFLKKYXENPTFVHV 211

>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 = 79.7 bits (195), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 49/142 (34%), Positives = 85/142 (59%), Gaps = 9/142 (6%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSV---LLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTREL+ QI    Q  +  L D  +V     +GG  V  D++K++  G +++ GT
Sbjct: 109 ALILAPTRELAVQI----QKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGT 163
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  R +++LVLDEAD +L+ GF++QI  +   LP   +  L SAT  
Sbjct: 164 PGRVFDMIRRRS-LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 222
Query: 119 EAVEELSKAGLRNPVRVEVRAE 140
             + E++   + +P+R+ V+ +
Sbjct: 223 HEILEMTNKFMTDPIRILVKRD 244

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 79.7 bits (195), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 48/141 (34%), Positives = 81/141 (57%), Gaps = 8/141 (5%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V       + D+K    +GG     D + + +  A +++GTPGR
Sbjct: 93  ALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--AQIVVGTPGR 149
Query: 62  LYDIMERMDVLDFRN--LEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE 119
           ++D ++R     FR   +++ +LDEAD +L  GF++QI  I + LP   +  L SAT   
Sbjct: 150 VFDNIQRRR---FRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPN 206
Query: 120 AVEELSKAGLRNPVRVEVRAE 140
            V E++   +RNPVR+ V+ +
Sbjct: 207 DVLEVTTKFMRNPVRILVKKD 227

>pdb|2J0Q|A Chain A, The Crystal Structure Of The Exon Junction Complex At 3.2 A Resolution Length = 410

Iteration: 1
 Score = 79.7 bits (195), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 49/142 (34%), Positives = 85/142 (59%), Gaps = 9/142 (6%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSV---LLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTREL+ QI    Q  +  L D  +V     +GG  V  D++K++  G +++ GT
Sbjct: 108 ALILAPTRELAVQI----QKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGT 162
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  R +++LVLDEAD +L+ GF++QI  +   LP   +  L SAT  
Sbjct: 163 PGRVFDMIRRRS-LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 221
Query: 119 EAVEELSKAGLRNPVRVEVRAE 140
             + E++   + +P+R+ V+ +
Sbjct: 222 HEILEMTNKFMTDPIRILVKRD 243

>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 = 79.7 bits (195), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 49/142 (34%), Positives = 85/142 (59%), Gaps = 9/142 (6%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSV---LLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTREL+ QI    Q  +  L D  +V     +GG  V  D++K++  G +++ GT
Sbjct: 109 ALILAPTRELAVQI----QKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGT 163
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  R +++LVLDEAD +L+ GF++QI  +   LP   +  L SAT  
Sbjct: 164 PGRVFDMIRRRS-LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 222
Query: 119 EAVEELSKAGLRNPVRVEVRAE 140
             + E++   + +P+R+ V+ +
Sbjct: 223 HEILEMTNKFMTDPIRILVKRD 244

>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 = 79.7 bits (195), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 48/141 (34%), Positives = 81/141 (57%), Gaps = 8/141 (5%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V       + D+K    +GG     D + + +  A +++GTPGR
Sbjct: 85  ALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--AQIVVGTPGR 141
Query: 62  LYDIMERMDVLDFRN--LEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE 119
           ++D ++R     FR   +++ +LDEAD +L  GF++QI  I + LP   +  L SAT   
Sbjct: 142 VFDNIQRRR---FRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPN 198
Query: 120 AVEELSKAGLRNPVRVEVRAE 140
            V E++   +RNPVR+ V+ +
Sbjct: 199 DVLEVTTKFMRNPVRILVKKD 219

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 79.7 bits (195), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 49/142 (34%), Positives = 85/142 (59%), Gaps = 9/142 (6%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSV---LLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTREL+ QI    Q  +  L D  +V     +GG  V  D++K++  G +++ GT
Sbjct: 87  ALILAPTRELAVQI----QKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGT 141
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  R +++LVLDEAD +L+ GF++QI  +   LP   +  L SAT  
Sbjct: 142 PGRVFDMIRRRS-LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 200
Query: 119 EAVEELSKAGLRNPVRVEVRAE 140
             + E++   + +P+R+ V+ +
Sbjct: 201 HEILEMTNKFMTDPIRILVKRD 222

>pdb|2J0U|A Chain A, The Crystal Structure Of Eif4aiii-Barentsz Complex At 3.0 A Resolution Length = 374

Iteration: 1
 Score = 79.3 bits (194), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 48/142 (33%), Positives = 85/142 (59%), Gaps = 9/142 (6%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSV---LLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTREL+ Q+    Q  +  L D  +V     +GG  V  D++K++  G +++ GT
Sbjct: 72  ALILAPTRELAVQV----QKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGT 126
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  R +++LVLDEAD +L+ GF++QI  +   LP   +  L SAT  
Sbjct: 127 PGRVFDMIRRRS-LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 185
Query: 119 EAVEELSKAGLRNPVRVEVRAE 140
             + E++   + +P+R+ V+ +
Sbjct: 186 HEILEMTNKFMTDPIRILVKRD 207

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score = 79.0 bits (193), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 47/139 (33%), Positives = 77/139 (55%), Gaps = 8/139 (5%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSV---LLVGGVEVKADVKKIEEEGANLLIGT 58
            ++++PTREL+ QI    Q  +  L D         +GG  V+A+V+ ++ E  ++++GT
Sbjct: 86  ALVLAPTRELAQQI----QXVVMALGDYMGASCHACIGGTNVRAEVQXLQMEAPHIIVGT 141
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L    + + VLDEAD +L  GF  QI  I   L    +  L SAT  
Sbjct: 142 PGRVFDMLNRR-YLSPXYIXMFVLDEADEMLSRGFXDQIYDIFQXLNSNTQVVLLSATMP 200
Query: 119 EAVEELSKAGLRNPVRVEV 137
             V E++   +R+P+R+ V
Sbjct: 201 SDVLEVTXXFMRDPIRILV 219

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 78.6 bits (192), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 48/138 (34%), Positives = 79/138 (57%), Gaps = 8/138 (5%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V       + D+K    +GG     D + + +  A +++GTPGR
Sbjct: 92  ALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--AQIVVGTPGR 148
Query: 62  LYDIMERMDVLDFRN--LEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE 119
           ++D ++R     FR   +++ +LDEAD +L  GF++QI  I + LP   +  L SAT   
Sbjct: 149 VFDNIQRRR---FRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPN 205
Query: 120 AVEELSKAGLRNPVRVEV 137
            V E++   +RNPVR+ V
Sbjct: 206 DVLEVTTKFMRNPVRILV 223

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 78.2 bits (191), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 45/135 (33%), Positives = 79/135 (58%), Gaps = 6/135 (4%)
Query: 3   MIISPTRELSSQIY-HVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
           ++++PTREL+ Q+  H+    I    D K   + GG+  KA + ++    A++++ TPGR
Sbjct: 60  LVVTPTRELTRQVASHIRD--IGRYMDTKVAEVYGGMPYKAQINRVR--NADIVVATPGR 115
Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           L D+  +  V+D  + EI+++DEAD + +MGF   I  I+++    + TGLFSAT  E +
Sbjct: 116 LLDLWSK-GVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEEI 174
Query: 122 EELSKAGLRNPVRVE 136
            ++ K  + N   +E
Sbjct: 175 RKVVKDFITNYEEIE 189

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 75.5 bits (184), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 49/141 (34%), Positives = 78/141 (55%), Gaps = 8/141 (5%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            + ++PTREL+ QI  V    ++   D+K    +GG     D + + +  A +++GTPGR
Sbjct: 92  ALXLAPTRELALQIQKVVXA-LAFHXDIKVHACIGGTSFVEDAEGLRD--AQIVVGTPGR 148
Query: 62  LYDIMERMDVLDFRNLEI--LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE 119
           ++D ++R     FR  +I   +LDEAD  L  GF++QI  I + LP   +  L SAT   
Sbjct: 149 VFDNIQRRR---FRTDKIKXFILDEADEXLSSGFKEQIYQIFTLLPPTTQVVLLSATXPN 205
Query: 120 AVEELSKAGLRNPVRVEVRAE 140
            V E++    RNPVR+ V+ +
Sbjct: 206 DVLEVTTKFXRNPVRILVKKD 226

>pdb|2DB3|A Chain A, Structural Basis For Rna Unwinding By The Dead-Box Protein Drosophila Vasa Length = 434

Iteration: 1
 Score = 75.1 bits (183), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 49/138 (35%), Positives = 84/138 (60%), Gaps = 7/138 (5%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I+SPTREL+ QI++ A+ F +    +K  ++ GG   +   + I   G +++I TPGRL
Sbjct: 133 VIVSPTRELAIQIFNEARKF-AFESYLKIGIVYGGTSFRHQNECITR-GCHVVIATPGRL 190
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRL---PKLRRTGLFSATQTE 119
            D ++R   + F +   +VLDEADR+LDMGF + +  I++ +   P+  +T +FSAT  E
Sbjct: 191 LDFVDRT-FITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPE-HQTLMFSATFPE 248
Query: 120 AVEELSKAGLRNPVRVEV 137
            ++ ++   L+N V V +
Sbjct: 249 EIQRMAGEFLKNYVFVAI 266

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 73.2 bits (178), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 37/141 (26%), Positives = 84/141 (59%), Gaps = 2/141 (1%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR+
Sbjct: 79  LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 138
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
              + R   L+ ++++  +LDEAD++L+ +  ++ +  I    P  ++  +FSAT ++ +
Sbjct: 139 L-ALARNKSLNLKHIKHFILDEADKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEI 197
Query: 122 EELSKAGLRNPVRVEVRAESK 142
             + +  +++P+ + V  E+K
Sbjct: 198 RPVCRKFMQDPMEIFVDDETK 218

>pdb|3IUY|A Chain A, Crystal Structure Of Ddx53 Dead-Box Domain Length = 228

Iteration: 1
 Score = 72.0 bits (175), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 43/135 (31%), Positives = 82/135 (60%), Gaps = 4/135 (2%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           ++++PTREL+  +      +  +   +KS+ + GG      ++ I + G +++I TPGRL
Sbjct: 98  LVLTPTRELALHVEAECSKY--SYKGLKSICIYGGRNRNGQIEDISK-GVDIIIATPGRL 154
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D ++  + ++ R++  LV+DEAD++LDM F+ QI  I+  +   R+T + SAT  + V 
Sbjct: 155 ND-LQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVR 213
Query: 123 ELSKAGLRNPVRVEV 137
           +L+ + L++P+ V V
Sbjct: 214 QLALSYLKDPMIVYV 228

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 72.0 bits (175), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/141 (25%), Positives = 83/141 (58%), Gaps = 2/141 (1%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR+
Sbjct: 80  LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 139
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
              + R   L+ ++++  +LDE D++L+ +  ++ +  I    P  ++  +FSAT ++ +
Sbjct: 140 L-ALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEI 198
Query: 122 EELSKAGLRNPVRVEVRAESK 142
             + +  +++P+ + V  E+K
Sbjct: 199 RPVCRKFMQDPMEIFVDDETK 219

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 71.6 bits (174), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 36/141 (25%), Positives = 83/141 (58%), Gaps = 2/141 (1%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR+
Sbjct: 80  LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 139
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
              + R   L+ ++++  +LDE D++L+ +  ++ +  I    P  ++  +FSAT ++ +
Sbjct: 140 L-ALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEI 198
Query: 122 EELSKAGLRNPVRVEVRAESK 142
             + +  +++P+ + V  E+K
Sbjct: 199 RPVCRKFMQDPMEIFVDDETK 219

>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 = 71.2 bits (173), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 47/134 (35%), Positives = 75/134 (55%), Gaps = 10/134 (7%)
Query: 2   GMIISPTRELSSQIYHVAQPFIST---LPDVKSVLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTR+L+ QI    +        L     V LVGG + +A + K+ +   N++I T
Sbjct: 98  AVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIAT 157
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLR-------RTG 111
           PGRL D++E+     FR ++  VLDEADRLL++GF+  +  I   L +         +T 
Sbjct: 158 PGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTL 217
Query: 112 LFSATQTEAVEELS 125
           LFSAT  + V++L+
Sbjct: 218 LFSATLDDKVQKLA 231

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 71.2 bits (173), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 47/134 (35%), Positives = 75/134 (55%), Gaps = 10/134 (7%)
Query: 2   GMIISPTRELSSQIYHVAQPFIST---LPDVKSVLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTR+L+ QI    +        L     V LVGG + +A + K+ +   N++I T
Sbjct: 98  AVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIAT 157
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLR-------RTG 111
           PGRL D++E+     FR ++  VLDEADRLL++GF+  +  I   L +         +T 
Sbjct: 158 PGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTL 217
Query: 112 LFSATQTEAVEELS 125
           LFSAT  + V++L+
Sbjct: 218 LFSATLDDKVQKLA 231

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 71.2 bits (173), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 43/139 (30%), Positives = 74/139 (53%), Gaps = 3/139 (2%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +I+ PTREL+ Q   V +  +     +  ++  GG  ++ D+ ++ E   ++L+GTPGR
Sbjct: 92  ALIMVPTRELALQTSQVVRT-LGKHCGISCMVTTGGTNLRDDILRLNET-VHILVGTPGR 149
Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           + D+  R  V D  +  + ++DEAD++L   F+  I  I+S LP   ++ LFSAT    V
Sbjct: 150 VLDLASR-KVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTV 208
Query: 122 EELSKAGLRNPVRVEVRAE 140
           +E     L  P  + +  E
Sbjct: 209 KEFMVKHLHKPYEINLMEE 227

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 71.2 bits (173), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 47/134 (35%), Positives = 75/134 (55%), Gaps = 10/134 (7%)
Query: 2   GMIISPTRELSSQIYHVAQPFIST---LPDVKSVLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTR+L+ QI    +        L     V LVGG + +A + K+ +   N++I T
Sbjct: 149 AVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIAT 208
Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLR-------RTG 111
           PGRL D++E+     FR ++  VLDEADRLL++GF+  +  I   L +         +T 
Sbjct: 209 PGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTL 268
Query: 112 LFSATQTEAVEELS 125
           LFSAT  + V++L+
Sbjct: 269 LFSATLDDKVQKLA 282

>pdb|2OXC|A Chain A, Human Dead-Box Rna Helicase Ddx20, Dead Domain In Complex With Adp Length = 230

Iteration: 1
 Score = 70.9 bits (172), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 41/138 (29%), Positives = 82/138 (59%), Gaps = 4/138 (2%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTRE++ QI+ V       +  ++  + +GG  +  D  ++++   ++ +G+PGR+
Sbjct: 96  LILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKK--CHIAVGSPGRI 153
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMG-FQKQISYIISRLPKLRRTGLFSATQTEAV 121
             ++E +D L+  ++ + +LDEAD+LL+ G FQ+QI++I S LP  ++    SAT  E +
Sbjct: 154 KQLIE-LDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFL 212
Query: 122 EELSKAGLRNPVRVEVRA 139
                  +R+P  V + +
Sbjct: 213 ANALTKYMRDPTFVRLNS 230

>pdb|1HV8|A Chain A, Crystal Structure Of A Dead Box Protein From The Hyperthermophile Methanococcus Jannaschii Length = 367

Iteration: 1
 Score = 70.1 bits (170), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 44/153 (28%), Positives = 83/153 (54%), Gaps = 6/153 (3%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +I++PTREL+ Q+    +       ++K   + GG  +   +K ++   AN+++GTPGR
Sbjct: 77  AIILTPTRELAIQVADEIESLKGN-KNLKIAKIYGGKAIYPQIKALK--NANIVVGTPGR 133
Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           + D + R   L+ +N++  +LDEAD  L+ GF K +  I++   K +R  LFSAT    +
Sbjct: 134 ILDHINR-GTLNLKNVKYFILDEADEXLNXGFIKDVEKILNACNKDKRILLFSATXPREI 192
Query: 122 EELSKA--GLRNPVRVEVRAESKSHHVSASSQQ 152
             L+K   G  + ++ ++ A  +  +V  +  +
Sbjct: 193 LNLAKKYXGDYSFIKAKINANIEQSYVEVNENE 225

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 69.7 bits (169), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 41/134 (30%), Positives = 77/134 (57%), Gaps = 2/134 (1%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            M+I PTREL+ Q+  +       +   K +   GG  ++ D+ ++++   +++I TPGR
Sbjct: 74  AMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT-VHVVIATPGR 132
Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           + D++++  V    +++++VLDEAD+LL   F + +  II  LPK R+  L+SAT   +V
Sbjct: 133 ILDLIKK-GVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSV 191
Query: 122 EELSKAGLRNPVRV 135
           ++   + L  P  +
Sbjct: 192 QKFMNSHLEKPYEI 205

>pdb|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score = 69.3 bits (168), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/136 (25%), Positives = 80/136 (58%), Gaps = 2/136 (1%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR+
Sbjct: 86  LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 145
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
              + R   L+ ++++  +LDE D++L+ +  ++ +  I    P  ++  +FSAT ++ +
Sbjct: 146 L-ALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEI 204
Query: 122 EELSKAGLRNPVRVEV 137
             + +  +++P+ + V
Sbjct: 205 RPVCRKFMQDPMEIFV 220

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 59.7 bits (143), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 43/138 (31%), Positives = 74/138 (53%), Gaps = 8/138 (5%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            + ++P+REL+ Q   V Q  +     + S L+V         +K ++  A +++GTPG 
Sbjct: 95  AICLAPSRELARQTLEVVQE-MGKFTKITSQLIVPD-----SFEKNKQINAQVIVGTPGT 148
Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           + D+M R  ++  + ++I VLDEAD +LD  G   Q   +   LPK  +  LFSAT  +A
Sbjct: 149 VLDLMRR-KLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADA 207
Query: 121 VEELSKAGLRNPVRVEVR 138
           V + +K  + N   +E++
Sbjct: 208 VRQYAKKIVPNANTLELQ 225

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 59.7 bits (143), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 43/139 (30%), Positives = 74/139 (53%), Gaps = 8/139 (5%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            + ++P+REL+ Q   V Q  +     + S L+V         +K ++  A +++GTPG 
Sbjct: 78  AICLAPSRELARQTLEVVQE-MGKFTKITSQLIV-----PDSFEKNKQINAQVIVGTPGT 131
Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           + D+M R  ++  + ++I VLDEAD +LD  G   Q   +   LPK  +  LFSAT  +A
Sbjct: 132 VLDLMRR-KLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADA 190
Query: 121 VEELSKAGLRNPVRVEVRA 139
           V + +K  + N   +E++ 
Sbjct: 191 VRQYAKKIVPNANTLELQT 209

>pdb|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 59.7 bits (143), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 43/139 (30%), Positives = 74/139 (53%), Gaps = 8/139 (5%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            + ++P+REL+ Q   V Q  +     + S L+V         +K ++  A +++GTPG 
Sbjct: 78  AICLAPSRELARQTLEVVQE-MGKFTKITSQLIV-----PDSFEKNKQINAQVIVGTPGT 131
Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           + D+M R  ++  + ++I VLDEAD +LD  G   Q   +   LPK  +  LFSAT  +A
Sbjct: 132 VLDLMRR-KLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADA 190
Query: 121 VEELSKAGLRNPVRVEVRA 139
           V + +K  + N   +E++ 
Sbjct: 191 VRQYAKKIVPNANTLELQT 209

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 45/156 (28%), Positives = 84/156 (53%), Gaps = 11/156 (7%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   +KI E+   ++IGTPG +
Sbjct: 99  LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-QKISEQ---IVIGTPGTV 154
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLL-DMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + +++ VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 155 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 214
Query: 122 EELSKAGLRNPVRVEVRAES------KSHHVSASSQ 151
            + ++  + +P  ++++ E       K ++V  SS+
Sbjct: 215 WKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSR 250

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 45/156 (28%), Positives = 84/156 (53%), Gaps = 11/156 (7%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   +KI E+   ++IGTPG +
Sbjct: 136 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-QKISEQ---IVIGTPGTV 191
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLL-DMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + +++ VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 192 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 251
Query: 122 EELSKAGLRNPVRVEVRAES------KSHHVSASSQ 151
            + ++  + +P  ++++ E       K ++V  SS+
Sbjct: 252 WKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSR 287

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 45/156 (28%), Positives = 84/156 (53%), Gaps = 11/156 (7%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   +KI E+   ++IGTPG +
Sbjct: 166 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-QKISEQ---IVIGTPGTV 221
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLL-DMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + +++ VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 222 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 281
Query: 122 EELSKAGLRNPVRVEVRAES------KSHHVSASSQ 151
            + ++  + +P  ++++ E       K ++V  SS+
Sbjct: 282 WKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSR 317

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 45/156 (28%), Positives = 84/156 (53%), Gaps = 11/156 (7%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   +KI E+   ++IGTPG +
Sbjct: 115 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-QKISEQ---IVIGTPGTV 170
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLL-DMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + +++ VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 171 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 230
Query: 122 EELSKAGLRNPVRVEVRAES------KSHHVSASSQ 151
            + ++  + +P  ++++ E       K ++V  SS+
Sbjct: 231 WKFAQKVVPDPNVIKLKREEETLDTIKQYYVLCSSR 266

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 57.4 bits (137), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 41/139 (29%), Positives = 77/139 (55%), Gaps = 5/139 (3%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   +KI E+   ++IGTPG +
Sbjct: 166 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-QKISEQ---IVIGTPGTV 221
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLL-DMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + +++ VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 222 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 281
Query: 122 EELSKAGLRNPVRVEVRAE 140
            + ++  + +P  ++++ E
Sbjct: 282 WKFAQKVVPDPNVIKLKRE 300

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 57.0 bits (136), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 41/139 (29%), Positives = 77/139 (55%), Gaps = 5/139 (3%)
Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   +KI E+   ++IGTPG +
Sbjct: 99  LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-QKISEQ---IVIGTPGTV 154
Query: 63  YDIMERMDVLDFRNLEILVLDEADRLL-DMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + +++ VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 155 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 214
Query: 122 EELSKAGLRNPVRVEVRAE 140
            + ++  + +P  ++++ E
Sbjct: 215 WKFAQKVVPDPNVIKLKRE 233

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 52.0 bits (123), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 45/146 (30%), Positives = 74/146 (50%), Gaps = 8/146 (5%)
Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +IISPTREL+SQI H     IS     +  ++               +  ++L+ TP R
Sbjct: 101 ALIISPTRELASQI-HRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNR 159
Query: 62  L-YDIMERMDVLDFRNLEILVLDEADRLLD---MGFQKQIS--YIISRLPKLRRTGLFSA 115
           L Y + +    +D  ++E LV+DE+D+L +    GF+ Q++  ++     K+RR  +FSA
Sbjct: 160 LIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRR-AMFSA 218
Query: 116 TQTEAVEELSKAGLRNPVRVEVRAES 141
           T    VE+  K  L N + V + A +
Sbjct: 219 TFAYDVEQWCKLNLDNVISVSIGARN 244

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	183
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	5e-54
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	7e-49
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	3e-47
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	4e-47
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-46
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	6e-43
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-41
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	1e-41
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	4e-41
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	1e-40
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	1e-39
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	1e-39
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	1e-39
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	2e-39
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	6e-39
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	2e-38
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	2e-38
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-38
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	3e-38
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	4e-38
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	6e-38
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	1e-37
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	1e-37
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	1e-37
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	2e-37
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	4e-37
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	4e-37
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	2e-34
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	1e-32
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	1e-32
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	1e-31
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	1e-07

>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 =  170 bits (433), Expect = 5e-54
 Identities = 58/140 (41%), Positives = 91/140 (65%), Gaps = 3/140 (2%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +IISPTREL+ Q + V +  +    D  + L++GG ++K + ++I     N+L+ TPGR
Sbjct: 100 VLIISPTRELAYQTFEVLRK-VGKNHDFSAGLIIGGKDLKHEAERIN--NINILVCTPGR 156

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           L   M+        +L++LVLDEADR+LDMGF   ++ +I  LPK R+T LFSATQT++V
Sbjct: 157 LLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSV 216

Query: 122 EELSKAGLRNPVRVEVRAES 141
           ++L++  L+NP  V V  ++
Sbjct: 217 KDLARLSLKNPEYVWVHEKA 236

>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 =  158 bits (401), Expect = 7e-49
 Identities = 55/134 (41%), Positives = 87/134 (64%), Gaps = 3/134 (2%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I+SPTREL+ Q + V +  ++        L++GG    A+ +K+   G N+++ TPGRL
Sbjct: 130 LILSPTRELAMQTFGVLKELMTHH-VHTYGLIMGGSNRSAEAQKLGN-GINIIVATPGRL 187

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D M+      ++NL+ LV+DEADR+LD+GF++++  II  LP  R+T LFSATQT  VE
Sbjct: 188 LDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVE 247

Query: 123 ELSKAGLRN-PVRV 135
           +L++  L+  P+ V
Sbjct: 248 DLARISLKKEPLYV 261

>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 =  161 bits (408), Expect = 3e-47
 Identities = 48/157 (30%), Positives = 80/157 (50%), Gaps = 10/157 (6%)

Query: 4   IISPTRELSSQIYHVAQ---PFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           I++PTR+L+ QI    +        L     V LVGG + +A + K+ +   N++I TPG
Sbjct: 151 IVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPG 210

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLR-------RTGLF 113
           RL D++E+     FR ++  VLDEADRLL++GF+  +  I   L +         +T LF
Sbjct: 211 RLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLF 270

Query: 114 SATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASS 150
           SAT  + V++L+   +     + +    K+   +   
Sbjct: 271 SATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHER 307

>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 =  153 bits (389), Expect = 4e-47
 Identities = 51/138 (36%), Positives = 90/138 (65%), Gaps = 2/138 (1%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI    +   S++  V+S ++VGG++  +    + +   +++I TPGR
Sbjct: 114 ALVLTPTRELAFQISEQFEALGSSIG-VQSAVIVGGIDSMSQSLALAK-KPHIIIATPGR 171

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           L D +E     + R L+ LV+DEADR+L+M F+ ++  I+  +P+ R+T LFSAT T+ V
Sbjct: 172 LIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKV 231

Query: 122 EELSKAGLRNPVRVEVRA 139
           ++L +A L+NPV+  V +
Sbjct: 232 QKLQRAALKNPVKCAVSS 249

>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 =  159 bits (404), Expect = 1e-46
 Identities = 48/159 (30%), Positives = 81/159 (50%), Gaps = 10/159 (6%)

Query: 2   GMIISPTRELSSQIYHVAQ---PFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTR+L+ QI    +        L     V LVGG + +A + K+ +   N++I T
Sbjct: 98  AVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIAT 157

Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLR-------RTG 111
           PGRL D++E+     FR ++  VLDEADRLL++GF+  +  I   L +         +T 
Sbjct: 158 PGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTL 217

Query: 112 LFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASS 150
           LFSAT  + V++L+   +     + +    K+   +   
Sbjct: 218 LFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPEAHER 256

>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 =  142 bits (360), Expect = 6e-43
 Identities = 39/141 (27%), Positives = 67/141 (47%), Gaps = 6/141 (4%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +IISPTREL+SQI+             +  ++               +  ++L+ TP R
Sbjct: 101 ALIISPTRELASQIHRELIKISEGTG-FRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNR 159

Query: 62  LYDIMER-MDVLDFRNLEILVLDEADRLLD---MGFQKQISYIISRL-PKLRRTGLFSAT 116
           L  ++++    +D  ++E LV+DE+D+L +    GF+ Q++ I         R  +FSAT
Sbjct: 160 LIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSAT 219

Query: 117 QTEAVEELSKAGLRNPVRVEV 137
               VE+  K  L N + V +
Sbjct: 220 FAYDVEQWCKLNLDNVISVSI 240

>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 =  138 bits (351), Expect = 1e-41
 Identities = 46/139 (33%), Positives = 82/139 (58%), Gaps = 2/139 (1%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V    +           +GG  V+ +++K++ E  ++++GTPGR
Sbjct: 101 ALVLAPTRELAQQIQKVILA-LGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGR 159

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           ++D++ R   L  + +++ VLDEAD +L  GF+ QI  I  +L    +  L SAT    V
Sbjct: 160 VFDMLNR-RYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDV 218

Query: 122 EELSKAGLRNPVRVEVRAE 140
            E++K  +R+P+R+ V+ E
Sbjct: 219 LEVTKKFMRDPIRILVKKE 237

>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 =  139 bits (352), Expect = 1e-41
 Identities = 54/148 (36%), Positives = 89/148 (60%), Gaps = 8/148 (5%)

Query: 4   IISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLY 63
           I++PTREL+ QI   +Q F    P ++S ++ GG +  + +++++  G +LL+ TPGRL 
Sbjct: 105 ILAPTRELAIQILSESQKFSLNTP-LRSCVVYGGADTHSQIREVQM-GCHLLVATPGRLV 162

Query: 64  DIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIIS--RLPKL--RRTGLFSATQTE 119
           D +E+  +      + +VLDEADR+LDMGF+ QI  II    +P    R+T +FSAT  +
Sbjct: 163 DFIEKNKI-SLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPK 221

Query: 120 AVEELSKAGLRNPVRVEV-RAESKSHHV 146
            +++L+   L N + + V R  S S  +
Sbjct: 222 EIQKLAADFLYNYIFMTVGRVGSTSDSI 249

>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 =  137 bits (347), Expect = 4e-41
 Identities = 43/137 (31%), Positives = 80/137 (58%), Gaps = 4/137 (2%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             ++++PTREL+  +      +      +KS+ + GG      ++ I + G +++I TPG
Sbjct: 96  GMLVLTPTRELALHVEAECSKYSYK--GLKSICIYGGRNRNGQIEDISK-GVDIIIATPG 152

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL D+    + ++ R++  LV+DEAD++LDM F+ QI  I+  +   R+T + SAT  + 
Sbjct: 153 RLNDLQM-NNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDT 211

Query: 121 VEELSKAGLRNPVRVEV 137
           V +L+ + L++P+ V V
Sbjct: 212 VRQLALSYLKDPMIVYV 228

>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 =  140 bits (356), Expect = 1e-40
 Identities = 48/139 (34%), Positives = 83/139 (59%), Gaps = 2/139 (1%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V       +        +GG  V+A+V+K++ E  ++++GTPGR
Sbjct: 111 ALVLAPTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGR 169

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           ++D++ R   L  + +++ VLDEAD +L  GF+ QI  I  +L    +  L SAT    V
Sbjct: 170 VFDMLNR-RYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDV 228

Query: 122 EELSKAGLRNPVRVEVRAE 140
            E++K  +R+P+R+ V+ E
Sbjct: 229 LEVTKKFMRDPIRILVKKE 247

>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 =  133 bits (337), Expect = 1e-39
 Identities = 46/139 (33%), Positives = 78/139 (56%), Gaps = 4/139 (2%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V       + D+K    +GG     D + +    A +++GTPGR
Sbjct: 85  ALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR--DAQIVVGTPGR 141

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           ++D ++R        +++ +LDEAD +L  GF++QI  I + LP   +  L SAT    V
Sbjct: 142 VFDNIQR-RRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDV 200

Query: 122 EELSKAGLRNPVRVEVRAE 140
            E++   +RNPVR+ V+ +
Sbjct: 201 LEVTTKFMRNPVRILVKKD 219

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  138 bits (349), Expect = 1e-39
 Identities = 55/150 (36%), Positives = 88/150 (58%), Gaps = 8/150 (5%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QIY  A+ F S    V+  ++ GG ++   ++ +E  G +LL+ TPGR
Sbjct: 104 SLVLAPTRELAVQIYEEARKF-SYRSRVRPCVVYGGADIGQQIRDLER-GCHLLVATPGR 161

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIIS----RLPKLRRTGLFSATQ 117
           L D+MER   +     + LVLDEADR+LDMGF+ QI  I+         +R T +FSAT 
Sbjct: 162 LVDMMER-GKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATF 220

Query: 118 TEAVEELSKAGLRNPVRVEV-RAESKSHHV 146
            + ++ L++  L   + + V R  S S ++
Sbjct: 221 PKEIQMLARDFLDEYIFLAVGRVGSTSENI 250

>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 =  133 bits (338), Expect = 1e-39
 Identities = 47/137 (34%), Positives = 80/137 (58%), Gaps = 3/137 (2%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           + ++++PTREL+ Q+  VA  +      +KS  + GG      ++ +E  G  + I TPG
Sbjct: 104 ICLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLER-GVEICIATPG 161

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL D +E     + R    LVLDEADR+LDMGF+ QI  I+ ++   R+T ++SAT  + 
Sbjct: 162 RLIDFLEC-GKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKE 220

Query: 121 VEELSKAGLRNPVRVEV 137
           V +L++  L++ + + +
Sbjct: 221 VRQLAEDFLKDYIHINI 237

>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 =  138 bits (349), Expect = 2e-39
 Identities = 48/147 (32%), Positives = 82/147 (55%), Gaps = 5/147 (3%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             +I+SPTREL+ QI++ A+ F      +K  ++ GG   +   + I   G +++I TPG
Sbjct: 131 QVVIVSPTRELAIQIFNEARKFAFES-YLKIGIVYGGTSFRHQNECITR-GCHVVIATPG 188

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIIS--RLPKLRRTGLFSATQT 118
           RL D ++R   + F +   +VLDEADR+LDMGF + +  I++   +    +T +FSAT  
Sbjct: 189 RLLDFVDR-TFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFP 247

Query: 119 EAVEELSKAGLRNPVRVEVRAESKSHH 145
           E ++ ++   L+N V V +     +  
Sbjct: 248 EEIQRMAGEFLKNYVFVAIGIVGGACS 274

>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 =  136 bits (344), Expect = 6e-39
 Identities = 46/139 (33%), Positives = 79/139 (56%), Gaps = 4/139 (2%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V    ++   D+K    +GG     D + +    A +++GTPGR
Sbjct: 92  ALMLAPTRELALQIQKVVMA-LAFHMDIKVHACIGGTSFVEDAEGLR--DAQIVVGTPGR 148

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           ++D ++R        +++ +LDEAD +L  GF++QI  I + LP   +  L SAT    V
Sbjct: 149 VFDNIQR-RRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDV 207

Query: 122 EELSKAGLRNPVRVEVRAE 140
            E++   +RNPVR+ V+ +
Sbjct: 208 LEVTTKFMRNPVRILVKKD 226

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  130 bits (329), Expect = 2e-38
 Identities = 52/147 (35%), Positives = 79/147 (53%), Gaps = 5/147 (3%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPD---VKSVLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I +PTREL++QIYH         P    + +  L+GG + +  ++K+     +++IGT
Sbjct: 75  AVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNV-QPHIVIGT 133

Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR+ D +     LD     ILV+DEAD +LDMGF   +  I +R+PK  +  +FSAT  
Sbjct: 134 PGRINDFIRE-QALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSATIP 192

Query: 119 EAVEELSKAGLRNPVRVEVRAESKSHH 145
           E ++   K  + NP  V V      HH
Sbjct: 193 EKLKPFLKKYMENPTFVHVLEHHHHHH 219

>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 =  134 bits (340), Expect = 2e-38
 Identities = 43/139 (30%), Positives = 73/139 (52%), Gaps = 3/139 (2%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +I+ PTREL+ Q   V +        +  ++  GG  ++ D+ ++ E   ++L+GTPGR
Sbjct: 92  ALIMVPTRELALQTSQVVRTL-GKHCGISCMVTTGGTNLRDDILRLNE-TVHILVGTPGR 149

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           + D+  R  V D  +  + ++DEAD++L   F+  I  I+S LP   ++ LFSAT    V
Sbjct: 150 VLDLASR-KVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTV 208

Query: 122 EELSKAGLRNPVRVEVRAE 140
           +E     L  P  + +  E
Sbjct: 209 KEFMVKHLHKPYEINLMEE 227

>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 =  132 bits (334), Expect = 2e-38
 Identities = 39/139 (28%), Positives = 73/139 (52%), Gaps = 5/139 (3%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   K        ++IGTPG +
Sbjct: 166 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI----SEQIVIGTPGTV 221

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + +++ VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 222 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 281

Query: 122 EELSKAGLRNPVRVEVRAE 140
            + ++  + +P  ++++ E
Sbjct: 282 WKFAQKVVPDPNVIKLKRE 300

>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 =  130 bits (328), Expect = 3e-38
 Identities = 41/139 (29%), Positives = 80/139 (57%), Gaps = 4/139 (2%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +I++PTRE++ QI+ V       +  ++  + +GG  +  D  +++    ++ +G+PGR
Sbjct: 95  ILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK--KCHIAVGSPGR 152

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMG-FQKQISYIISRLPKLRRTGLFSATQTEA 120
           +  ++E  D L+  ++ + +LDEAD+LL+ G FQ+QI++I S LP  ++    SAT  E 
Sbjct: 153 IKQLIEL-DYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEF 211

Query: 121 VEELSKAGLRNPVRVEVRA 139
           +       +R+P  V + +
Sbjct: 212 LANALTKYMRDPTFVRLNS 230

>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 =  133 bits (338), Expect = 4e-38
 Identities = 46/139 (33%), Positives = 83/139 (59%), Gaps = 3/139 (2%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +I++PTREL+ QI          + +V+    +GG  V  D++K++  G +++ GTPGR
Sbjct: 108 ALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDY-GQHVVAGTPGR 165

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           ++D++ R   L  R +++LVLDEAD +L+ GF++QI  +   LP   +  L SAT    +
Sbjct: 166 VFDMIRR-RSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEI 224

Query: 122 EELSKAGLRNPVRVEVRAE 140
            E++   + +P+R+ V+ +
Sbjct: 225 LEMTNKFMTDPIRILVKRD 243

>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 =  128 bits (324), Expect = 6e-38
 Identities = 41/134 (30%), Positives = 77/134 (57%), Gaps = 2/134 (1%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            M+I PTREL+ Q+  +       +   K +   GG  ++ D+ ++++   +++I TPGR
Sbjct: 74  AMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDD-TVHVVIATPGR 132

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           + D++++  V    +++++VLDEAD+LL   F + +  II  LPK R+  L+SAT   +V
Sbjct: 133 ILDLIKK-GVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSV 191

Query: 122 EELSKAGLRNPVRV 135
           ++   + L  P  +
Sbjct: 192 QKFMNSHLEKPYEI 205

>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 =  128 bits (323), Expect = 1e-37
 Identities = 33/137 (24%), Positives = 79/137 (57%), Gaps = 2/137 (1%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR
Sbjct: 85  VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGR 144

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           +  +      L+ ++++  +LDE D++L+ +  ++ +  I    P  ++  +FSAT ++ 
Sbjct: 145 ILALARN-KSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKE 203

Query: 121 VEELSKAGLRNPVRVEV 137
           +  + +  +++P+ + V
Sbjct: 204 IRPVCRKFMQDPMEIFV 220

>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 =  127 bits (322), Expect = 1e-37
 Identities = 48/135 (35%), Positives = 79/135 (58%), Gaps = 5/135 (3%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           ++++PTREL+ Q   VA    +  P +K V + GG       + +   GA+ ++ TPGR 
Sbjct: 76  LVLTPTRELALQ---VASELTAVAPHLKVVAVYGGTGYGKQKEALLR-GADAVVATPGRA 131

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D + +  VLD   +E+ VLDEAD +L MGF++++  ++S  P  R+T LFSAT     +
Sbjct: 132 LDYLRQ-GVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAK 190

Query: 123 ELSKAGLRNPVRVEV 137
            L++  ++NPV + V
Sbjct: 191 RLAERYMKNPVLINV 205

>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 =  132 bits (335), Expect = 1e-37
 Identities = 39/139 (28%), Positives = 73/139 (52%), Gaps = 5/139 (3%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   K        ++IGTPG +
Sbjct: 99  LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI----SEQIVIGTPGTV 154

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + +++ VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 155 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 214

Query: 122 EELSKAGLRNPVRVEVRAE 140
            + ++  + +P  ++++ E
Sbjct: 215 WKFAQKVVPDPNVIKLKRE 233

>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 =  131 bits (333), Expect = 2e-37
 Identities = 35/142 (24%), Positives = 82/142 (57%), Gaps = 2/142 (1%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR
Sbjct: 79  VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGR 138

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           +  +      L+ ++++  +LDE D++L+ +  ++ +  I    P  ++  +FSAT ++ 
Sbjct: 139 ILALARN-KSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKE 197

Query: 121 VEELSKAGLRNPVRVEVRAESK 142
           +  + +  +++P+ + V  E+K
Sbjct: 198 IRPVCRKFMQDPMEIFVDDETK 219

>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 =  132 bits (334), Expect = 4e-37
 Identities = 39/139 (28%), Positives = 73/139 (52%), Gaps = 5/139 (3%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   K        ++IGTPG +
Sbjct: 166 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI----SEQIVIGTPGTV 221

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + +++ VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 222 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 281

Query: 122 EELSKAGLRNPVRVEVRAE 140
            + ++  + +P  ++++ E
Sbjct: 282 WKFAQKVVPDPNVIKLKRE 300

>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 =  122 bits (310), Expect = 2e-34
 Identities = 46/136 (33%), Positives = 77/136 (56%), Gaps = 8/136 (5%)

Query: 4   IISPTRELSSQIYHVAQPF--ISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
           +++PTREL+ Q   VA     I    D K   + GG+  KA + ++    A++++ TPGR
Sbjct: 61  VVTPTRELTRQ---VASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR--NADIVVATPGR 115

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           L D+  +  V+D  + EI+++DEAD + +MGF   I  I+++    + TGLFSAT  E +
Sbjct: 116 LLDLWSK-GVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEEI 174

Query: 122 EELSKAGLRNPVRVEV 137
            ++ K  + N   +E 
Sbjct: 175 RKVVKDFITNYEEIEA 190

>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 =  119 bits (300), Expect = 1e-32
 Identities = 43/139 (30%), Positives = 72/139 (51%), Gaps = 8/139 (5%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + ++P+REL+ Q   V Q  +     + S L+V     K       +  A +++GTPG +
Sbjct: 79  ICLAPSRELARQTLEVVQE-MGKFTKITSQLIVPDSFEKNK-----QINAQVIVGTPGTV 132

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDM-GFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D+M R  ++  + ++I VLDEAD +LD  G   Q   +   LPK  +  LFSAT  +AV
Sbjct: 133 LDLMRR-KLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAV 191

Query: 122 EELSKAGLRNPVRVEVRAE 140
            + +K  + N   +E++  
Sbjct: 192 RQYAKKIVPNANTLELQTN 210

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A* Length = 414

 Score =  119 bits (300), Expect = 1e-32
 Identities = 21/135 (15%), Positives = 46/135 (34%), Gaps = 8/135 (5%)

Query: 4   IISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKA---DVKKIEEEGANLLIGTPG 60
           ++ PT  L  Q     Q        VK       ++ +      K  EE+  ++L+ +  
Sbjct: 69  LVFPTVTLVKQTLERLQKLADE--KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQ 126

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
            +       + L  +  + + +D+ D +L          ++  +P+      FS  +   
Sbjct: 127 FVSK---NREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTIKQGK 183

Query: 121 VEELSKAGLRNPVRV 135
           + E  K      + V
Sbjct: 184 IYERPKNLKPGILVV 198

>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 =  116 bits (292), Expect = 1e-31
 Identities = 44/147 (29%), Positives = 80/147 (54%), Gaps = 8/147 (5%)

Query: 2   GMIISPTRELSSQIYHVAQPF--ISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTP 59
            +I++PTREL+ Q   VA     +    ++K   + GG  +   +K ++   AN+++GTP
Sbjct: 77  AIILTPTRELAIQ---VADEIESLKGNKNLKIAKIYGGKAIYPQIKALK--NANIVVGTP 131

Query: 60  GRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE 119
           GR+ D + R   L+ +N++  +LDEAD +L+MGF K +  I++   K +R  LFSAT   
Sbjct: 132 GRILDHINR-GTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPR 190

Query: 120 AVEELSKAGLRNPVRVEVRAESKSHHV 146
            +  L+K  + +   ++ +  +     
Sbjct: 191 EILNLAKKYMGDYSFIKAKINANIEQS 217

>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 = 49.4 bits (117), Expect = 1e-07
 Identities = 24/124 (19%), Positives = 49/124 (39%), Gaps = 4/124 (3%)

Query: 4   IISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLY 63
           +++PT+ L  Q     +     LP  K V L G  E   + +      A +++ TP  + 
Sbjct: 57  MLAPTKPLVLQHAESFRRLF-NLPPEKIVALTG--EKSPEERSKAWARAKVIVATPQTIE 113

Query: 64  DIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEE 123
           + +     +   ++ ++V DEA R +       I+    R  K       +A+     E+
Sbjct: 114 NDLLA-GRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEK 172

Query: 124 LSKA 127
           + + 
Sbjct: 173 IMEV 176

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	183
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.96
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	99.96
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.96
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.95
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.94
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.94
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.94
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.94
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.94
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.94
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	99.94
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	99.94
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.94
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.93
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.93
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.93
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.92
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.92
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.92
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.91
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.9
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.89
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.88
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.88
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.88
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.88
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	99.87
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.87
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.86
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.81
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.81
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.8
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.77
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.76
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.75
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.74
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.71
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.71
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.7
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.69
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.68
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.64
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.64
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.63
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.63
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.63
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.62
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.61
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.6
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.59
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.58
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.58
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.57
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.55
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.53
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.53
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.52
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.51
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.47
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.43
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.43
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.29
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.28
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.26
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.24
3h1t_A	590	Type I site-specific restriction-modification syst	99.23
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.23
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.22
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.22
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.17
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.12
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.1
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.08
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.73
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	98.62
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.42
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.41
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.3
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.17
3jux_A	822	Protein translocase subunit SECA; protein transloc	97.53
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.25
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	96.14
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	96.08
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	95.97
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	95.75
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	95.71
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	95.63
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	95.48
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	95.13
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	95.09
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	95.02
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	94.69
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	94.3
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	94.27
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	94.17
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	94.11
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	94.08
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	94.03
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	93.92
1yks_A	440	Genome polyprotein [contains: flavivirin protease	93.85
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	93.62
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	93.38
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	93.34
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	93.33
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	93.09
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	92.93
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	92.88
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	92.43
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	92.39
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	91.37
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	90.65
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	90.68
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	90.56
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	90.36
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	90.23
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	89.34
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	89.23
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	88.24
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	88.08
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	87.85
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	87.68
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	86.55
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	85.87
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	85.14
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	84.27
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	83.6
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	83.57
4gl2_A	699	Interferon-induced helicase C domain-containing P;	83.1
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	82.41
3kta_B	173	Chromosome segregation protein SMC; structural mai	82.04
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	81.95
3h1t_A	590	Type I site-specific restriction-modification syst	81.93
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	80.8
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	80.19
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	80.06

>3fe2_A Probable ATP-dependent RNA helicase DDX5; DEAD, ADP, ATP-binding, hydrolase, nucleotide- RNA-binding, methylation, mRNA processing, mRNA S nucleus; HET: ADP; 2.60A {Homo sapiens} PDB: 4a4d_A

Probab=99.96  E-value=3.3e-28  Score=189.53  Aligned_cols=137  Identities=35%  Similarity=0.588  Sum_probs=127.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++|||+||.|+++.++++.... ++++..++||.....+...+. .+++|+||||+++.+++.+ +..++++++++
T Consensus       104 ~~lil~Pt~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~-~~~~I~v~Tp~~l~~~l~~-~~~~~~~~~~l  180 (242)
T 3fe2_A          104 ICLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLE-RGVEICIATPGRLIDFLEC-GKTNLRRTTYL  180 (242)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHHHHHT-TCCEEEECTTSCHHHHHHHHH-HCCSEEEECHHHHHHHHHH-TSCCCTTCCEE
T ss_pred             EEEEEeCcHHHHHHHHHHHHHHHhhc-CceEEEEECCCChHHHHHHhc-CCCCEEEECHHHHHHHHHc-CCCCcccccEE
Confidence            37999999999999999999998887 899999999999888877774 5899999999999999988 77889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccC
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAE  140 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~  140 (183)
                      |+||||.+++.+|...+..+++.+++++|+++||||++++++.+++.++++|+.|.++.+
T Consensus       181 ViDEah~l~~~~~~~~~~~i~~~~~~~~q~~~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  240 (242)
T 3fe2_A          181 VLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVRQLAEDFLKDYIHINIGAL  240 (242)
T ss_dssp             EETTHHHHHHTTCHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEEEECC-
T ss_pred             EEeCHHHHhhhCcHHHHHHHHHhCCccceEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            999999999999999999999999999999999999999999999999999999998765

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=99.96  E-value=7.7e-28  Score=202.21  Aligned_cols=163  Identities=30%  Similarity=0.454  Sum_probs=147.1

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++||||||.|+++.+++++... ++++..++||.....+...+ ..+++|+||||++|.+++.+ +.+++++++++
T Consensus       131 ~~lil~PtreLa~Q~~~~~~~~~~~~-~~~~~~~~gg~~~~~~~~~l-~~~~~Ivv~Tp~~l~~~l~~-~~~~l~~~~~l  207 (434)
T 2db3_A          131 QVVIVSPTRELAIQIFNEARKFAFES-YLKIGIVYGGTSFRHQNECI-TRGCHVVIATPGRLLDFVDR-TFITFEDTRFV  207 (434)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHHTTTS-SCCCCEECTTSCHHHHHHHH-TTCCSEEEECHHHHHHHHHT-TSCCCTTCCEE
T ss_pred             cEEEEecCHHHHHHHHHHHHHHhccC-CcEEEEEECCCCHHHHHHHh-hcCCCEEEEChHHHHHHHHh-CCcccccCCeE
Confidence            48999999999999999999998765 78999999999988887776 46899999999999999988 77889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhC--CCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCC
Q 030094           81 VLDEADRLLDMGFQKQISYIISRL--PKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKT  158 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l--~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (183)
                      |+||||+|++.+|...+..++..+  ++.+|+++||||+++++..++..++.+|..+.+...               ...
T Consensus       208 VlDEah~~~~~gf~~~~~~i~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~---------------~~~  272 (434)
T 2db3_A          208 VLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFPEEIQRMAGEFLKNYVFVAIGIV---------------GGA  272 (434)
T ss_dssp             EEETHHHHTSTTTHHHHHHHHHCTTSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEESST---------------TCC
T ss_pred             EEccHhhhhccCcHHHHHHHHHhcCCCCCceEEEEeccCCHHHHHHHHHhccCCEEEEeccc---------------ccc
Confidence            999999999999999999999885  578999999999999999999999999999988776               456


Q ss_pred             ccCceEEEEEecCcchhhhhhcc
Q 030094          159 PLGLHLEVIWNVNQMRNHHNLLI  181 (183)
Q Consensus       159 ~~~l~q~~i~~~~~~k~~~ll~l  181 (183)
                      ..++.|.++.++..+|...++.+
T Consensus       273 ~~~i~~~~~~~~~~~k~~~l~~~  295 (434)
T 2db3_A          273 CSDVKQTIYEVNKYAKRSKLIEI  295 (434)
T ss_dssp             CTTEEEEEEECCGGGHHHHHHHH
T ss_pred             ccccceEEEEeCcHHHHHHHHHH
Confidence            77899999999998888877654

>3fmo_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 2.51A {Homo sapiens}

Probab=99.96  E-value=2.7e-28  Score=196.21  Aligned_cols=136  Identities=28%  Similarity=0.422  Sum_probs=122.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +|||++||||||.|+++.+++++++.+++++....|+.......    ..+++|+||||++|.+++.+.+.+++++++++
T Consensus       164 ~~lil~PtreLa~Q~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~----~~~~~IlV~TP~~l~~~l~~~~~~~l~~l~~l  239 (300)
T 3fmo_B          164 QCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ----KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVF  239 (300)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEESTTCCCCTTC----CCCCSEEEECHHHHHHHHTTTCCCCGGGCSEE
T ss_pred             eEEEEcCcHHHHHHHHHHHHHHHhhCCCcEEEEEeCCccHhhhh----cCCCCEEEECHHHHHHHHHhcCCCChhhceEE
Confidence            48999999999999999999999887789999999887754332    45799999999999999976466789999999


Q ss_pred             EEcccchhhc-cchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccC
Q 030094           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAE  140 (183)
Q Consensus        81 VvDEad~ll~-~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~  140 (183)
                      |+||||.|++ .+|...+..|++.+++.+|+++||||+++++..+++.++++|+.|.+..+
T Consensus       240 VlDEad~l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~~e  300 (300)
T 3fmo_B          240 VLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE  300 (300)
T ss_dssp             EETTHHHHHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEEEECCC
T ss_pred             EEeCHHHHhhccCcHHHHHHHHHhCCCCCEEEEEeccCCHHHHHHHHHHCCCCeEEEecCC
Confidence            9999999998 68999999999999999999999999999999999999999999987653

>1wrb_A DJVLGB; RNA helicase, DEAD BOX, VASA, structural genomics, NPPSFA, N project on protein structural and functional analyses; 2.40A {Dugesia japonica} SCOP: c.37.1.19

Probab=99.95  E-value=1.3e-27  Score=187.02  Aligned_cols=148  Identities=35%  Similarity=0.576  Sum_probs=123.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++|||+||.|+++.++++.... ++++..+.||.....+...+ ..+++|+||||+++.+++.. +.+++++++++
T Consensus       102 ~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~-~~~~~Ivv~Tp~~l~~~l~~-~~~~~~~~~~l  178 (253)
T 1wrb_A          102 KCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREV-QMGCHLLVATPGRLVDFIEK-NKISLEFCKYI  178 (253)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHH-SSCCSEEEECHHHHHHHHHT-TSBCCTTCCEE
T ss_pred             eEEEEECCHHHHHHHHHHHHHHhccC-CceEEEEECCCCHHHHHHHh-CCCCCEEEECHHHHHHHHHc-CCCChhhCCEE
Confidence            37999999999999999999998765 78899999999888777776 46899999999999999988 77889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHh--CCC--CCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccC
Q 030094           81 VLDEADRLLDMGFQKQISYIISR--LPK--LRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASS  156 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~--l~~--~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~  156 (183)
                      |+||||.+++.+|...+..+++.  ++.  .+|+++||||+++++..+++.++++|..|.++..               .
T Consensus       179 ViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~---------------~  243 (253)
T 1wrb_A          179 VLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRV---------------G  243 (253)
T ss_dssp             EEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC------------------
T ss_pred             EEeCHHHHHhCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCC---------------C
Confidence            99999999999999999999995  444  7899999999999999999999999999998877               5


Q ss_pred             CCccCceEEE
Q 030094          157 KTPLGLHLEV  166 (183)
Q Consensus       157 ~~~~~l~q~~  166 (183)
                      ...++|+|++
T Consensus       244 ~~~~~i~q~~  253 (253)
T 1wrb_A          244 STSDSIKQEI  253 (253)
T ss_dssp             ----------
T ss_pred             CCcCCceecC
Confidence            5677888764

>3bor_A Human initiation factor 4A-II; translation initiation, DEAD BOX, structural genomics, helic binding, HOST-virus interaction, hydrolase; 1.85A {Homo sapiens} PDB: 2g9n_A*

Probab=99.94  E-value=1e-26  Score=180.71  Aligned_cols=137  Identities=33%  Similarity=0.587  Sum_probs=113.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++|||+||.|+++.+++++... ++++..+.|+.....+...+...+++|+|+||+++.+++.. +.+.+++++++
T Consensus       100 ~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l~~~~~~Ilv~Tp~~l~~~l~~-~~~~~~~~~~l  177 (237)
T 3bor_A          100 QALVLAPTRELAQQIQKVILALGDYM-GATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGRVFDMLNR-RYLSPKWIKMF  177 (237)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECC-------------CCCSEEEECHHHHHHHHHT-TSSCSTTCCEE
T ss_pred             eEEEEECcHHHHHHHHHHHHHHhhhc-CceEEEEECCCchHHHHHHHhcCCCCEEEECHHHHHHHHHh-CCcCcccCcEE
Confidence            47999999999999999999998766 78888999998877777777555599999999999999987 77889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRA  139 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~  139 (183)
                      |+||||.+++.+|...+..+++.+++.+|++++|||+++++.++++.++++|..|.++.
T Consensus       178 ViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~l~~p~~i~v~~  236 (237)
T 3bor_A          178 VLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDVLEVTKKFMRDPIRILVKK  236 (237)
T ss_dssp             EEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCSSCEEEC---
T ss_pred             EECCchHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHCCCCEEEEecC
Confidence            99999999999999999999999999999999999999999999999999999997654

>3iuy_A Probable ATP-dependent RNA helicase DDX53; REC-A-like, DEAD-BOX, structural genomics, structural genomi consortium, SGC, ATP-binding, hydrolase; HET: AMP; 2.40A {Homo sapiens}

Probab=99.94  E-value=1.3e-26  Score=178.69  Aligned_cols=132  Identities=33%  Similarity=0.554  Sum_probs=116.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||++|||+||.|+++.++++. . +++++..++||.....+...+ ..+++|+|+||+++.+++.. +.+++++++++|
T Consensus        97 ~lil~Pt~~L~~q~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~~~-~~~~~iiv~Tp~~l~~~~~~-~~~~~~~~~~lV  172 (228)
T 3iuy_A           97 MLVLTPTRELALHVEAECSKYS-Y-KGLKSICIYGGRNRNGQIEDI-SKGVDIIIATPGRLNDLQMN-NSVNLRSITYLV  172 (228)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHC-C-TTCCEEEECC------CHHHH-HSCCSEEEECHHHHHHHHHT-TCCCCTTCCEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHHhc-c-cCceEEEEECCCChHHHHHHh-cCCCCEEEECHHHHHHHHHc-CCcCcccceEEE
Confidence            7999999999999999999985 2 378899999998887777776 46899999999999999987 788899999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEE
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEV  137 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~  137 (183)
                      +||||.+++.+|...+..+++.+++++|++++|||++++++++++.++++|+.|.+
T Consensus       173 iDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i~v  228 (228)
T 3iuy_A          173 IDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVRQLALSYLKDPMIVYV  228 (228)
T ss_dssp             ECCHHHHHHTTCHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHHTTCSSCEEEEC
T ss_pred             EECHHHHhccchHHHHHHHHHhCCcCCeEEEEEeeCCHHHHHHHHHHCCCCEEEeC
Confidence            99999999999999999999999999999999999999999999999999998864

>3ber_A Probable ATP-dependent RNA helicase DDX47; DEAD, AMP, structural genomics, structural GEN consortium, SGC, ATP-binding, hydrolase; HET: AMP PGE; 1.40A {Homo sapiens}

Probab=99.94  E-value=2.9e-26  Score=179.66  Aligned_cols=136  Identities=38%  Similarity=0.660  Sum_probs=124.1

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++|||+||.|+++.++++.... ++++..++||.....+...+ ..+++|+|+||+++.+++.+.+.+++++++++
T Consensus       113 ~~lil~Ptr~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~-~~~~~I~v~Tp~~l~~~l~~~~~~~l~~~~~l  190 (249)
T 3ber_A          113 FALVLTPTRELAFQISEQFEALGSSI-GVQSAVIVGGIDSMSQSLAL-AKKPHIIIATPGRLIDHLENTKGFNLRALKYL  190 (249)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHGGG-TCCEEEECTTSCHHHHHHHH-HTCCSEEEECHHHHHHHHHHSTTCCCTTCCEE
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhccC-CeeEEEEECCCChHHHHHHh-cCCCCEEEECHHHHHHHHHcCCCcCccccCEE
Confidence            38999999999999999999998776 78999999998877776666 46899999999999999987456789999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVR  138 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~  138 (183)
                      |+||||++++.+|...+..+++.+++.+|+++||||+++++.++++.++++|+.|.++
T Consensus       191 ViDEah~l~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~p~~i~v~  248 (249)
T 3ber_A          191 VMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKVQKLQRAALKNPVKCAVS  248 (249)
T ss_dssp             EECSHHHHHHTTCHHHHHHHHHSSCSSSEEEEEESSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             EEcChhhhhccChHHHHHHHHHhCCCCCeEEEEeccCCHHHHHHHHHHCCCCEEEEec
Confidence            9999999999999999999999999999999999999999999999999999998764

>2oxc_A Probable ATP-dependent RNA helicase DDX20; DEAD, structural genomics, structural genomics consortium, SGC, hydrolase; HET: ADP; 1.30A {Homo sapiens} PDB: 3b7g_A*

Probab=99.94  E-value=2.1e-26  Score=178.06  Aligned_cols=135  Identities=30%  Similarity=0.532  Sum_probs=122.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++|||+|+.|+++.++++....+++++..+.||....++...+  .+++|+|+||+++.+++.. +.+++++++++
T Consensus        94 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~--~~~~Iiv~Tp~~l~~~~~~-~~~~~~~~~~l  170 (230)
T 2oxc_A           94 QILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRL--KKCHIAVGSPGRIKQLIEL-DYLNPGSIRLF  170 (230)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTSCHHHHHHHT--TSCSEEEECHHHHHHHHHT-TSSCGGGCCEE
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhcccCCceEEEEeCCCCHHHHHHhc--cCCCEEEECHHHHHHHHhc-CCcccccCCEE
Confidence            37999999999999999999998776689999999998877766555  4799999999999999987 77889999999


Q ss_pred             EEcccchhhccc-hHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEc
Q 030094           81 VLDEADRLLDMG-FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVR  138 (183)
Q Consensus        81 VvDEad~ll~~~-~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~  138 (183)
                      |+||||.+++.+ |...+..+++.+++.+|++++|||+++++.++++.++++|..|.++
T Consensus       171 ViDEah~~~~~~~~~~~~~~i~~~~~~~~~~l~lSAT~~~~~~~~~~~~~~~p~~i~~~  229 (230)
T 2oxc_A          171 ILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFLANALTKYMRDPTFVRLN  229 (230)
T ss_dssp             EESSHHHHHSTTSSHHHHHHHHHHSCSSCEEEEEESCCCHHHHHHHTTTCSSCEEECC-
T ss_pred             EeCCchHhhcCcchHHHHHHHHHhCCCCCeEEEEEeccCHHHHHHHHHHcCCCeEEEcC
Confidence            999999999887 9999999999999999999999999999999999999999998653

>2pl3_A Probable ATP-dependent RNA helicase DDX10; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; HET: ADP; 2.15A {Homo sapiens}

Probab=99.94  E-value=5.3e-26  Score=176.08  Aligned_cols=137  Identities=42%  Similarity=0.656  Sum_probs=121.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++|||+||.|+++.++++.... ++++..+.|+.....+...+  .+++|+|+||+++.+++.....+++++++++
T Consensus        99 ~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~--~~~~iiv~Tp~~l~~~l~~~~~~~~~~~~~l  175 (236)
T 2pl3_A           99 GVLIISPTRELAYQTFEVLRKVGKNH-DFSAGLIIGGKDLKHEAERI--NNINILVCTPGRLLQHMDETVSFHATDLQML  175 (236)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTS-SCCEEEECCC--CHHHHHHH--TTCSEEEECHHHHHHHHHHCSSCCCTTCCEE
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhCCC-CeeEEEEECCCCHHHHHHhC--CCCCEEEECHHHHHHHHHhcCCcccccccEE
Confidence            37999999999999999999997665 78999999998877776665  4799999999999999987446788999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccC
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAE  140 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~  140 (183)
                      |+||||.+++.+|...+..+++.+++.+|++++|||+++++..+++.++++|..|.++++
T Consensus       176 ViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~~~  235 (236)
T 2pl3_A          176 VLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHEK  235 (236)
T ss_dssp             EETTHHHHHHTTTHHHHHHHHHTSCTTSEEEEEESSCCHHHHHHHHHSCSSCEEEECCC-
T ss_pred             EEeChHHHhcCCcHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            999999999999999999999999999999999999999999999999999999987653

>1t6n_A Probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; HET: FLC; 1.94A {Homo sapiens} SCOP: c.37.1.19

Probab=99.94  E-value=4.4e-26  Score=174.66  Aligned_cols=136  Identities=24%  Similarity=0.536  Sum_probs=124.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++||++|+.|+++.++++.+..+++++..+.|+.....+...+...+++|+|+||+++..++.+ +.+.+++++++
T Consensus        84 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~v~~~~g~~~~~~~~~~~~~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~l  162 (220)
T 1t6n_A           84 SVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN-KSLNLKHIKHF  162 (220)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT-TSSCCTTCCEE
T ss_pred             EEEEEeCCHHHHHHHHHHHHHHHhhCCCceEEEEeCCCChHHHHHHHhcCCCCEEEeCHHHHHHHHHh-CCCCcccCCEE
Confidence            37999999999999999999998877789999999998888877777666789999999999999988 77889999999


Q ss_pred             EEcccchhhc-cchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEE
Q 030094           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEV  137 (183)
Q Consensus        81 VvDEad~ll~-~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~  137 (183)
                      |+||||.+++ .+|...+..+++.+++.+|++++|||+++++.++++.++++|..|.+
T Consensus       163 ViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~v  220 (220)
T 1t6n_A          163 ILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV  220 (220)
T ss_dssp             EEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEEC
T ss_pred             EEcCHHHHhcccCcHHHHHHHHHhCCCcCeEEEEEeecCHHHHHHHHHHcCCCeEEeC
Confidence            9999999987 58899999999999999999999999999999999999999998863

>1vec_A ATP-dependent RNA helicase P54; DEAD-box protein, RNA binding protein; HET: TLA; 2.01A {Homo sapiens} SCOP: c.37.1.19

Probab=99.94  E-value=7.4e-26  Score=171.49  Aligned_cols=132  Identities=31%  Similarity=0.571  Sum_probs=122.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||++||++|+.|+++.++++.+..+++++..+.|+....++...+ ..+++|+|+||+++.+++.+ +...+++++++|
T Consensus        74 ~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~lV  151 (206)
T 1vec_A           74 AMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRL-DDTVHVVIATPGRILDLIKK-GVAKVDHVQMIV  151 (206)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHT-TSCCSEEEECHHHHHHHHHT-TCSCCTTCCEEE
T ss_pred             EEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhc-CCCCCEEEeCHHHHHHHHHc-CCcCcccCCEEE
Confidence            7999999999999999999998877788999999998887776665 46899999999999999987 778899999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEE
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRV  135 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i  135 (183)
                      +||||.+.+.+|...+..+++.+++++|++++|||+++++.++++.++++|..|
T Consensus       152 iDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          152 LDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             EETHHHHTSTTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             EEChHHhHhhCcHHHHHHHHHhCCccceEEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence            999999999899999999999999999999999999999999999999999876

>3ly5_A ATP-dependent RNA helicase DDX18; alpha-beta, structural genomics, structural genomics consort ATP-binding, hydrolase, nucleotide-binding, RNA-B; 2.80A {Homo sapiens}

Probab=99.94  E-value=1e-25  Score=177.78  Aligned_cols=131  Identities=40%  Similarity=0.649  Sum_probs=119.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++|||+||.|+++.++++.... +.++..++|+.....+...+. .+++|+||||+++.+++.....+.+++++++
T Consensus       128 ~~lil~Pt~~La~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~-~~~~Iiv~Tp~~l~~~~~~~~~~~~~~l~~l  205 (262)
T 3ly5_A          128 GVLILSPTRELAMQTFGVLKELMTHH-VHTYGLIMGGSNRSAEAQKLG-NGINIIVATPGRLLDHMQNTPGFMYKNLQCL  205 (262)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTC-CSCEEEECSSSCHHHHHHHHH-HCCSEEEECHHHHHHHHHHCTTCCCTTCCEE
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHHhhc-CceEEEEECCCCHHHHHHHhc-CCCCEEEEcHHHHHHHHHccCCcccccCCEE
Confidence            48999999999999999999998776 788999999998887777764 4799999999999999988455789999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCe
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPV  133 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~  133 (183)
                      |+||||++++.+|...+..+++.+++.+|+++||||+++++..+++.+++++.
T Consensus       206 ViDEah~l~~~~~~~~l~~i~~~~~~~~q~l~~SAT~~~~v~~~~~~~l~~~~  258 (262)
T 3ly5_A          206 VIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVEDLARISLKKEP  258 (262)
T ss_dssp             EECSHHHHHHTTCHHHHHHHHHHSCSSSEEEEECSSCCHHHHHHHHHHCSSCC
T ss_pred             EEcChHHHhhhhHHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHcCCCC
Confidence            99999999999999999999999999999999999999999999999998654

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.94  E-value=3.4e-26  Score=175.39  Aligned_cols=138  Identities=36%  Similarity=0.582  Sum_probs=121.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCC---CceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLP---DVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~---~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||++|||+||.|+++.++++....+   ++++..+.|+.....+...+ ..+++|+|+||+++.+++.. +.++++++
T Consensus        74 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~~Iiv~Tp~~l~~~l~~-~~~~~~~~  151 (219)
T 1q0u_A           74 QAVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKL-NVQPHIVIGTPGRINDFIRE-QALDVHTA  151 (219)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCC-SSCCSEEEECHHHHHHHHHT-TCCCGGGC
T ss_pred             eEEEEcCcHHHHHHHHHHHHHHhhhcccccceEEEEEeCCCCHHHHHHHc-CCCCCEEEeCHHHHHHHHHc-CCCCcCcc
Confidence            379999999999999999999987653   57888889988766554444 35799999999999999987 77889999


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccC
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAE  140 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~  140 (183)
                      +++|+||||.+.+.+|...+..+++.+++.+|++++|||+++++.++++.++++|..|.+...
T Consensus       152 ~~lViDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~~~~~~~  214 (219)
T 1q0u_A          152 HILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHVLEH  214 (219)
T ss_dssp             CEEEECSHHHHHHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEECC--
T ss_pred             eEEEEcCchHHhhhChHHHHHHHHHhCCcccEEEEEecCCCHHHHHHHHHHcCCCeEEEeecc
Confidence            999999999999999999999999999999999999999999999999999999999876543

>2gxq_A Heat resistant RNA dependent ATPase; RNA helicase, atomic resolution, AMP complex, ribosome biogenesis, thermophilic, hydrolase; HET: AMP; 1.20A {Thermus thermophilus HB27} PDB: 2gxs_A* 2gxu_A 3mwj_A 3mwk_A* 3mwl_A* 3nbf_A* 3nej_A

Probab=99.93  E-value=3.9e-25  Score=167.46  Aligned_cols=133  Identities=34%  Similarity=0.560  Sum_probs=120.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++||++|+.|+++.++++..   .+++..+.|+.....+...+. .+++|+|+||+++.+++.. +.+++++++++
T Consensus        74 ~~lil~P~~~L~~q~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~-~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~i  148 (207)
T 2gxq_A           74 RALVLTPTRELALQVASELTAVAP---HLKVVAVYGGTGYGKQKEALL-RGADAVVATPGRALDYLRQ-GVLDLSRVEVA  148 (207)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHHCT---TSCEEEECSSSCSHHHHHHHH-HCCSEEEECHHHHHHHHHH-TSSCCTTCSEE
T ss_pred             cEEEEECCHHHHHHHHHHHHHHhh---cceEEEEECCCChHHHHHHhh-CCCCEEEECHHHHHHHHHc-CCcchhhceEE
Confidence            379999999999999999998864   467888899888777766664 5899999999999999988 78889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVR  138 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~  138 (183)
                      |+||||.+.+.+|...+..+++.+++.+|++++|||++++++.+++.++.+|..|.+.
T Consensus       149 ViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~p~~i~~~  206 (207)
T 2gxq_A          149 VLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAKRLAERYMKNPVLINVI  206 (207)
T ss_dssp             EEESHHHHHHTTCHHHHHHHHHTSCTTSEEEEECSSCCHHHHHHHHHHCSSCEEEECC
T ss_pred             EEEChhHhhccchHHHHHHHHHhCCccCeEEEEEEecCHHHHHHHHHHcCCCeEEEcC
Confidence            9999999999999999999999999999999999999999999999999999998764

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.93  E-value=1.4e-24  Score=179.92  Aligned_cols=162  Identities=35%  Similarity=0.595  Sum_probs=140.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||++|||+||.|+++.++++.... ++++..+.||....++...+ ..+++|+|+||++|.+++.. +.+.+++++++|
T Consensus       104 ~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~-~~~~~I~v~Tp~~l~~~l~~-~~~~~~~~~~iV  180 (417)
T 2i4i_A          104 SLVLAPTRELAVQIYEEARKFSYRS-RVRPCVVYGGADIGQQIRDL-ERGCHLLVATPGRLVDMMER-GKIGLDFCKYLV  180 (417)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCHHHHHHHH-TTCCSEEEECHHHHHHHHHT-TSBCCTTCCEEE
T ss_pred             EEEECCcHHHHHHHHHHHHHHhCcC-CceEEEEECCCCHHHHHHHh-hCCCCEEEEChHHHHHHHHc-CCcChhhCcEEE
Confidence            7999999999999999999997665 78999999999888887777 46899999999999999988 778899999999


Q ss_pred             EcccchhhccchHHHHHHHHHh--CCC--CCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCC
Q 030094           82 LDEADRLLDMGFQKQISYIISR--LPK--LRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSK  157 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~--l~~--~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~  157 (183)
                      +||||.+++.+|...+..++..  +++  .+|++++|||+++.+..+...++.+|..+.+...               ..
T Consensus       181 iDEah~~~~~~~~~~~~~i~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~---------------~~  245 (417)
T 2i4i_A          181 LDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATFPKEIQMLARDFLDEYIFLAVGRV---------------GS  245 (417)
T ss_dssp             ESSHHHHHHTTCHHHHHHHHTSSSCCCBTTBEEEEEESCCCHHHHHHHHHHCSSCEEEEEC-------------------
T ss_pred             EEChhHhhccCcHHHHHHHHHhccCCCcCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEeCCC---------------CC
Confidence            9999999999999999999885  333  6899999999999999999999999999888766               56


Q ss_pred             CccCceEEEEEecCcchhhhhhcc
Q 030094          158 TPLGLHLEVIWNVNQMRNHHNLLI  181 (183)
Q Consensus       158 ~~~~l~q~~i~~~~~~k~~~ll~l  181 (183)
                      .+.++.+.++.++..+|...+..+
T Consensus       246 ~~~~i~~~~~~~~~~~~~~~l~~~  269 (417)
T 2i4i_A          246 TSENITQKVVWVEESDKRSFLLDL  269 (417)
T ss_dssp             CCSSEEEEEEECCGGGHHHHHHHH
T ss_pred             CccCceEEEEEeccHhHHHHHHHH
Confidence            678899999999888887766543

>1qde_A EIF4A, translation initiation factor 4A; DEAD box protein family, gene regulation; 2.00A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 1qva_A

Probab=99.93  E-value=3.6e-25  Score=169.86  Aligned_cols=136  Identities=34%  Similarity=0.592  Sum_probs=113.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++|||+|+.|+++.++++.... ++++..+.|+.....+...+  .+++|+|+||+++.+++.+ +.+.+++++++
T Consensus        84 ~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~--~~~~iiv~Tp~~l~~~~~~-~~~~~~~~~~i  159 (224)
T 1qde_A           84 QALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGL--RDAQIVVGTPGRVFDNIQR-RRFRTDKIKMF  159 (224)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECC----------C--TTCSEEEECHHHHHHHHHT-TSSCCTTCCEE
T ss_pred             eEEEEECCHHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHhcC--CCCCEEEECHHHHHHHHHh-CCcchhhCcEE
Confidence            37999999999999999999998766 78999999988877666554  3499999999999999988 77889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccC
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAE  140 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~  140 (183)
                      |+||||.+.+.+|...+..+++.+++.+|++++|||+++++.++++.++++|..|.+..+
T Consensus       160 ViDEah~~~~~~~~~~l~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~p~~i~~~~~  219 (224)
T 1qde_A          160 ILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKD  219 (224)
T ss_dssp             EEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC----
T ss_pred             EEcChhHHhhhhhHHHHHHHHHhCCccCeEEEEEeecCHHHHHHHHHHCCCCEEEEecCC
Confidence            999999999999999999999999999999999999999999999999999999987765

>2j0s_A ATP-dependent RNA helicase DDX48; mRNA processing, phosphorylation, rRNA processing, mRNA splicing, mRNA transport; HET: ANP; 2.21A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 2j0q_A* 2hyi_C* 3ex7_C* 2xb2_A* 2hxy_A 2j0u_A 2j0u_B 2zu6_A

Probab=99.92  E-value=1.3e-24  Score=180.11  Aligned_cols=161  Identities=30%  Similarity=0.490  Sum_probs=142.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++|||+||.|+++.+.+++... ++++..+.|+....++...+. .+++|+|+||+++.+++.. +.+.+.+++++
T Consensus       107 ~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~-~~~~ivv~Tp~~l~~~l~~-~~~~~~~~~~v  183 (410)
T 2j0s_A          107 QALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLD-YGQHVVAGTPGRVFDMIRR-RSLRTRAIKML  183 (410)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHHH-HCCSEEEECHHHHHHHHHT-TSSCCTTCCEE
T ss_pred             eEEEEcCcHHHHHHHHHHHHHHhccC-CeEEEEEECCCCHHHHHHHhh-cCCCEEEcCHHHHHHHHHh-CCccHhheeEE
Confidence            47999999999999999999998776 889999999999888877774 5899999999999999988 77889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||.+++.+|...+..+++.+++.+|++++|||+++++..+...++.+|..+.+...               .....
T Consensus       184 ViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~  248 (410)
T 2j0s_A          184 VLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVKRD---------------ELTLE  248 (410)
T ss_dssp             EEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCCGG---------------GCSCT
T ss_pred             EEccHHHHHhhhhHHHHHHHHHhCccCceEEEEEcCCCHHHHHHHHHHcCCCEEEEecCc---------------cccCC
Confidence            999999999999999999999999999999999999999999999999999998877665               55677


Q ss_pred             CceEEEEEecCcc-hhhhhh
Q 030094          161 GLHLEVIWNVNQM-RNHHNL  179 (183)
Q Consensus       161 ~l~q~~i~~~~~~-k~~~ll  179 (183)
                      ++.++++.++..+ |...+.
T Consensus       249 ~~~~~~~~~~~~~~k~~~l~  268 (410)
T 2j0s_A          249 GIKQFFVAVEREEWKFDTLC  268 (410)
T ss_dssp             TEEEEEEEESSTTHHHHHHH
T ss_pred             CceEEEEEeCcHHhHHHHHH
Confidence            8899998887665 554443

>3dkp_A Probable ATP-dependent RNA helicase DDX52; DEAD, ADP, structural genomics, structural GEN consortium, SGC, rRNA, ATP-binding, hydrolase; HET: ADP; 2.10A {Homo sapiens}

Probab=99.92  E-value=4e-25  Score=171.98  Aligned_cols=139  Identities=29%  Similarity=0.400  Sum_probs=116.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcC-CcCCCCceE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMD-VLDFRNLEI   79 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~-~~~l~~l~~   79 (183)
                      .+||++|||+||.|+++.++++.... ++++..+.|+.....+.......+++|+||||+++.+++.... .++++++++
T Consensus       100 ~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~I~v~Tp~~l~~~l~~~~~~~~~~~~~~  178 (245)
T 3dkp_A          100 RALIISPTRELASQIHRELIKISEGT-GFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNRLIYLLKQDPPGIDLASVEW  178 (245)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTS-CCCEECCCHHHHHHTTTSTTSCCCCCEEEECHHHHHHHHHSSSCSCCCTTCCE
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhccc-CceEEEEecCccHHHHhhhhhcCCCCEEEECHHHHHHHHHhCCCCcccccCcE
Confidence            38999999999999999999998776 7888777776544333222334679999999999999998722 578999999


Q ss_pred             EEEcccchhhc---cchHHHHHHHHHhCC-CCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccC
Q 030094           80 LVLDEADRLLD---MGFQKQISYIISRLP-KLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAE  140 (183)
Q Consensus        80 lVvDEad~ll~---~~~~~~l~~i~~~l~-~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~  140 (183)
                      +|+||||.+++   .+|...+..++..+. ++.|+++||||+++++..+++.++++|+.|.++.+
T Consensus       179 lViDEah~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~SAT~~~~v~~~~~~~l~~p~~i~~~~~  243 (245)
T 3dkp_A          179 LVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSATFAYDVEQWCKLNLDNVISVSIGAR  243 (245)
T ss_dssp             EEESSHHHHHHHC--CHHHHHHHHHHHCCCTTCEEEEEESSCCHHHHHHHHHHSSSCEEEEECC-
T ss_pred             EEEeChHHhcccccccHHHHHHHHHHhcCCCCcEEEEEeccCCHHHHHHHHHhCCCCEEEEeCCC
Confidence            99999999998   578999999988764 57899999999999999999999999999998765

>1xti_A Probable ATP-dependent RNA helicase P47; alpha-beta fold, gene regulation; 1.95A {Homo sapiens} SCOP: c.37.1.19 c.37.1.19 PDB: 1xtj_A* 1xtk_A

Probab=99.92  E-value=1.9e-23  Score=171.63  Aligned_cols=165  Identities=23%  Similarity=0.462  Sum_probs=145.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||++||++|+.|+++.++++....+++++..+.|+.....+...+...+++|+|+||+++..++.. ..+.+++++++|
T Consensus        79 ~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~iiv~T~~~l~~~~~~-~~~~~~~~~~vV  157 (391)
T 1xti_A           79 VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN-KSLNLKHIKHFI  157 (391)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHTTTCTTCCEEEECTTSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT-TSSCCTTCSEEE
T ss_pred             EEEECCCHHHHHHHHHHHHHHHhhCCCeEEEEEeCCCCHHHHHHHHhcCCCCEEEECHHHHHHHHHc-CCccccccCEEE
Confidence            7999999999999999999998887789999999999888777777666799999999999999987 778899999999


Q ss_pred             Ecccchhhc-cchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           82 LDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        82 vDEad~ll~-~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      +||||.+.+ .++...+..++...++.+|++++|||+++.+..++..++.+|..+.+....              .....
T Consensus       158 iDEaH~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~  223 (391)
T 1xti_A          158 LDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFVDDET--------------KLTLH  223 (391)
T ss_dssp             ECSHHHHTSSHHHHHHHHHHHHTSCSSSEEEEEESSCCSTHHHHHHHHCSSCEEEECCCCC--------------CCCCT
T ss_pred             EeCHHHHhhccchHHHHHHHHhhCCCCceEEEEEeeCCHHHHHHHHHHcCCCeEEEecCcc--------------ccCcc
Confidence            999999987 478899999999999999999999999999999999999999998876652              44567


Q ss_pred             CceEEEEEecCcchhhhhhcc
Q 030094          161 GLHLEVIWNVNQMRNHHNLLI  181 (183)
Q Consensus       161 ~l~q~~i~~~~~~k~~~ll~l  181 (183)
                      ++.++++.+...+|...+..+
T Consensus       224 ~~~~~~~~~~~~~~~~~l~~~  244 (391)
T 1xti_A          224 GLQQYYVKLKDNEKNRKLFDL  244 (391)
T ss_dssp             TCEEEEEECCGGGHHHHHHHH
T ss_pred             cceEEEEEcCchhHHHHHHHH
Confidence            788999888888877666543

>3eiq_A Eukaryotic initiation factor 4A-I; PDCD4, anti-oncogene, apoptosis, cell cycle, nucleus, phosph RNA-binding, ATP-binding, helicase, hydrolase; 3.50A {Homo sapiens}

Probab=99.91  E-value=1.2e-23  Score=174.01  Aligned_cols=161  Identities=32%  Similarity=0.509  Sum_probs=143.8

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++||++|+.|+++.++++.... +..+..+.|+.....+...+...+++|+|+||+++.+++.. +.+.+++++++
T Consensus       110 ~~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~iiv~T~~~l~~~l~~-~~~~~~~~~~v  187 (414)
T 3eiq_A          110 QALVLAPTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNR-RYLSPKYIKMF  187 (414)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHGGGS-CCCEEECCCCTTHHHHHHHHTTTCCSEEEECHHHHHHHHHH-TSSCSTTCCEE
T ss_pred             eEEEEeChHHHHHHHHHHHHHHhccc-CceEEEEECCcchHHHHHHHhcCCCCEEEECHHHHHHHHHc-CCcccccCcEE
Confidence            37999999999999999999998776 78999999999888887777667899999999999999988 78889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||.+.+.++...+..++..+++.+|++++|||+++.+..+...++.+|..+.....               .....
T Consensus       188 ViDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~  252 (414)
T 3eiq_A          188 VLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVKKE---------------ELTLE  252 (414)
T ss_dssp             EECSHHHHHHTTTHHHHHHHHTTSCTTCEEEEECSCCCHHHHHHHTTTCSSCEEECCCCC---------------CCCTT
T ss_pred             EEECHHHhhccCcHHHHHHHHHhCCCCCeEEEEEEecCHHHHHHHHHHcCCCEEEEecCC---------------ccCCC
Confidence            999999999999999999999999999999999999999999999999999999887766               66778


Q ss_pred             CceEEEEEecCcc-hhhhh
Q 030094          161 GLHLEVIWNVNQM-RNHHN  178 (183)
Q Consensus       161 ~l~q~~i~~~~~~-k~~~l  178 (183)
                      ++.++++.+...+ |...+
T Consensus       253 ~~~~~~~~~~~~~~~~~~l  271 (414)
T 3eiq_A          253 GIRQFYINVEREEWKLDTL  271 (414)
T ss_dssp             SCCEEEEECSSSTTHHHHH
T ss_pred             CceEEEEEeChHHhHHHHH
Confidence            8888888887665 44444

>3fmp_B ATP-dependent RNA helicase DDX19B; nuclear porin, nuclear pore complex, nucleocytoplasmic trans mRNA export, protein interaction, beta-propeller; HET: ADP; 3.19A {Homo sapiens}

Probab=99.90  E-value=1.5e-23  Score=177.63  Aligned_cols=159  Identities=25%  Similarity=0.344  Sum_probs=119.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++|||+||.|+++.++++.++.+++.+....|+.......    ..+++|+||||+++.+++.+.+.+++++++++
T Consensus       164 ~~lil~Pt~~La~Q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~Ivv~Tp~~l~~~l~~~~~~~~~~~~~i  239 (479)
T 3fmp_B          164 QCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ----KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVF  239 (479)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHTTSTTCCEEEESTTCCCCTTC----CCCCSEEEECHHHHHHHHTTSCCCCGGGCCEE
T ss_pred             cEEEEeChHHHHHHHHHHHHHHHhhCCCceEEEEeCCccccccc----cCCCCEEEECchHHHHHHHhcCCcCcccCCEE
Confidence            48999999999999999999999887788888888877643321    34689999999999999976566788999999


Q ss_pred             EEcccchhhc-cchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCc
Q 030094           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTP  159 (183)
Q Consensus        81 VvDEad~ll~-~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (183)
                      |+||||.+++ .++...+..+.+.+++.+|++++|||+++++..++..++++|..+.+..+               ....
T Consensus       240 ViDEah~~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~i~~~~~---------------~~~~  304 (479)
T 3fmp_B          240 VLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE---------------EETL  304 (479)
T ss_dssp             EECCHHHHHTSTTHHHHHHHHHTTSCTTSEEEEEESCCCHHHHHHHHHHSSSEEEEEEC---------------------
T ss_pred             EEECHHHHhhcCCcHHHHHHHHhhCCccceEEEEeCCCCHHHHHHHHHHcCCCeEEecccc---------------ccCc
Confidence            9999999987 58889999999999999999999999999999999999999999998877               5567


Q ss_pred             cCceEEEEEecCc-chhhhh
Q 030094          160 LGLHLEVIWNVNQ-MRNHHN  178 (183)
Q Consensus       160 ~~l~q~~i~~~~~-~k~~~l  178 (183)
                      .++.|+++.+... .|...+
T Consensus       305 ~~~~~~~~~~~~~~~~~~~l  324 (479)
T 3fmp_B          305 DTIKQYYVLCSSRDEKFQAL  324 (479)
T ss_dssp             --------------------
T ss_pred             CCceEEEEEeCCHHHHHHHH
Confidence            7788888877653 344433

>1fuu_A Yeast initiation factor 4A; IF4A, helicase, DEAD-box protein, translation; 2.50A {Saccharomyces cerevisiae} SCOP: c.37.1.19 PDB: 2vso_A* 2vsx_A*

Probab=99.89  E-value=2.1e-22  Score=165.31  Aligned_cols=154  Identities=31%  Similarity=0.512  Sum_probs=123.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++||++|+.|+++.+.++.... ++++..+.|+....++...+.  +++|+|+||+++...+.. +.+.+.+++++
T Consensus        91 ~~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~--~~~i~v~T~~~l~~~~~~-~~~~~~~~~~v  166 (394)
T 1fuu_A           91 QALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR--DAQIVVGTPGRVFDNIQR-RRFRTDKIKMF  166 (394)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECSSCCHHHHHHHHH--HCSEEEECHHHHHHHHHT-TSSCCTTCCEE
T ss_pred             CEEEEcCCHHHHHHHHHHHHHHhccC-CeeEEEEeCCCchHHHHhhcC--CCCEEEECHHHHHHHHHh-CCcchhhCcEE
Confidence            37999999999999999999997765 789999999988877766653  689999999999999987 77888999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||.+.+.++...+..++..+++.+|++++|||+++.+..+...++.+|..+.....               ...+.
T Consensus       167 IiDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~  231 (394)
T 1fuu_A          167 ILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILVKKD---------------ELTLE  231 (394)
T ss_dssp             EEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEECSSCCHHHHHHHHHHCCSCEEEEECC---------------------
T ss_pred             EEEChHHhhCCCcHHHHHHHHHhCCCCceEEEEEEecCHHHHHHHHHhcCCCeEEEecCc---------------cccCC
Confidence            999999999989999999999999999999999999999999999999999999887665               44455


Q ss_pred             CceEEEEEecCcc
Q 030094          161 GLHLEVIWNVNQM  173 (183)
Q Consensus       161 ~l~q~~i~~~~~~  173 (183)
                      ++.++++.++..+
T Consensus       232 ~~~~~~~~~~~~~  244 (394)
T 1fuu_A          232 GIKQFYVNVEEEE  244 (394)
T ss_dssp             -------------
T ss_pred             CceEEEEEcCchh
Confidence            6666666655444

>1s2m_A Putative ATP-dependent RNA helicase DHH1; ATP-binding, RNA-binding, RNA binding protein; 2.10A {Saccharomyces cerevisiae} SCOP: c.37.1.19 c.37.1.19 PDB: 2wax_A* 2way_A

Probab=99.88  E-value=7.4e-22  Score=162.81  Aligned_cols=160  Identities=29%  Similarity=0.476  Sum_probs=137.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++||++|+.|+++.++++.... ++++....|+.....+...+ ..+++|+|+||+++.+++.. +...+++++++
T Consensus        91 ~~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~-~~~~~Ivv~T~~~l~~~~~~-~~~~~~~~~~v  167 (400)
T 1s2m_A           91 QALIMVPTRELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRL-NETVHILVGTPGRVLDLASR-KVADLSDCSLF  167 (400)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHT-TSCCSEEEECHHHHHHHHHT-TCSCCTTCCEE
T ss_pred             cEEEEcCCHHHHHHHHHHHHHHhccc-CceEEEEeCCcchHHHHHHh-cCCCCEEEEchHHHHHHHHh-CCcccccCCEE
Confidence            37999999999999999999998766 78899999988877766555 46899999999999999987 67789999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPL  160 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (183)
                      |+||||.+.+.+|...+..++..+++..|++++|||++..+..+...++.+|..+....+                ....
T Consensus       168 IiDEaH~~~~~~~~~~~~~i~~~~~~~~~~i~lSAT~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~  231 (400)
T 1s2m_A          168 IMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLMEE----------------LTLK  231 (400)
T ss_dssp             EEESHHHHSSHHHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCCSS----------------CBCT
T ss_pred             EEeCchHhhhhchHHHHHHHHHhCCcCceEEEEEecCCHHHHHHHHHHcCCCeEEEeccc----------------cccC
Confidence            999999999988999999999999999999999999999999999999999987754432                3456


Q ss_pred             CceEEEEEecCcchhhhhh
Q 030094          161 GLHLEVIWNVNQMRNHHNL  179 (183)
Q Consensus       161 ~l~q~~i~~~~~~k~~~ll  179 (183)
                      ++.+++..++...|...+.
T Consensus       232 ~~~~~~~~~~~~~k~~~l~  250 (400)
T 1s2m_A          232 GITQYYAFVEERQKLHCLN  250 (400)
T ss_dssp             TEEEEEEECCGGGHHHHHH
T ss_pred             CceeEEEEechhhHHHHHH
Confidence            7788888887777765544

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.88  E-value=3.9e-22  Score=172.84  Aligned_cols=161  Identities=30%  Similarity=0.439  Sum_probs=132.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhh---hCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFIS---TLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~---~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||++|||+||.|+++.++++..   ..+...+..+.||.....+...+...+++|+||||++|.+++.......++++
T Consensus        97 ~~lvl~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~gg~~~~~~~~~l~~~~~~IlV~Tp~~l~~~l~~~~~~~~~~~  176 (579)
T 3sqw_A           97 KAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFV  176 (579)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTC
T ss_pred             eEEEEcchHHHHHHHHHHHHHHHhhcccccceEEEEEECCccHHHHHHHHhcCCCCEEEECHHHHHHHHHhccccccccC
Confidence            379999999999999999999875   33467888999999988888887667899999999999999987334578999


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCC-------CCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccch
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLP-------KLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASS  150 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~-------~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~  150 (183)
                      +++|+||||.+++++|...+..|+..++       ..+|+++||||+++.+..++..++.+|..+.+......       
T Consensus       177 ~~lViDEah~l~~~gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~~-------  249 (579)
T 3sqw_A          177 DYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKN-------  249 (579)
T ss_dssp             CEEEEETHHHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSS-------
T ss_pred             CEEEEEChHHhhcCCCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCcc-------
Confidence            9999999999999999999999887764       36799999999999999999999999988876543211       


Q ss_pred             hhcccCCCccCceEEEEEecCc
Q 030094          151 QQLASSKTPLGLHLEVIWNVNQ  172 (183)
Q Consensus       151 ~~~~~~~~~~~l~q~~i~~~~~  172 (183)
                          .......+.+.++.++..
T Consensus       250 ----~~~~~~~i~~~~~~~~~~  267 (579)
T 3sqw_A          250 ----EPEAHERIDQSVVISEKF  267 (579)
T ss_dssp             ----SCSSCTTEEEEEEEESST
T ss_pred             ----ccccccccceEEEEecch
Confidence                134455677777766543

>3fht_A ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box helicase, RNA dependent ATPase, mRNA export, nucleocytoplasmic transport, NUP214, CAN; HET: ANP; 2.20A {Homo sapiens} PDB: 3ews_A* 3g0h_A* 3fhc_B

Probab=99.88  E-value=3.5e-22  Score=164.89  Aligned_cols=154  Identities=25%  Similarity=0.359  Sum_probs=133.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++||++||.|+++.++++....+++++....|+.......    ..+++|+|+||+++.+++.+.+.+++++++++
T Consensus        97 ~~lil~P~~~L~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~ivv~T~~~l~~~~~~~~~~~~~~~~~i  172 (412)
T 3fht_A           97 QCLCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQ----KISEQIVIGTPGTVLDWCSKLKFIDPKKIKVF  172 (412)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTSTTCCEEEECTTCCCCTTC----CCCCSEEEECHHHHHHHHTTSCSSCGGGCCEE
T ss_pred             CEEEECCCHHHHHHHHHHHHHHHhhcccceEEEeecCcchhhhh----cCCCCEEEECchHHHHHHHhcCCcChhhCcEE
Confidence            37999999999999999999998887789999888887654332    35789999999999999976466788999999


Q ss_pred             EEcccchhhc-cchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCc
Q 030094           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTP  159 (183)
Q Consensus        81 VvDEad~ll~-~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (183)
                      |+||||.+++ .++...+..+.+.+++.+|++++|||+++.+..+...++.+|..+.+...               ....
T Consensus       173 ViDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~  237 (412)
T 3fht_A          173 VLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKRE---------------EETL  237 (412)
T ss_dssp             EEETHHHHHSTTTTHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEECCCGG---------------GSSC
T ss_pred             EEeCHHHHhhcCCcHHHHHHHHhhCCCCceEEEEEeecCHHHHHHHHHhcCCCeEEeeccc---------------cccc
Confidence            9999999987 67889999999999999999999999999999999999999999987776               5667


Q ss_pred             cCceEEEEEecCcc
Q 030094          160 LGLHLEVIWNVNQM  173 (183)
Q Consensus       160 ~~l~q~~i~~~~~~  173 (183)
                      ..+.++++.+...+
T Consensus       238 ~~~~~~~~~~~~~~  251 (412)
T 3fht_A          238 DTIKQYYVLCSSRD  251 (412)
T ss_dssp             TTEEEEEEECSSHH
T ss_pred             cCceEEEEEcCChH
Confidence            78888888876543

>3i5x_A ATP-dependent RNA helicase MSS116; protein-RNA complex, RNA helicase, DEAD-BOX, ATP-binding, HE hydrolase, mitochondrion; HET: ANP; 1.90A {Saccharomyces cerevisiae} PDB: 3i5y_A* 3i61_A* 3i62_A* 3sqx_A* 4db2_A 4db4_A

Probab=99.88  E-value=7.7e-22  Score=170.01  Aligned_cols=160  Identities=31%  Similarity=0.449  Sum_probs=130.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhh---CCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFIST---LPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~---~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+|||+|||+||.|+++.++++...   .+...+..+.|+.....+...+...+++|+||||+++.+++.+.....++++
T Consensus       148 ~~lil~Ptr~La~Q~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~Iiv~Tp~~l~~~l~~~~~~~~~~~  227 (563)
T 3i5x_A          148 KAVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPGRLIDVLEKYSNKFFRFV  227 (563)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHHCGGGTTSCEEEECTTSCHHHHHHHHHHHCCSEEEECHHHHHHHHHHHHHHHCTTC
T ss_pred             eEEEEcCcHHHHHHHHHHHHHHHhhccccCceeEEEEECCcCHHHHHHHHhcCCCCEEEECcHHHHHHHHhccccccccc
Confidence            3799999999999999999998653   3457788999999988888877667899999999999999987334568899


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCC-------CCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccch
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLP-------KLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASS  150 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~-------~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~  150 (183)
                      +++|+||||.+++++|...+..++..++       ..+|+++||||+++.+..++..++.+|..+.+......       
T Consensus       228 ~~lViDEah~l~~~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~~-------  300 (563)
T 3i5x_A          228 DYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDKN-------  300 (563)
T ss_dssp             CEEEEETHHHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCSS-------
T ss_pred             eEEEEeCHHHHhccchHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCCC-------
Confidence            9999999999999999999999887763       37799999999999999999999999988876543211       


Q ss_pred             hhcccCCCccCceEEEEEecC
Q 030094          151 QQLASSKTPLGLHLEVIWNVN  171 (183)
Q Consensus       151 ~~~~~~~~~~~l~q~~i~~~~  171 (183)
                          .......+.+.++.++.
T Consensus       301 ----~~~~~~~~~~~~~~~~~  317 (563)
T 3i5x_A          301 ----EPEAHERIDQSVVISEK  317 (563)
T ss_dssp             ----SCSSCTTEEEEEEEESS
T ss_pred             ----CccccccCceEEEECch
Confidence                13345566676666654

>1hv8_A Putative ATP-dependent RNA helicase MJ0669; RNA-binding protein, ATPase, RNA binding protein; 3.00A {Methanocaldococcus jannaschii} SCOP: c.37.1.19 c.37.1.19

Probab=99.87  E-value=4.1e-21  Score=155.90  Aligned_cols=157  Identities=27%  Similarity=0.456  Sum_probs=135.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||++||++|+.|+++.+.++.... ++++....|+.....+...+.  +++|+|+||+++.+.+.. +.+.+++++++|
T Consensus        77 ~lil~P~~~L~~q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~~--~~~iiv~T~~~l~~~~~~-~~~~~~~~~~iI  152 (367)
T 1hv8_A           77 AIILTPTRELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKALK--NANIVVGTPGRILDHINR-GTLNLKNVKYFI  152 (367)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHHH--TCSEEEECHHHHHHHHHT-TCSCTTSCCEEE
T ss_pred             EEEEcCCHHHHHHHHHHHHHHhCCC-CceEEEEECCcchHHHHhhcC--CCCEEEecHHHHHHHHHc-CCcccccCCEEE
Confidence            7999999999999999999997664 788999999988877766663  789999999999999987 778899999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCccC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTPLG  161 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (183)
                      +||||.+.+.++...+..++..+++..|++++|||+++....+...++.++..+....                   ..+
T Consensus       153 iDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~-------------------~~~  213 (367)
T 1hv8_A          153 LDEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKI-------------------NAN  213 (367)
T ss_dssp             EETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECCS-------------------SSS
T ss_pred             EeCchHhhhhchHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEecC-------------------CCC
Confidence            9999999999999999999999999999999999999999999999999887765322                   346


Q ss_pred             ceEEEEEecCcchhhhhhcc
Q 030094          162 LHLEVIWNVNQMRNHHNLLI  181 (183)
Q Consensus       162 l~q~~i~~~~~~k~~~ll~l  181 (183)
                      +.+.++.+...+|...+..+
T Consensus       214 ~~~~~~~~~~~~~~~~l~~~  233 (367)
T 1hv8_A          214 IEQSYVEVNENERFEALCRL  233 (367)
T ss_dssp             SEEEEEECCGGGHHHHHHHH
T ss_pred             ceEEEEEeChHHHHHHHHHH
Confidence            77888888877777666543

>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=99.87  E-value=1.2e-20  Score=151.62  Aligned_cols=132  Identities=33%  Similarity=0.594  Sum_probs=119.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++||++|+.|+++.++++.... +.++..+.|+.....+...+  .+++|+|+||+++.+++.. +.+++.+++++
T Consensus        58 ~~liv~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~--~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~i  133 (337)
T 2z0m_A           58 KSLVVTPTRELTRQVASHIRDIGRYM-DTKVAEVYGGMPYKAQINRV--RNADIVVATPGRLLDLWSK-GVIDLSSFEIV  133 (337)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECTTSCHHHHHHHH--TTCSEEEECHHHHHHHHHT-TSCCGGGCSEE
T ss_pred             CEEEEeCCHHHHHHHHHHHHHHhhhc-CCcEEEEECCcchHHHHhhc--CCCCEEEECHHHHHHHHHc-CCcchhhCcEE
Confidence            37999999999999999999997766 78999999998887776666  3599999999999999887 77788999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEE
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVE  136 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~  136 (183)
                      |+||||.+.+.++...+..++...+...|++++|||+++.+......++.++..+.
T Consensus       134 ViDEah~~~~~~~~~~~~~~~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~  189 (337)
T 2z0m_A          134 IIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIE  189 (337)
T ss_dssp             EEESHHHHHHTTCHHHHHHHHHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEE
T ss_pred             EEEChHHhhccccHHHHHHHHhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeee
Confidence            99999999999999999999999999999999999999999999999999988774

>3pey_A ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, ATPase, helicase, mRNA-export, nuclear pore, hydrolase-RNA complex; HET: ADP; 1.40A {Saccharomyces cerevisiae} PDB: 3pew_A* 3pex_A* 3pez_A* 3rrm_A* 3rrn_A* 2kbe_A 3gfp_A 2kbf_A 3pev_A* 3peu_A*

Probab=99.86  E-value=8.4e-21  Score=155.49  Aligned_cols=150  Identities=29%  Similarity=0.414  Sum_probs=127.8

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++||++|+.|+++.++++.... ++.+....|+......     ..+++|+|+||+++..++.+ +...+.+++++
T Consensus        77 ~~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~-----~~~~~iiv~T~~~l~~~~~~-~~~~~~~~~~i  149 (395)
T 3pey_A           77 QAICLAPSRELARQTLEVVQEMGKFT-KITSQLIVPDSFEKNK-----QINAQVIVGTPGTVLDLMRR-KLMQLQKIKIF  149 (395)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEESTTSSCTTS-----CBCCSEEEECHHHHHHHHHT-TCBCCTTCCEE
T ss_pred             cEEEECCCHHHHHHHHHHHHHHhccc-CeeEEEEecCchhhhc-----cCCCCEEEEcHHHHHHHHHc-CCcccccCCEE
Confidence            37999999999999999999997665 7888877776543222     34799999999999999987 77889999999


Q ss_pred             EEcccchhhc-cchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCcccccccchhhcccCCCc
Q 030094           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESKSHHVSASSQQLASSKTP  159 (183)
Q Consensus        81 VvDEad~ll~-~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (183)
                      |+||||.+.+ .++...+..+.+.+++.+|++++|||+++.+..+...++.++..+.....               ....
T Consensus       150 IiDEah~~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~  214 (395)
T 3pey_A          150 VLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAVRQYAKKIVPNANTLELQTN---------------EVNV  214 (395)
T ss_dssp             EEETHHHHHHSTTHHHHHHHHHHTSCTTCEEEEEESCCCHHHHHHHHHHSCSCEEECCCGG---------------GCSC
T ss_pred             EEEChhhhcCccccHHHHHHHHHhCCCCcEEEEEEecCCHHHHHHHHHhCCCCeEEEcccc---------------cccc
Confidence            9999999987 67899999999999999999999999999999999999999998877666               5556


Q ss_pred             cCceEEEEEecCc
Q 030094          160 LGLHLEVIWNVNQ  172 (183)
Q Consensus       160 ~~l~q~~i~~~~~  172 (183)
                      ..+.+.+..+...
T Consensus       215 ~~~~~~~~~~~~~  227 (395)
T 3pey_A          215 DAIKQLYMDCKNE  227 (395)
T ss_dssp             TTEEEEEEECSSH
T ss_pred             ccccEEEEEcCch
Confidence            7777777776544

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.81  E-value=3.6e-20  Score=153.92  Aligned_cols=147  Identities=18%  Similarity=0.177  Sum_probs=112.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcch---HHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEV---KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~---~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||++|||+||.|+++.+++++.  .++++..+.|+.+.   ..+...+..+.++|+||||+++.+++..   +.++++
T Consensus        66 ~~lil~Pt~~L~~q~~~~~~~~~~--~~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~---~~~~~~  140 (414)
T 3oiy_A           66 KSALVFPTVTLVKQTLERLQKLAD--EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK---LSQKRF  140 (414)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHHCC--SSCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH---HTTCCC
T ss_pred             EEEEEECCHHHHHHHHHHHHHHcc--CCceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH---hccccc
Confidence            489999999999999999999876  48999999999887   5556666555599999999999988865   667899


Q ss_pred             eEEEEcccchh----------hc-cchHHH-HHHHHHhCC-----------CCCeEEEEeec-CChHHH-HHHHhhCCCC
Q 030094           78 EILVLDEADRL----------LD-MGFQKQ-ISYIISRLP-----------KLRRTGLFSAT-QTEAVE-ELSKAGLRNP  132 (183)
Q Consensus        78 ~~lVvDEad~l----------l~-~~~~~~-l~~i~~~l~-----------~~~Q~v~~SAT-~~~~v~-~~~~~~~~~~  132 (183)
                      +++|+||||.+          ++ .+|.+. +..+++.++           +.+|++++||| .++.+. .+.+.++.  
T Consensus       141 ~~iViDEaH~~~~~~~~~d~~l~~~~~~~~~~~~i~~~~~~~~~~~~l~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~--  218 (414)
T 3oiy_A          141 DFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN--  218 (414)
T ss_dssp             SEEEESCHHHHHHCHHHHHHHHHHTTCCHHHHHHHHHHHHHTCCCCCCTTCCCCEEEESSCCSSCCSSTTHHHHHHHS--
T ss_pred             cEEEEeChHhhhhccchhhhHHhhcCCcHHHHHHHHHhcccchhhhhcccCCCceEEEEecCCCcchhHHHHHHHhhc--
Confidence            99999999654          44 677777 888888776           78999999999 565544 33333332  


Q ss_pred             eEEEEccCCcccccccchhhcccCCCccCceEEEEEecC
Q 030094          133 VRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNVN  171 (183)
Q Consensus       133 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~l~q~~i~~~~  171 (183)
                        +.+...               ...+.++.|.++.++.
T Consensus       219 --~~~~~~---------------~~~~~~i~~~~~~~~~  240 (414)
T 3oiy_A          219 --FTVGRL---------------VSVARNITHVRISSRS  240 (414)
T ss_dssp             --CCSSCC---------------CCCCCSEEEEEESSCC
T ss_pred             --cCcCcc---------------ccccccchheeeccCH
Confidence              222222               4556778888876643

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.80  E-value=8.1e-20  Score=168.21  Aligned_cols=146  Identities=19%  Similarity=0.181  Sum_probs=115.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcch---HHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEV---KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~---~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||++||||||.|+++.+++++ . .++++..++|+.+.   ..+...+..+.++|+||||++|.+++..   ++++++
T Consensus       123 ~~Lil~PtreLa~Q~~~~l~~l~-~-~~i~v~~l~Gg~~~~er~~~~~~l~~g~~~IlV~Tp~rL~~~l~~---l~~~~l  197 (1104)
T 4ddu_A          123 KSALVFPTVTLVKQTLERLQKLA-D-EKVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK---LSQKRF  197 (1104)
T ss_dssp             CEEEEESSHHHHHHHHHHHHTTS-C-TTSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH---HHTSCC
T ss_pred             eEEEEechHHHHHHHHHHHHHhh-C-CCCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh---hcccCc
Confidence            48999999999999999999986 4 38999999999887   6666677555599999999999998864   677899


Q ss_pred             eEEEEccc----------chhhc-cchHHH-HHHHHHhCC-----------CCCeEEEEeec-CChHHH-HHHHhhCCCC
Q 030094           78 EILVLDEA----------DRLLD-MGFQKQ-ISYIISRLP-----------KLRRTGLFSAT-QTEAVE-ELSKAGLRNP  132 (183)
Q Consensus        78 ~~lVvDEa----------d~ll~-~~~~~~-l~~i~~~l~-----------~~~Q~v~~SAT-~~~~v~-~~~~~~~~~~  132 (183)
                      +++|+|||          |++++ .||... +..+++.++           +.+|+++|||| .+..+. .+.+.++.  
T Consensus       198 ~~lViDEaH~l~~~~r~~Dr~L~~~gf~~~~i~~il~~l~~~~~~~~~~~~~~~q~ll~SAT~~p~~~~~~~~~~~l~--  275 (1104)
T 4ddu_A          198 DFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPGILVVSSATAKPRGIRPLLFRDLLN--  275 (1104)
T ss_dssp             SEEEESCHHHHTTSSHHHHHHHHTSSCCHHHHHHHHHHHHHTSCCCCCSSCCCCEEEEECBSSCCCSSTTHHHHHHTC--
T ss_pred             CEEEEeCCCccccccccchhhhHhcCCCHHHHHHHHHhcccchhhhhhccCCCceEEEEcCCCCcHHHHHHHhhccee--
Confidence            99999999          45666 788888 889998877           88999999999 555544 23343333  


Q ss_pred             eEEEEccCCcccccccchhhcccCCCccCceEEEEEec
Q 030094          133 VRVEVRAESKSHHVSASSQQLASSKTPLGLHLEVIWNV  170 (183)
Q Consensus       133 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~l~q~~i~~~  170 (183)
                        +.+...               ...+.++.|.++.++
T Consensus       276 --i~v~~~---------------~~~~~~i~~~~~~~~  296 (1104)
T 4ddu_A          276 --FTVGRL---------------VSVARNITHVRISSR  296 (1104)
T ss_dssp             --CCCCBC---------------CCCCCCEEEEEESCC
T ss_pred             --EEeccC---------------CCCcCCceeEEEecC
Confidence              333333               556788888887774

>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=99.77  E-value=3.7e-19  Score=157.74  Aligned_cols=102  Identities=20%  Similarity=0.257  Sum_probs=73.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhcC-----CcCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMD-----VLDF   74 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~~-----~~~l   74 (183)
                      +|+|++||||||.|+++.+..+.+++ ++++.+++||.+...+  .+ ..+|||+||||++| .++++.+-     .+.+
T Consensus       117 ~vlVltPTreLA~Q~~e~~~~l~~~l-gl~v~~i~GG~~~~~r--~~-~~~~dIvvgTpgrl~fDyLrd~~~~~~~~~~~  192 (853)
T 2fsf_A          117 GVHVVTVNDYLAQRDAENNRPLFEFL-GLTVGINLPGMPAPAK--RE-AYAADITYGTNNEYGFDYLRDNMAFSPEERVQ  192 (853)
T ss_dssp             CCEEEESSHHHHHHHHHHHHHHHHHT-TCCEEECCTTCCHHHH--HH-HHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCC
T ss_pred             cEEEEcCCHHHHHHHHHHHHHHHHhc-CCeEEEEeCCCCHHHH--HH-hcCCCEEEECCchhhHHHHHhhhhccHhHhcc
Confidence            57999999999999999999999998 8999999999876433  33 23799999999999 78887521     3668


Q ss_pred             CCceEEEEcccchhh-cc---------------chHHHHHHHHHhCCC
Q 030094           75 RNLEILVLDEADRLL-DM---------------GFQKQISYIISRLPK  106 (183)
Q Consensus        75 ~~l~~lVvDEad~ll-~~---------------~~~~~l~~i~~~l~~  106 (183)
                      ++++++|+||||.|| +.               +|...+..|+..+++
T Consensus       193 ~~l~~lVlDEaD~mLiD~a~tpLIiSg~~~~~~~~y~~i~~iv~~L~~  240 (853)
T 2fsf_A          193 RKLHYALVDEVDSILIDEARTPLIISGPAEDSSEMYKRVNKIIPHLIR  240 (853)
T ss_dssp             CSCCEEEESCHHHHTTTTTTCEEEEEEC--------------------
T ss_pred             cCCcEEEECchHHHHHhcCcccccccCCCccchhHHHHHHHHHHhchh
Confidence            999999999999999 43               367889999998874

>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=99.76  E-value=1.6e-19  Score=165.86  Aligned_cols=141  Identities=15%  Similarity=0.184  Sum_probs=110.8

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCc----eEEEEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCcC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDV----KSVLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLD   73 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~----~~~~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~~   73 (183)
                      .+||++|||+||.|+++.+++++... ++    ++..++|+.+..++.   ..+ .. ++|+||||++|.+++.+     
T Consensus       101 ~~lil~PtreLa~Q~~~~l~~l~~~~-~i~~~~~v~~~~Gg~~~~~~~~~~~~l-~~-~~IlV~TP~~L~~~l~~-----  172 (1054)
T 1gku_B          101 RCYVIFPTSLLVIQAAETIRKYAEKA-GVGTENLIGYYHGRIPKREKENFMQNL-RN-FKIVITTTQFLSKHYRE-----  172 (1054)
T ss_dssp             CEEEEESCHHHHHHHHHHHHHHHTTT-CCSGGGSEEECCSSCCSHHHHHHHHSG-GG-CSEEEEEHHHHHHCSTT-----
T ss_pred             eEEEEeccHHHHHHHHHHHHHHHhhc-CCCccceEEEEeCCCChhhHHHHHhhc-cC-CCEEEEcHHHHHHHHHH-----
Confidence            48999999999999999999998876 67    899999998876643   333 33 99999999999987754     


Q ss_pred             CCCceEEEEcccchhhccchHHHHHHHHHhCC-----------CCCeEEEEeecCChHHHHHHHhhCCCCeEEEEccCCc
Q 030094           74 FRNLEILVLDEADRLLDMGFQKQISYIISRLP-----------KLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRAESK  142 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~-----------~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~~~~  142 (183)
                      +++++++|+||||.+++  +..++..++..++           ..+|+++||||+++. ..++..++.++..+.+...  
T Consensus       173 L~~l~~lViDEah~~l~--~~~~~~~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~~~--  247 (1054)
T 1gku_B          173 LGHFDFIFVDDVDAILK--ASKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIGSS--  247 (1054)
T ss_dssp             SCCCSEEEESCHHHHHT--STHHHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCSCC--
T ss_pred             hccCCEEEEeChhhhhh--ccccHHHHHHHhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEccCc--
Confidence            66899999999999987  5678888887773           568999999999998 6566666655555544443  


Q ss_pred             ccccccchhhcccCCCccCceEEEE
Q 030094          143 SHHVSASSQQLASSKTPLGLHLEVI  167 (183)
Q Consensus       143 ~~~~~~~~~~~~~~~~~~~l~q~~i  167 (183)
                                   .....++.|+++
T Consensus       248 -------------~~~~~~i~~~~~  259 (1054)
T 1gku_B          248 -------------RITVRNVEDVAV  259 (1054)
T ss_dssp             -------------EECCCCEEEEEE
T ss_pred             -------------ccCcCCceEEEe
Confidence                         344556666665

>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=99.75  E-value=1.7e-17  Score=152.91  Aligned_cols=125  Identities=22%  Similarity=0.191  Sum_probs=107.3

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      ++|++|||+||.|+++.+.++..     .+..+.|+...        ..+++|+|+||++|..++.+ +...+++++++|
T Consensus       230 vlvl~PtraLa~Q~~~~l~~~~~-----~VglltGd~~~--------~~~~~IlV~Tpe~L~~~L~~-~~~~l~~l~lVV  295 (1108)
T 3l9o_A          230 VIYTSPIKALSNQKYRELLAEFG-----DVGLMTGDITI--------NPDAGCLVMTTEILRSMLYR-GSEVMREVAWVI  295 (1108)
T ss_dssp             EEEEESSHHHHHHHHHHHHHHTS-----SEEEECSSCBC--------CCSCSEEEEEHHHHHHHHHH-CSSHHHHEEEEE
T ss_pred             EEEEcCcHHHHHHHHHHHHHHhC-----CccEEeCcccc--------CCCCCEEEeChHHHHHHHHc-CccccccCCEEE
Confidence            79999999999999999998753     56778887763        35789999999999999988 777789999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChH--HHHHHHhhCCCCeEEEEccC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA--VEELSKAGLRNPVRVEVRAE  140 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~--v~~~~~~~~~~~~~i~~~~~  140 (183)
                      +||||.+.+.++...+..++..+++..|++++|||+++.  +..+......+|..+.....
T Consensus       296 IDEaH~l~d~~rg~~~e~ii~~l~~~~qvl~lSATipn~~e~a~~l~~~~~~~~~vi~~~~  356 (1108)
T 3l9o_A          296 FDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTNF  356 (1108)
T ss_dssp             EETGGGTTSHHHHHHHHHHHHHSCTTSEEEEEECSCSSCHHHHHHHHHHTCSCEEEEEECC
T ss_pred             EhhhhhccccchHHHHHHHHHhcCCCceEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecCC
Confidence            999999999999999999999999999999999999875  44666777778877765443

>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=99.74  E-value=4.9e-18  Score=150.81  Aligned_cols=116  Identities=18%  Similarity=0.218  Sum_probs=97.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhc-----CCcCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERM-----DVLDF   74 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~-----~~~~l   74 (183)
                      +|+||+||||||.|+++.+..+.+++ ++++.+++||.+..++...   .+|||+||||++| .+++..+     +.+.+
T Consensus       126 ~vlVltptreLA~qd~e~~~~l~~~l-gl~v~~i~gg~~~~~r~~~---~~~dIv~gTpgrlgfD~L~D~m~~~~~~l~l  201 (844)
T 1tf5_A          126 GVHVVTVNEYLASRDAEQMGKIFEFL-GLTVGLNLNSMSKDEKREA---YAADITYSTNNELGFDYLRDNMVLYKEQMVQ  201 (844)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHHHHHT-TCCEEECCTTSCHHHHHHH---HHSSEEEEEHHHHHHHHHHHTTCSSGGGCCC
T ss_pred             CEEEEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHHHHh---cCCCEEEECchhhhHHHHHHhhhcchhhhcc
Confidence            48999999999999999999999988 9999999999876544322   4799999999999 6666541     24678


Q ss_pred             CCceEEEEcccchhh-cc---------------chHHHHHHHHHhCC---------CCCeEE-----------------E
Q 030094           75 RNLEILVLDEADRLL-DM---------------GFQKQISYIISRLP---------KLRRTG-----------------L  112 (183)
Q Consensus        75 ~~l~~lVvDEad~ll-~~---------------~~~~~l~~i~~~l~---------~~~Q~v-----------------~  112 (183)
                      +.++++|+||||.|| +.               +|...+..|++.++         +.+|+.                 +
T Consensus       202 r~~~~lVlDEaD~mLiDea~tplIisg~~~~~~~~~~~i~~iv~~l~~~~~y~vd~k~rq~~lt~~g~~~~e~~~~i~~L  281 (844)
T 1tf5_A          202 RPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNL  281 (844)
T ss_dssp             CCCCEEEEETHHHHHTTTTTCEEEEEEEEECCCHHHHHHHHHHTTCCSSSSBCCCSSSCCCCBCHHHHHHHHHHTTCSCT
T ss_pred             cCCCEEEECchhhhhhhccccchhhcCCcccchhHHHHHHHHHHhCcccccceeccccceEEecHHHHHHHHHHhCcccc
Confidence            999999999999998 55               37899999999997         478988                 9


Q ss_pred             EeecCChH
Q 030094          113 FSATQTEA  120 (183)
Q Consensus       113 ~SAT~~~~  120 (183)
                      ||||.+.-
T Consensus       282 fsat~~~~  289 (844)
T 1tf5_A          282 FDVKHVAL  289 (844)
T ss_dssp             TSGGGHHH
T ss_pred             CCCccchh
Confidence            99998743

>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=99.71  E-value=3.9e-17  Score=145.33  Aligned_cols=116  Identities=16%  Similarity=0.240  Sum_probs=99.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhc-----CCcCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERM-----DVLDF   74 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~-----~~~~l   74 (183)
                      +|+||+||++||.|+++.+..+.+++ ++++.+++||.+...+.  . ..+|||++|||++| .+++..+     +.+.+
T Consensus       154 ~v~VvTpTreLA~Qdae~m~~l~~~l-GLsv~~i~gg~~~~~r~--~-~y~~DIvygTpgrlgfDyLrD~m~~~~~~l~l  229 (922)
T 1nkt_A          154 GVHIVTVNDYLAKRDSEWMGRVHRFL-GLQVGVILATMTPDERR--V-AYNADITYGTNNEFGFDYLRDNMAHSLDDLVQ  229 (922)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHHHHHT-TCCEEECCTTCCHHHHH--H-HHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCC
T ss_pred             CeEEEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHHH--H-hcCCCEEEECchHhhHHHHHhhhhccHhhhcc
Confidence            48999999999999999999999998 99999999998754333  2 23699999999999 7777652     24678


Q ss_pred             CCceEEEEcccchhh-c---------------cchHHHHHHHHHhCC---------CCCeEE-----------------E
Q 030094           75 RNLEILVLDEADRLL-D---------------MGFQKQISYIISRLP---------KLRRTG-----------------L  112 (183)
Q Consensus        75 ~~l~~lVvDEad~ll-~---------------~~~~~~l~~i~~~l~---------~~~Q~v-----------------~  112 (183)
                      +.+.++|+||||.|| +               .+|...+..|+..++         +.+|+.                 +
T Consensus       230 r~l~~lIVDEaDsmLiDeartPLiiSg~~~~~~~~y~~i~~iv~~L~~~~dy~vDek~rqv~Lte~G~~~~e~~l~i~~L  309 (922)
T 1nkt_A          230 RGHHYAIVDEVDSILIDEARTPLIISGPADGASNWYTEFARLAPLMEKDVHYEVDLRKRTVGVHEKGVEFVEDQLGIDNL  309 (922)
T ss_dssp             CCCCEEEETTHHHHHTTGGGSCEEEEEECCCCHHHHHHHHHHHHHSCBTTTEEEETTTTEEEECHHHHHHHHHHHTCSST
T ss_pred             CCCCEEEEeChHHHHHhcCccceeecCCCCcchhHHHHHHHHHHhCcccccceeccCcceEEecHhHHHHHHHHhCCccc
Confidence            999999999999999 3               358899999999998         789999                 9


Q ss_pred             EeecCChH
Q 030094          113 FSATQTEA  120 (183)
Q Consensus       113 ~SAT~~~~  120 (183)
                      ||||.++-
T Consensus       310 fsat~~~l  317 (922)
T 1nkt_A          310 YEAANSPL  317 (922)
T ss_dssp             TCSTTCCH
T ss_pred             cCCcchhH
Confidence            99998753

>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=99.71  E-value=9.7e-17  Score=124.20  Aligned_cols=119  Identities=16%  Similarity=0.178  Sum_probs=88.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +++++|||++|.|+.+.+........+..+.........      ....+++|+||||+++.+++..    ++++++++|
T Consensus       112 ~l~~~p~~~la~q~~~~~~~~~~~~~~~~~g~~~~~~~~------~~~~~~~Ivv~Tpg~l~~~l~~----~l~~~~~lV  181 (235)
T 3llm_A          112 IVVTQPRRISAVSVAERVAFERGEEPGKSCGYSVRFESI------LPRPHASIMFCTVGVLLRKLEA----GIRGISHVI  181 (235)
T ss_dssp             EEEEESSHHHHHHHHHHHHHTTTCCTTSSEEEEETTEEE------CCCSSSEEEEEEHHHHHHHHHH----CCTTCCEEE
T ss_pred             EEEeccchHHHHHHHHHHHHHhccccCceEEEeechhhc------cCCCCCeEEEECHHHHHHHHHh----hhcCCcEEE
Confidence            688999999999998888766443223444332222111      1124689999999999999976    389999999


Q ss_pred             Ecccchh-hccchH-HHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCe
Q 030094           82 LDEADRL-LDMGFQ-KQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPV  133 (183)
Q Consensus        82 vDEad~l-l~~~~~-~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~  133 (183)
                      +||||.+ ++.+|. ..++.+.... ++.|+++||||++.+.  +.+.+..+|+
T Consensus       182 lDEah~~~~~~~~~~~~l~~i~~~~-~~~~~il~SAT~~~~~--~~~~~~~~pv  232 (235)
T 3llm_A          182 VDEIHERDINTDFLLVVLRDVVQAY-PEVRIVLMSATIDTSM--FCEYFFNCPI  232 (235)
T ss_dssp             ECCTTSCCHHHHHHHHHHHHHHHHC-TTSEEEEEECSSCCHH--HHHHTTSCCC
T ss_pred             EECCccCCcchHHHHHHHHHHHhhC-CCCeEEEEecCCCHHH--HHHHcCCCCE
Confidence            9999996 777776 5677777776 4799999999999886  6666666665

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.70  E-value=4.3e-16  Score=142.46  Aligned_cols=124  Identities=22%  Similarity=0.204  Sum_probs=103.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||++||++|+.|+++.+.++..     ++..++|+....        .+++|+|+||++|..++.+ +...+++++++|
T Consensus       132 vL~l~PtkaLa~Q~~~~l~~~~~-----~vglltGd~~~~--------~~~~IvV~Tpe~L~~~L~~-~~~~l~~l~lVV  197 (1010)
T 2xgj_A          132 VIYTSPIKALSNQKYRELLAEFG-----DVGLMTGDITIN--------PDAGCLVMTTEILRSMLYR-GSEVMREVAWVI  197 (1010)
T ss_dssp             EEEEESSHHHHHHHHHHHHHHHS-----CEEEECSSCEEC--------TTCSEEEEEHHHHHHHHHH-TCTTGGGEEEEE
T ss_pred             EEEECChHHHHHHHHHHHHHHhC-----CEEEEeCCCccC--------CCCCEEEEcHHHHHHHHHc-CcchhhcCCEEE
Confidence            79999999999999999998753     577788877642        3689999999999999988 777889999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHh---hCCCCeEEEEccC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKA---GLRNPVRVEVRAE  140 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~---~~~~~~~i~~~~~  140 (183)
                      +||||.+.+.++...++.++..+++..|++++|||+++. .+++.+   ...+|..+...+.
T Consensus       198 iDEaH~l~d~~rg~~~e~il~~l~~~~~il~LSATi~n~-~e~a~~l~~~~~~~~~vi~~~~  258 (1010)
T 2xgj_A          198 FDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNA-MEFAEWICKIHSQPCHIVYTNF  258 (1010)
T ss_dssp             EETGGGGGCTTTHHHHHHHHHHSCTTCEEEEEECCCTTH-HHHHHHHHHHHTSCEEEEEECC
T ss_pred             EechhhhcccchhHHHHHHHHhcCCCCeEEEEcCCCCCH-HHHHHHHHhhcCCCeEEEecCC
Confidence            999999998888888999999999999999999999876 334443   3456776655433

>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=99.69  E-value=1.7e-16  Score=135.63  Aligned_cols=115  Identities=13%  Similarity=0.157  Sum_probs=89.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCc-CCCCceE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL-DFRNLEI   79 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~-~l~~l~~   79 (183)
                      .+||++||++|+.|+++.++++.... ++++..+.|+.....+...+. .+++|+|+||++|.+++.. +.+ .++++++
T Consensus        57 ~~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~-~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~~  133 (556)
T 4a2p_A           57 KVVFLATKVPVYEQQKNVFKHHFERQ-GYSVQGISGENFSNVSVEKVI-EDSDIIVVTPQILVNSFED-GTLTSLSIFTL  133 (556)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHGGG-TCCEEECCCC-----CHHHHH-HHCSEEEECHHHHHHHHHS-SSCCCSTTCSE
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHhccc-CceEEEEeCCCCcchhHHHhh-CCCCEEEECHHHHHHHHHh-CcccccccCCE
Confidence            37999999999999999999998776 789999999887766655553 4699999999999999987 666 7999999


Q ss_pred             EEEcccchhhccchHHHH-HHHHHh-C---CCCCeEEEEeecCC
Q 030094           80 LVLDEADRLLDMGFQKQI-SYIISR-L---PKLRRTGLFSATQT  118 (183)
Q Consensus        80 lVvDEad~ll~~~~~~~l-~~i~~~-l---~~~~Q~v~~SAT~~  118 (183)
                      +|+||||++.+.+....+ ...+.. +   ++..|++++|||++
T Consensus       134 vViDEah~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT~~  177 (556)
T 4a2p_A          134 MIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVG  177 (556)
T ss_dssp             EEEETGGGCSTTSHHHHHHHHHHHHHHCC---CCEEEEEESCCC
T ss_pred             EEEECCcccCCcchHHHHHHHHHHhhhcccCCCCeEEEEeCCcc
Confidence            999999999877644333 233322 1   45689999999995

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.68  E-value=1.5e-16  Score=135.69  Aligned_cols=116  Identities=13%  Similarity=0.175  Sum_probs=94.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCc-CCCCceE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL-DFRNLEI   79 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~-~l~~l~~   79 (183)
                      .+||++||++|+.|+++.+++++... ++++..+.|+.....+...+. .+++|+|+||+++..++.. +.+ .+.++++
T Consensus        54 ~~lil~P~~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~~-~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~~  130 (555)
T 3tbk_A           54 KVVFFANQIPVYEQQATVFSRYFERL-GYNIASISGATSDSVSVQHII-EDNDIIILTPQILVNNLNN-GAIPSLSVFTL  130 (555)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHTT-TCCEEEECTTTGGGSCHHHHH-HHCSEEEECHHHHHHHHHT-SSSCCGGGCSE
T ss_pred             EEEEEeCCHHHHHHHHHHHHHHhccC-CcEEEEEcCCCcchhhHHHHh-cCCCEEEECHHHHHHHHhc-CcccccccCCE
Confidence            37999999999999999999998876 899999999987766655553 4699999999999999987 666 7899999


Q ss_pred             EEEcccchhhccc-hHHHHHHHHHhC-----CCCCeEEEEeecCCh
Q 030094           80 LVLDEADRLLDMG-FQKQISYIISRL-----PKLRRTGLFSATQTE  119 (183)
Q Consensus        80 lVvDEad~ll~~~-~~~~l~~i~~~l-----~~~~Q~v~~SAT~~~  119 (183)
                      +|+||||++.+.+ +...+...+...     ++..|++++|||++.
T Consensus       131 vViDEah~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT~~~  176 (555)
T 3tbk_A          131 MIFDECHNTSKNHPYNQIMFRYLDHKLGESRDPLPQVVGLTASVGV  176 (555)
T ss_dssp             EEETTGGGCSTTCHHHHHHHHHHHHHTSSCCSCCCEEEEEESCCCC
T ss_pred             EEEECccccCCcchHHHHHHHHHHhhhccccCCCCeEEEEecCccc
Confidence            9999999998764 333333443332     256799999999954

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.64  E-value=5.3e-16  Score=141.76  Aligned_cols=115  Identities=26%  Similarity=0.266  Sum_probs=98.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||++||++|+.|+++.+.++.   +++++..++|+...        ...++|+|+||++|..++.. ....+++++++|
T Consensus        85 vlvl~PtraLa~Q~~~~l~~~~---~~~~v~~l~G~~~~--------~~~~~IlV~Tpe~L~~~l~~-~~~~l~~l~lvV  152 (997)
T 4a4z_A           85 TIYTSPIKALSNQKFRDFKETF---DDVNIGLITGDVQI--------NPDANCLIMTTEILRSMLYR-GADLIRDVEFVI  152 (997)
T ss_dssp             EEEEESCGGGHHHHHHHHHTTC-----CCEEEECSSCEE--------CTTSSEEEEEHHHHHHHHHH-TCSGGGGEEEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHHHc---CCCeEEEEeCCCcc--------CCCCCEEEECHHHHHHHHHh-CchhhcCCCEEE
Confidence            7999999999999999888864   36788889988763        34689999999999999987 677789999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGL  129 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~  129 (183)
                      +||||.+.+.++...+..++..+++..|++++|||+++.. +++.++.
T Consensus       153 iDEaH~l~d~~~g~~~e~ii~~l~~~v~iIlLSAT~~n~~-ef~~~l~  199 (997)
T 4a4z_A          153 FDEVHYVNDQDRGVVWEEVIIMLPQHVKFILLSATVPNTY-EFANWIG  199 (997)
T ss_dssp             ECCTTCCCTTCTTCCHHHHHHHSCTTCEEEEEECCCTTHH-HHHHHHH
T ss_pred             EECcccccccchHHHHHHHHHhcccCCCEEEEcCCCCChH-HHHHHHh
Confidence            9999999998888889999999999999999999998763 6666553

>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=99.64  E-value=2.1e-15  Score=135.06  Aligned_cols=115  Identities=13%  Similarity=0.144  Sum_probs=90.1

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCc-CCCCceE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL-DFRNLEI   79 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~-~l~~l~~   79 (183)
                      .+||++||++|+.|+++.+++++... ++++..++|+.....+...+. .+++|+|+||++|.+++.. +.+ .++++++
T Consensus       298 ~~Lvl~Pt~~L~~Q~~~~~~~~~~~~-~~~v~~~~g~~~~~~~~~~~~-~~~~Ivv~Tp~~l~~~l~~-~~~~~~~~~~~  374 (797)
T 4a2q_A          298 KVVFLATKVPVYEQQKNVFKHHFERQ-GYSVQGISGENFSNVSVEKVI-EDSDIIVVTPQILVNSFED-GTLTSLSIFTL  374 (797)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHGGG-TCCEEEECCC-----CHHHHH-HTCSEEEECHHHHHHHHHS-SSCCCGGGCSE
T ss_pred             eEEEEeCCHHHHHHHHHHHHHhcccC-CceEEEEeCCcchhhhHHHhh-CCCCEEEEchHHHHHHHHh-ccccccccCCE
Confidence            37999999999999999999998776 889999999987776665553 5799999999999999987 666 7899999


Q ss_pred             EEEcccchhhccch-HHHHHHHHHhC----CCCCeEEEEeecCC
Q 030094           80 LVLDEADRLLDMGF-QKQISYIISRL----PKLRRTGLFSATQT  118 (183)
Q Consensus        80 lVvDEad~ll~~~~-~~~l~~i~~~l----~~~~Q~v~~SAT~~  118 (183)
                      +|+||||++.+.+. ...+..+....    .+.+|++++|||++
T Consensus       375 iViDEaH~~~~~~~~~~i~~~~~~~~~~~~~~~~~~l~lSATp~  418 (797)
T 4a2q_A          375 MIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVG  418 (797)
T ss_dssp             EEETTGGGCSTTSHHHHHHHHHHHHHHTTCCCCCEEEEEESCCC
T ss_pred             EEEECccccCCCccHHHHHHHHHHHhhccCCCCCeEEEEcCCcc
Confidence            99999999987643 33333333321    45689999999995

>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=99.63  E-value=3.9e-16  Score=118.09  Aligned_cols=113  Identities=14%  Similarity=0.219  Sum_probs=76.9

Q ss_pred             CEEEEeCcHHHHHH-HHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcC-----CcCC
Q 030094            1 MGMIISPTRELSSQ-IYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMD-----VLDF   74 (183)
Q Consensus         1 ~alIl~PtreLa~Q-i~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~-----~~~l   74 (183)
                      .+||++||++|+.| +.+.+.++...  ++++..+.|+.....+...+. .+++|+|+||+++...+....     .+.+
T Consensus        84 ~~lil~p~~~L~~q~~~~~~~~~~~~--~~~v~~~~g~~~~~~~~~~~~-~~~~i~v~T~~~l~~~~~~~~~~~~~~~~~  160 (216)
T 3b6e_A           84 KVIVLVNKVLLVEQLFRKEFQPFLKK--WYRVIGLSGDTQLKISFPEVV-KSCDIIISTAQILENSLLNLENGEDAGVQL  160 (216)
T ss_dssp             CEEEEESSHHHHHHHHHHTHHHHHTT--TSCEEECCC---CCCCHHHHH-HHCSEEEEEHHHHHHHHHC-------CCCG
T ss_pred             cEEEEECHHHHHHHHHHHHHHHHhcc--CceEEEEeCCcccchhHHhhc-cCCCEEEECHHHHHHHHhccCcccccccch
Confidence            37999999999999 78888888654  678888888776554444443 369999999999999987622     1567


Q ss_pred             CCceEEEEcccchhhccchHHHHH-HHHHhC-------------CCCCeEEEEeec
Q 030094           75 RNLEILVLDEADRLLDMGFQKQIS-YIISRL-------------PKLRRTGLFSAT  116 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~~~~~~~l~-~i~~~l-------------~~~~Q~v~~SAT  116 (183)
                      .+++++|+||||.+.+.++...+. .++...             .+..|++++|||
T Consensus       161 ~~~~~iIiDEah~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT  216 (216)
T 3b6e_A          161 SDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTAS  216 (216)
T ss_dssp             GGCSEEEETTC-------CHHHHHHHHHHHHHHHHHHHHTTCCCCCCCEEEEEECC
T ss_pred             hcccEEEEECchhhccCCcHHHHHHHHHHHhcccccccccccCCCCcceEEEeecC
Confidence            899999999999998765555443 332221             157899999998

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.63  E-value=2.8e-15  Score=131.95  Aligned_cols=114  Identities=12%  Similarity=0.174  Sum_probs=91.3

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCc-CCCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL-DFRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~-~l~~l~~l   80 (183)
                      +||++||++|+.|+++.+++++... ++++..+.|+.....+...+. .+++|+|+||++|.+.+.. +.+ .+++++++
T Consensus        64 ~lvl~Pt~~L~~Q~~~~~~~~~~~~-~~~v~~~~g~~~~~~~~~~~~-~~~~Iiv~Tp~~L~~~l~~-~~~~~l~~~~~v  140 (696)
T 2ykg_A           64 VVFFANQIPVYEQNKSVFSKYFERH-GYRVTGISGATAENVPVEQIV-ENNDIIILTPQILVNNLKK-GTIPSLSIFTLM  140 (696)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECSSSCSSSCHHHHH-HTCSEEEECHHHHHHHHHT-TSSCCGGGCSEE
T ss_pred             EEEEECCHHHHHHHHHHHHHHhccC-CceEEEEeCCccccccHHHhc-cCCCEEEECHHHHHHHHhc-CcccccccccEE
Confidence            7999999999999999999998665 789999999887655555553 4799999999999999987 666 78999999


Q ss_pred             EEcccchhhccc-hHHHHHHHHHh-----CCCCCeEEEEeecCC
Q 030094           81 VLDEADRLLDMG-FQKQISYIISR-----LPKLRRTGLFSATQT  118 (183)
Q Consensus        81 VvDEad~ll~~~-~~~~l~~i~~~-----l~~~~Q~v~~SAT~~  118 (183)
                      |+||||++.+.. +...+...+..     .++..|++++|||+.
T Consensus       141 ViDEaH~~~~~~~~~~i~~~~l~~~~~~~~~~~~~il~LTATp~  184 (696)
T 2ykg_A          141 IFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVG  184 (696)
T ss_dssp             EEETGGGCSTTCHHHHHHHHHHHHHHTTCCSCCCEEEEEESCCC
T ss_pred             EEeCCCcccCcccHHHHHHHHHHHhhcccCCCCCeEEEEeCccc
Confidence            999999987553 33333333332     246789999999997

>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=99.63  E-value=3e-15  Score=130.21  Aligned_cols=127  Identities=17%  Similarity=0.148  Sum_probs=95.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHH-----HhcCCcEEEeCcHHHH---HHHHh-cCCc
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKI-----EEEGANLLIGTPGRLY---DIMER-MDVL   72 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l-----~~~~~~IiV~TP~~l~---~~l~~-~~~~   72 (183)
                      +||++|+++|+.|+.+.+.++     ++++..+.|+....+....+     ...+++|+|+||++|.   .++.. .+..
T Consensus        87 ~lVisP~~~L~~q~~~~l~~~-----gi~~~~l~~~~~~~~~~~~~~~l~~~~~~~~Ilv~Tpe~L~~~~~~~~~l~~~~  161 (591)
T 2v1x_A           87 TLVICPLISLMEDQLMVLKQL-----GISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAY  161 (591)
T ss_dssp             EEEECSCHHHHHHHHHHHHHH-----TCCEEECCSSCCHHHHHHHHHHHHCTTCCCCEEEECHHHHHSCHHHHHHHHHHH
T ss_pred             EEEEeCHHHHHHHHHHHHHhc-----CCcEEEEeCCCCHHHHHHHHHHhhcccCCCCEEEEChhHhhccHHHHHHHHhhh
Confidence            799999999999999998886     57788888887765554332     2357999999999874   22221 0234


Q ss_pred             CCCCceEEEEcccchhhccc--hHHHHHH--HHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCe
Q 030094           73 DFRNLEILVLDEADRLLDMG--FQKQISY--IISRLPKLRRTGLFSATQTEAVEELSKAGLRNPV  133 (183)
Q Consensus        73 ~l~~l~~lVvDEad~ll~~~--~~~~l~~--i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~  133 (183)
                      .+.++.++|+||||.+.++|  |.+.+..  ++....+..|++++|||+++.+...+..++..+.
T Consensus       162 ~~~~i~~iViDEAH~is~~g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~  226 (591)
T 2v1x_A          162 EARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEK  226 (591)
T ss_dssp             HTTCEEEEEEETGGGGSTTCTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCCS
T ss_pred             hccCCcEEEEECcccccccccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCCC
Confidence            57889999999999998876  6555543  3333345799999999999999888888777554

>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=99.62  E-value=5.2e-15  Score=123.23  Aligned_cols=123  Identities=20%  Similarity=0.209  Sum_probs=97.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||+|||++|+.|+.+.+.++.+ .+..++..+.|+..........  .+++|+|+||+.+...+.. +.+.+.++.++|
T Consensus        55 ~liv~P~~~L~~q~~~~~~~~~~-~~~~~v~~~~g~~~~~~~~~~~--~~~~ivv~T~~~l~~~~~~-~~~~~~~~~~vI  130 (494)
T 1wp9_A           55 VLMLAPTKPLVLQHAESFRRLFN-LPPEKIVALTGEKSPEERSKAW--ARAKVIVATPQTIENDLLA-GRISLEDVSLIV  130 (494)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHBC-SCGGGEEEECSCSCHHHHHHHH--HHCSEEEECHHHHHHHHHT-TSCCTTSCSEEE
T ss_pred             EEEEECCHHHHHHHHHHHHHHhC-cchhheEEeeCCcchhhhhhhc--cCCCEEEecHHHHHHHHhc-CCcchhhceEEE
Confidence            79999999999999999999863 2466888888888766544433  3689999999999999987 778899999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChH---HHHHHHhh
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA---VEELSKAG  128 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~---v~~~~~~~  128 (183)
                      +||||.+.+......+...+....+..+++++|||+...   +..+....
T Consensus       131 iDEaH~~~~~~~~~~~~~~~~~~~~~~~~l~lTaTp~~~~~~~~~l~~~l  180 (494)
T 1wp9_A          131 FDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVINNL  180 (494)
T ss_dssp             EETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEESCSCSSHHHHHHHHHHT
T ss_pred             EECCcccCCCCcHHHHHHHHHhcCCCCeEEEEecCCCCCcHHHHHHHHhc
Confidence            999999986655555666666666789999999999744   44444443

>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=99.61  E-value=2e-15  Score=133.82  Aligned_cols=119  Identities=17%  Similarity=0.224  Sum_probs=99.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +++++|+|+||.|+++.++++.. . ++++...+|+.......    ..+++|+|+||+++..++.+ +...+++++++|
T Consensus        71 ~l~i~P~raLa~q~~~~~~~l~~-~-g~~v~~~~G~~~~~~~~----~~~~~Iiv~Tpe~l~~~~~~-~~~~l~~~~~vI  143 (720)
T 2zj8_A           71 AVYIVPLKALAEEKFQEFQDWEK-I-GLRVAMATGDYDSKDEW----LGKYDIIIATAEKFDSLLRH-GSSWIKDVKILV  143 (720)
T ss_dssp             EEEECSSGGGHHHHHHHTGGGGG-G-TCCEEEECSCSSCCCGG----GGGCSEEEECHHHHHHHHHH-TCTTGGGEEEEE
T ss_pred             EEEEcCcHHHHHHHHHHHHHHHh-c-CCEEEEecCCCCccccc----cCCCCEEEECHHHHHHHHHc-ChhhhhcCCEEE
Confidence            79999999999999999977654 3 78899999876543321    24789999999999999987 666689999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhh
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAG  128 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~  128 (183)
                      +||||.+.+.++...+..++..+++..|++++|||+++. ..+++++
T Consensus       144 iDE~H~l~~~~r~~~~~~ll~~l~~~~~ii~lSATl~n~-~~~~~~l  189 (720)
T 2zj8_A          144 ADEIHLIGSRDRGATLEVILAHMLGKAQIIGLSATIGNP-EELAEWL  189 (720)
T ss_dssp             EETGGGGGCTTTHHHHHHHHHHHBTTBEEEEEECCCSCH-HHHHHHT
T ss_pred             EECCcccCCCcccHHHHHHHHHhhcCCeEEEEcCCcCCH-HHHHHHh
Confidence            999999988788999999999887789999999999864 6666654

>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=99.60  E-value=3e-15  Score=132.36  Aligned_cols=120  Identities=16%  Similarity=0.232  Sum_probs=97.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+++++|+|+||.|+++.++++. .. ++++...+|+....++.    ..+++|+|+||+++..++.+ +...+++++++
T Consensus        70 ~~l~i~P~r~La~q~~~~~~~~~-~~-g~~v~~~~G~~~~~~~~----~~~~~Iiv~Tpe~l~~~l~~-~~~~l~~~~~v  142 (702)
T 2p6r_A           70 KSLYVVPLRALAGEKYESFKKWE-KI-GLRIGISTGDYESRDEH----LGDCDIIVTTSEKADSLIRN-RASWIKAVSCL  142 (702)
T ss_dssp             CEEEEESSHHHHHHHHHHHTTTT-TT-TCCEEEECSSCBCCSSC----STTCSEEEEEHHHHHHHHHT-TCSGGGGCCEE
T ss_pred             cEEEEeCcHHHHHHHHHHHHHHH-hc-CCEEEEEeCCCCcchhh----ccCCCEEEECHHHHHHHHHc-ChhHHhhcCEE
Confidence            37999999999999999997664 33 78999999977654321    23799999999999999987 55568899999


Q ss_pred             EEcccchhhccchHHHHHHHHHhC---CCCCeEEEEeecCChHHHHHHHhh
Q 030094           81 VLDEADRLLDMGFQKQISYIISRL---PKLRRTGLFSATQTEAVEELSKAG  128 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l---~~~~Q~v~~SAT~~~~v~~~~~~~  128 (183)
                      |+||||.+.+.++...+..++..+   ++..|++++|||+++ ...+++++
T Consensus       143 IiDE~H~l~~~~r~~~~~~ll~~l~~~~~~~~ii~lSATl~n-~~~~~~~l  192 (702)
T 2p6r_A          143 VVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAEWL  192 (702)
T ss_dssp             EETTGGGGGCTTTHHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHHHHT
T ss_pred             EEeeeeecCCCCcccHHHHHHHHHHhcCcCceEEEECCCcCC-HHHHHHHh
Confidence            999999998877777777776665   578999999999996 46777654

>4f92_B U5 small nuclear ribonucleoprotein 200 kDa helica; RNP remodeling, PRE-mRNA splicing, spliceosome catalytic ACT DEXD/H-box RNA helicase; HET: SAN; 2.66A {Homo sapiens} PDB: 4f93_B* 4f91_B

Probab=99.59  E-value=8.7e-15  Score=139.52  Aligned_cols=125  Identities=19%  Similarity=0.228  Sum_probs=92.9

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhc-CCcCCCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM-DVLDFRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~-~~~~l~~l~~l   80 (183)
                      ||+++|||+||.|+++.+++..+...++++..++|+...+..  ..  .+++|+|+||+++..++++. ..-.+++++++
T Consensus       975 avyi~P~raLa~q~~~~~~~~f~~~~g~~V~~ltGd~~~~~~--~~--~~~~IiV~TPEkld~llr~~~~~~~l~~v~lv 1050 (1724)
T 4f92_B          975 CVYITPMEALAEQVYMDWYEKFQDRLNKKVVLLTGETSTDLK--LL--GKGNIIISTPEKWDILSRRWKQRKNVQNINLF 1050 (1724)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHTTTSCCCEEECCSCHHHHHH--HH--HHCSEEEECHHHHHHHHTTTTTCHHHHSCSEE
T ss_pred             EEEEcChHHHHHHHHHHHHHHhchhcCCEEEEEECCCCcchh--hc--CCCCEEEECHHHHHHHHhCcccccccceeeEE
Confidence            799999999999999998764433238899998887654332  22  35899999999998887652 22247899999


Q ss_pred             EEcccchhhccchHHHHHHHH-------HhCCCCCeEEEEeecCChHHHHHHHhhCCCC
Q 030094           81 VLDEADRLLDMGFQKQISYII-------SRLPKLRRTGLFSATQTEAVEELSKAGLRNP  132 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~-------~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~  132 (183)
                      |+||+|.+.+. .+..++.++       ...++..|++++|||+++. ++++++.-.++
T Consensus      1051 ViDE~H~l~d~-rg~~le~il~rl~~i~~~~~~~~riI~lSATl~N~-~dla~WL~~~~ 1107 (1724)
T 4f92_B         1051 VVDEVHLIGGE-NGPVLEVICSRMRYISSQIERPIRIVALSSSLSNA-KDVAHWLGCSA 1107 (1724)
T ss_dssp             EECCGGGGGST-THHHHHHHHHHHHHHHHTTSSCCEEEEEESCBTTH-HHHHHHHTCCS
T ss_pred             EeechhhcCCC-CCccHHHHHHHHHHHHhhcCCCceEEEEeCCCCCH-HHHHHHhCCCC
Confidence            99999988653 344444333       4457789999999999875 78888765444

>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=99.58  E-value=8.6e-15  Score=133.22  Aligned_cols=114  Identities=13%  Similarity=0.175  Sum_probs=89.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCc-CCCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL-DFRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~-~l~~l~~l   80 (183)
                      +||++||++|+.|+++.++++.... ++++..++|+.....+...+. .+++|+|+||++|.+++.. +.+ .+++++++
T Consensus       299 vLvl~Pt~~L~~Q~~~~~~~~~~~~-~~~v~~~~G~~~~~~~~~~~~-~~~~IvI~Tp~~L~~~l~~-~~~~~l~~~~li  375 (936)
T 4a2w_A          299 VVFLATKVPVYEQQKNVFKHHFERQ-GYSVQGISGENFSNVSVEKVI-EDSDIIVVTPQILVNSFED-GTLTSLSIFTLM  375 (936)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHHTT-TCCEEEECCC-----CCHHHH-HHCSEEEECHHHHHHHHHS-SSCCCGGGCSEE
T ss_pred             EEEEeCCHHHHHHHHHHHHHHhccc-CceEEEEECCcchhhHHHHhc-cCCCEEEecHHHHHHHHHc-CccccccCCCEE
Confidence            7999999999999999999998766 899999999987666555553 4699999999999999987 666 78999999


Q ss_pred             EEcccchhhccc-hHHHHHHHHHhC----CCCCeEEEEeecCC
Q 030094           81 VLDEADRLLDMG-FQKQISYIISRL----PKLRRTGLFSATQT  118 (183)
Q Consensus        81 VvDEad~ll~~~-~~~~l~~i~~~l----~~~~Q~v~~SAT~~  118 (183)
                      |+||||++.+.+ +...+..+....    ++..|++++|||+.
T Consensus       376 ViDEaH~~~~~~~~~~i~~~~~~~~~~~~~~~~~~l~LSATp~  418 (936)
T 4a2w_A          376 IFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVG  418 (936)
T ss_dssp             EEETGGGCSTTCHHHHHHHHHHHHHHTTCSCCCEEEEEESCCC
T ss_pred             EEECccccCCCccHHHHHHHHHHHhhccCCCcCeEEEecCCcc
Confidence            999999998654 333333443331    45689999999995

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.58  E-value=6e-15  Score=130.55  Aligned_cols=119  Identities=18%  Similarity=0.194  Sum_probs=98.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +++++|+|+||.|+++.++++.. . ++++...+|+....++  .+  .+++|+|+||+++..++.+ +...+++++++|
T Consensus        78 il~i~P~r~La~q~~~~~~~~~~-~-g~~v~~~~G~~~~~~~--~~--~~~~Iiv~Tpe~l~~~~~~-~~~~l~~~~~vI  150 (715)
T 2va8_A           78 AIYVTPLRALTNEKYLTFKDWEL-I-GFKVAMTSGDYDTDDA--WL--KNYDIIITTYEKLDSLWRH-RPEWLNEVNYFV  150 (715)
T ss_dssp             EEEECSCHHHHHHHHHHHGGGGG-G-TCCEEECCSCSSSCCG--GG--GGCSEEEECHHHHHHHHHH-CCGGGGGEEEEE
T ss_pred             EEEEeCcHHHHHHHHHHHHHhhc-C-CCEEEEEeCCCCCchh--hc--CCCCEEEEcHHHHHHHHhC-ChhHhhccCEEE
Confidence            78999999999999999976643 3 7888888887665433  12  3789999999999999988 666689999999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGL  129 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~  129 (183)
                      +||||.+.+.++...++.++.+++ ..|++++|||+++. ..+++++.
T Consensus       151 iDE~H~l~~~~~~~~l~~i~~~~~-~~~ii~lSATl~n~-~~~~~~l~  196 (715)
T 2va8_A          151 LDELHYLNDPERGPVVESVTIRAK-RRNLLALSATISNY-KQIAKWLG  196 (715)
T ss_dssp             ECSGGGGGCTTTHHHHHHHHHHHH-TSEEEEEESCCTTH-HHHHHHHT
T ss_pred             EechhhcCCcccchHHHHHHHhcc-cCcEEEEcCCCCCH-HHHHHHhC
Confidence            999999887778888888888886 89999999999864 66666543

>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=99.57  E-value=1e-14  Score=127.69  Aligned_cols=103  Identities=14%  Similarity=0.110  Sum_probs=85.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      ++||++||||||.|+++.+.+..    +.++...+|+..        ...+++|+|+||++|   +.. ..+++++++++
T Consensus       259 ~vLVl~PTReLA~Qia~~l~~~~----g~~vg~~vG~~~--------~~~~~~IlV~TPGrL---l~~-~~l~l~~l~~l  322 (666)
T 3o8b_A          259 KVLVLNPSVAATLGFGAYMSKAH----GIDPNIRTGVRT--------ITTGAPVTYSTYGKF---LAD-GGCSGGAYDII  322 (666)
T ss_dssp             CEEEEESCHHHHHHHHHHHHHHH----SCCCEEECSSCE--------ECCCCSEEEEEHHHH---HHT-TSCCTTSCSEE
T ss_pred             eEEEEcchHHHHHHHHHHHHHHh----CCCeeEEECcEe--------ccCCCCEEEECcHHH---HhC-CCcccCcccEE
Confidence            48999999999999998766654    445666777655        246899999999997   455 67889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCe--EEEEeecCChH
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRR--TGLFSATQTEA  120 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q--~v~~SAT~~~~  120 (183)
                      |+||| ++++.+|...+..+++.++..+|  .+++|||+++.
T Consensus       323 VlDEA-H~l~~~~~~~l~~Il~~l~~~~~~llil~SAT~~~~  363 (666)
T 3o8b_A          323 ICDEC-HSTDSTTILGIGTVLDQAETAGARLVVLATATPPGS  363 (666)
T ss_dssp             EETTT-TCCSHHHHHHHHHHHHHTTTTTCSEEEEEESSCTTC
T ss_pred             EEccc-hhcCccHHHHHHHHHHhhhhcCCceEEEECCCCCcc
Confidence            99999 55678899999999999988877  67779999985

>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=99.55  E-value=1.3e-14  Score=138.21  Aligned_cols=122  Identities=16%  Similarity=0.154  Sum_probs=93.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCC--cCCCCceE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDV--LDFRNLEI   79 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~--~~l~~l~~   79 (183)
                      ||+++|+|+||.|+++.+++..+.. ++++..++|+.....+.    ..+++|+|+||+++..++++ ..  -.++++++
T Consensus       137 ~lyiaP~kALa~e~~~~l~~~~~~~-gi~V~~~tGd~~~~~~~----~~~~~IlVtTpEkld~llr~-~~~~~~l~~v~~  210 (1724)
T 4f92_B          137 IIYIAPMRSLVQEMVGSFGKRLATY-GITVAELTGDHQLCKEE----ISATQIIVCTPEKWDIITRK-GGERTYTQLVRL  210 (1724)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHTTT-TCCEEECCSSCSSCCTT----GGGCSEEEECHHHHHHHTTS-STTHHHHTTEEE
T ss_pred             EEEECCHHHHHHHHHHHHHHHHhhC-CCEEEEEECCCCCCccc----cCCCCEEEECHHHHHHHHcC-CccchhhcCcCE
Confidence            7999999999999999998887776 89999999987654321    24699999999998766654 22  23789999


Q ss_pred             EEEcccchhhccchHHHHHHHHH-------hCCCCCeEEEEeecCChHHHHHHHhhCCC
Q 030094           80 LVLDEADRLLDMGFQKQISYIIS-------RLPKLRRTGLFSATQTEAVEELSKAGLRN  131 (183)
Q Consensus        80 lVvDEad~ll~~~~~~~l~~i~~-------~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~  131 (183)
                      +|+||+|.+-+ ..+..++.++.       ..++..|++++|||+++. ++++++.-.+
T Consensus       211 vIiDEvH~l~d-~RG~~lE~~l~rl~~~~~~~~~~~riI~LSATl~N~-~dvA~wL~~~  267 (1724)
T 4f92_B          211 IILDEIHLLHD-DRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPNY-EDVATFLRVD  267 (1724)
T ss_dssp             EEETTGGGGGS-TTHHHHHHHHHHHHHHHHHHTCCCEEEEEECSCTTH-HHHHHHTTCC
T ss_pred             EEEecchhcCC-ccHHHHHHHHHHHHHHHHhCCCCCcEEEEecccCCH-HHHHHHhCCC
Confidence            99999997643 44555554443       346789999999999864 7777765433

>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=99.53  E-value=5.3e-14  Score=130.28  Aligned_cols=124  Identities=19%  Similarity=0.267  Sum_probs=96.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHH---HHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKAD---VKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~---~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +++|+|||++||.|+++.+.+..... ++++..+.|.....+.   ...+..+.+||+||||+.+    .  +.+.++++
T Consensus       654 ~vlvlvPt~~La~Q~~~~~~~~~~~~-~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll----~--~~~~~~~l  726 (1151)
T 2eyq_A          654 QVAVLVPTTLLAQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLL----Q--SDVKFKDL  726 (1151)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHH----H--SCCCCSSE
T ss_pred             eEEEEechHHHHHHHHHHHHHHhhcC-CCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHH----h--CCcccccc
Confidence            47999999999999999999877665 6888888876554433   3345455699999999654    2  45778999


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEE
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVE  136 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~  136 (183)
                      +++|+||+|++ +    .....+++.++...|++++|||+.++...+....+.++..+.
T Consensus       727 ~lvIiDEaH~~-g----~~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~  780 (1151)
T 2eyq_A          727 GLLIVDEEHRF-G----VRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIA  780 (1151)
T ss_dssp             EEEEEESGGGS-C----HHHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEECC
T ss_pred             ceEEEechHhc-C----hHHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEEe
Confidence            99999999995 2    233455666667899999999999888888887777666554

>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=99.53  E-value=6.9e-15  Score=116.53  Aligned_cols=108  Identities=20%  Similarity=0.156  Sum_probs=84.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||++||++|+.|+++.++++... +..++..+.||......    ...+++|+|+||+++...    ....+++++++|
T Consensus       160 ~lil~Pt~~L~~q~~~~l~~~~~~-~~~~~~~~~~~~~~~~~----~~~~~~I~v~T~~~l~~~----~~~~~~~~~~vI  230 (282)
T 1rif_A          160 ILIIVPTTALTTQMADDFVDYRLF-SHAMIKKIGGGASKDDK----YKNDAPVVVGTWQTVVKQ----PKEWFSQFGMMM  230 (282)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTSC-CGGGEEECSTTCSSTTC----CCTTCSEEEECHHHHTTS----CGGGGGGEEEEE
T ss_pred             EEEEECCHHHHHHHHHHHHHhccc-ccceEEEEeCCCcchhh----hccCCcEEEEchHHHHhh----HHHHHhhCCEEE
Confidence            799999999999999999998543 36777788777654321    125689999999876432    334567899999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHH
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE  122 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~  122 (183)
                      +||||++.+    ..+..+++.+++.+|++++|||+++...
T Consensus       231 iDEaH~~~~----~~~~~il~~~~~~~~~l~lSATp~~~~~  267 (282)
T 1rif_A          231 NDECHLATG----KSISSIISGLNNCMFKFGLSGSLRDGKA  267 (282)
T ss_dssp             EETGGGCCH----HHHHHHTTTCTTCCEEEEECSSCCTTST
T ss_pred             EECCccCCc----ccHHHHHHHhhcCCeEEEEeCCCCCcch
Confidence            999999963    4777888888889999999999986643

>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=99.52  E-value=9.3e-14  Score=119.20  Aligned_cols=127  Identities=20%  Similarity=0.185  Sum_probs=91.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||++|+++|+.|+.+.+.++     ++++..+.|+....+..   ..+..+.++|+++||+++...... ..+...++.
T Consensus        68 ~lvi~P~~aL~~q~~~~l~~~-----gi~~~~l~~~~~~~~~~~~~~~~~~~~~~ilv~Tpe~l~~~~~~-~~l~~~~~~  141 (523)
T 1oyw_A           68 TVVVSPLISLMKDQVDQLQAN-----GVAAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFL-EHLAHWNPV  141 (523)
T ss_dssp             EEEECSCHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHH-HHHTTSCEE
T ss_pred             EEEECChHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhChHHH-HHHhhCCCC
Confidence            689999999999999988875     56788888877655443   334456799999999998533222 234558899


Q ss_pred             EEEEcccchhhccc--hHHHH---HHHHHhCCCCCeEEEEeecCChHHHHH-HHhh-CCCCeEE
Q 030094           79 ILVLDEADRLLDMG--FQKQI---SYIISRLPKLRRTGLFSATQTEAVEEL-SKAG-LRNPVRV  135 (183)
Q Consensus        79 ~lVvDEad~ll~~~--~~~~l---~~i~~~l~~~~Q~v~~SAT~~~~v~~~-~~~~-~~~~~~i  135 (183)
                      ++|+||||.+.++|  |....   ..+.+.+| +.+++++|||.++.+..- .+.. +.+|..+
T Consensus       142 ~vViDEaH~i~~~g~~fr~~~~~l~~l~~~~~-~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~  204 (523)
T 1oyw_A          142 LLAVDEAHCISQWGHDFRPEYAALGQLRQRFP-TLPFMALTATADDTTRQDIVRLLGLNDPLIQ  204 (523)
T ss_dssp             EEEESSGGGGCTTSSCCCHHHHGGGGHHHHCT-TSCEEEEESCCCHHHHHHHHHHHTCCSCEEE
T ss_pred             EEEEeCccccCcCCCccHHHHHHHHHHHHhCC-CCCEEEEeCCCCHHHHHHHHHHhCCCCCeEE
Confidence            99999999998765  54444   34455564 689999999999987653 3333 3455544

>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=99.51  E-value=6.8e-14  Score=124.89  Aligned_cols=113  Identities=21%  Similarity=0.314  Sum_probs=85.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +++|++||++||.|+++.+.++.... ++++..++|+....+..   ..+..+.++|+||||+.+.+      .+.++++
T Consensus       419 qvlvlaPtr~La~Q~~~~l~~~~~~~-gi~v~~l~G~~~~~~r~~~~~~l~~g~~~IvVgT~~ll~~------~~~~~~l  491 (780)
T 1gm5_A          419 QTAFMVPTSILAIQHYRRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQE------DVHFKNL  491 (780)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHHH------CCCCSCC
T ss_pred             eEEEEeCcHHHHHHHHHHHHHHhhhc-CceEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHhh------hhhccCC
Confidence            58999999999999999999998766 79999999998765543   34445569999999986632      4678999


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHH
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELS  125 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~  125 (183)
                      +++|+||+|++-   +..  ...+......+|++++|||..++...+.
T Consensus       492 ~lVVIDEaHr~g---~~q--r~~l~~~~~~~~vL~mSATp~p~tl~~~  534 (780)
T 1gm5_A          492 GLVIIDEQHRFG---VKQ--REALMNKGKMVDTLVMSATPIPRSMALA  534 (780)
T ss_dssp             CEEEEESCCCC----------CCCCSSSSCCCEEEEESSCCCHHHHHH
T ss_pred             ceEEecccchhh---HHH--HHHHHHhCCCCCEEEEeCCCCHHHHHHH
Confidence            999999999962   221  1223333457899999999887755544

>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=99.47  E-value=2.2e-14  Score=126.24  Aligned_cols=114  Identities=13%  Similarity=0.209  Sum_probs=83.7

Q ss_pred             EEEEeCcHHHHHHH-HHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHH------hcCCcCC
Q 030094            2 GMIISPTRELSSQI-YHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIME------RMDVLDF   74 (183)
Q Consensus         2 alIl~PtreLa~Qi-~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~------~~~~~~l   74 (183)
                      +||++||++|+.|+ ++.++++...  ++++..+.|+....++...+. .+++|+|+||++|...+.      . ..+.+
T Consensus        59 vlvl~P~~~L~~Q~~~~~l~~~~~~--~~~v~~~~g~~~~~~~~~~~~-~~~~Ilv~Tp~~L~~~l~~~~~~~~-~~~~~  134 (699)
T 4gl2_A           59 VIVLVNKVLLVEQLFRKEFQPFLKK--WYRVIGLSGDTQLKISFPEVV-KSCDIIISTAQILENSLLNLENGED-AGVQL  134 (699)
T ss_dssp             BCCEESCSHHHHHHHHHTHHHHHTT--TSCEEEEC----CCCCHHHHH-HSCSEEEEEHHHHHHHTC---------CCCG
T ss_pred             EEEEECCHHHHHHHHHHHHHHHcCc--CceEEEEeCCcchhhHHHhhh-cCCCEEEECHHHHHHHHhccccccc-cceec
Confidence            68999999999999 9999998754  488999999877665555553 579999999999999883      3 45778


Q ss_pred             CCceEEEEcccchhhccc-hHHHHHHHHHh----C---------CCCCeEEEEeecCCh
Q 030094           75 RNLEILVLDEADRLLDMG-FQKQISYIISR----L---------PKLRRTGLFSATQTE  119 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~~~-~~~~l~~i~~~----l---------~~~~Q~v~~SAT~~~  119 (183)
                      .+++++|+||||++...+ +...+...+..    .         .+..|++++|||.+.
T Consensus       135 ~~~~lvViDEaH~~~~~~~~~~i~~~~l~~~~~~~~~~~~~~~~~~~~~il~lTATp~~  193 (699)
T 4gl2_A          135 SDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTASPGV  193 (699)
T ss_dssp             GGCSEEEEESGGGCBTTBSSCSHHHHHHHHHHHHHHHHC----CCCCCEEEEECSCCCC
T ss_pred             ccCcEEEEECccccCccchHHHHHHHHHHhhhcccccccccccCCCCCEEEEecccccc
Confidence            999999999999986543 22222222221    1         256899999999986

>2ipc_A Preprotein translocase SECA subunit; nucleotide binding fold, ATPase, parallel dimer; 2.80A {Thermus thermophilus}

Probab=99.43  E-value=3.7e-13  Score=120.05  Aligned_cols=85  Identities=16%  Similarity=0.137  Sum_probs=72.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhcC-----CcCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMD-----VLDF   74 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~~-----~~~l   74 (183)
                      +|+|++||++||.|+++.+..+..++ ++++.+++||.+.....  . ..++||+||||+++ .++++.+-     .+.+
T Consensus       122 qv~VvTPTreLA~Qdae~m~~l~~~l-GLsv~~i~Gg~~~~~r~--~-ay~~DIvyGTpgrlgfDyLrd~m~~~~~~l~~  197 (997)
T 2ipc_A          122 GVHVVTVNDYLARRDAEWMGPVYRGL-GLSVGVIQHASTPAERR--K-AYLADVTYVTNSELGFDYLRDNMAISPDQLVL  197 (997)
T ss_dssp             CCEEEESSHHHHHHHHHHHHHHHHTT-TCCEEECCTTCCHHHHH--H-HHTSSEEEEEHHHHHHHHHHHTSCSSTTTCCS
T ss_pred             CEEEEeCCHHHHHHHHHHHHHHHHhc-CCeEEEEeCCCCHHHHH--H-HcCCCEEEECchhhhhHHHHHhhhcchhhccc
Confidence            47999999999999999999999988 89999999998754332  2 24799999999999 88887621     3567


Q ss_pred             C---CceEEEEcccchhh
Q 030094           75 R---NLEILVLDEADRLL   89 (183)
Q Consensus        75 ~---~l~~lVvDEad~ll   89 (183)
                      +   ++.++|+||||.||
T Consensus       198 r~d~~l~~lIIDEaDsmL  215 (997)
T 2ipc_A          198 RHDHPLHYAIIDEVDSIL  215 (997)
T ss_dssp             CSSSSSCEEEETTHHHHT
T ss_pred             ccCCCcceEEEechHHHH
Confidence            8   99999999999987

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.43  E-value=1.9e-13  Score=116.22  Aligned_cols=108  Identities=20%  Similarity=0.162  Sum_probs=87.1

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+|||+||++|+.|+++.++++... ++.++..+.|+....++    ...+++|+||||+.+..   . ....++++.++
T Consensus       159 ~vlvl~P~~~L~~Q~~~~~~~~~~~-~~~~v~~~~~~~~~~~~----~~~~~~I~i~T~~~l~~---~-~~~~~~~~~li  229 (510)
T 2oca_A          159 KILIIVPTTALTTQMADDFVDYRLF-SHAMIKKIGGGASKDDK----YKNDAPVVVGTWQTVVK---Q-PKEWFSQFGMM  229 (510)
T ss_dssp             EEEEEESSHHHHHHHHHHHHHTTSS-CGGGEEECGGGCCTTGG----GCTTCSEEEEEHHHHTT---S-CGGGGGGEEEE
T ss_pred             eEEEEECcHHHHHHHHHHHHHhhcC-CccceEEEecCCccccc----cccCCcEEEEeHHHHhh---c-hhhhhhcCCEE
Confidence            3799999999999999999988543 46788888888776544    24679999999996543   2 34567889999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHH
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV  121 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v  121 (183)
                      |+||+|++..    .....+++.+++..+++++|||+++..
T Consensus       230 IiDE~H~~~~----~~~~~il~~~~~~~~~l~lSATp~~~~  266 (510)
T 2oca_A          230 MNDECHLATG----KSISSIISGLNNCMFKFGLSGSLRDGK  266 (510)
T ss_dssp             EEETGGGCCH----HHHHHHGGGCTTCCEEEEEESCGGGCS
T ss_pred             EEECCcCCCc----ccHHHHHHhcccCcEEEEEEeCCCCCc
Confidence            9999999854    457778888888899999999997664

>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=99.29  E-value=2.7e-11  Score=108.29  Aligned_cols=125  Identities=18%  Similarity=0.118  Sum_probs=81.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +++++|+|+||.|+++.+....    +.++...+|+....+.   ....+++|+++|||++.+.+..  ...+.+++++|
T Consensus       143 ilvl~P~r~La~q~~~~l~~~~----~~~v~~~vG~~i~~~~---~~~~~~~I~v~T~G~l~r~l~~--~~~l~~~~~lI  213 (773)
T 2xau_A          143 VACTQPRRVAAMSVAQRVAEEM----DVKLGEEVGYSIRFEN---KTSNKTILKYMTDGMLLREAME--DHDLSRYSCII  213 (773)
T ss_dssp             EEEEESCHHHHHHHHHHHHHHT----TCCBTTTEEEEETTEE---ECCTTCSEEEEEHHHHHHHHHH--STTCTTEEEEE
T ss_pred             EEecCchHHHHHHHHHHHHHHh----CCchhheecceecccc---ccCCCCCEEEECHHHHHHHHhh--CccccCCCEEE
Confidence            6889999999999987665543    2222222221110000   0124689999999999988866  35689999999


Q ss_pred             Ecccch-hhccch-HHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEcc
Q 030094           82 LDEADR-LLDMGF-QKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRA  139 (183)
Q Consensus        82 vDEad~-ll~~~~-~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~  139 (183)
                      +||+|. .++..+ ...+..+.... ++.|++++|||++.  +.+.+ ++.++..+.+..
T Consensus       214 lDEah~R~ld~d~~~~~l~~l~~~~-~~~~iIl~SAT~~~--~~l~~-~~~~~~vi~v~g  269 (773)
T 2xau_A          214 LDEAHERTLATDILMGLLKQVVKRR-PDLKIIIMSATLDA--EKFQR-YFNDAPLLAVPG  269 (773)
T ss_dssp             ECSGGGCCHHHHHHHHHHHHHHHHC-TTCEEEEEESCSCC--HHHHH-HTTSCCEEECCC
T ss_pred             ecCccccccchHHHHHHHHHHHHhC-CCceEEEEeccccH--HHHHH-HhcCCCcccccC
Confidence            999996 665432 34455555544 57899999999974  34544 555555555443

>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=99.28  E-value=8.7e-12  Score=105.03  Aligned_cols=94  Identities=20%  Similarity=0.159  Sum_probs=74.8

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCce-EEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVK-SVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEI   79 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~-~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~   79 (183)
                      .+||+|||++|+.|+++.+.++     +++ +..+.|+..          ..++|+|+||+.+...+...    .+++.+
T Consensus       135 ~~Lvl~P~~~L~~Q~~~~~~~~-----~~~~v~~~~g~~~----------~~~~Ivv~T~~~l~~~~~~~----~~~~~l  195 (472)
T 2fwr_A          135 PTLIVVPTLALAEQWKERLGIF-----GEEYVGEFSGRIK----------ELKPLTVSTYDSAYVNAEKL----GNRFML  195 (472)
T ss_dssp             CEEEEESSHHHHHHHHHHGGGG-----CGGGEEEBSSSCB----------CCCSEEEEEHHHHHHTHHHH----TTTCSE
T ss_pred             CEEEEECCHHHHHHHHHHHHhC-----CCcceEEECCCcC----------CcCCEEEEEcHHHHHHHHHh----cCCCCE
Confidence            4799999999999999988884     566 777777654          35799999999988776541    245889


Q ss_pred             EEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC
Q 030094           80 LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        80 lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      +|+||||.+.+.+|..    +++.+ +..+++++|||+.
T Consensus       196 iIvDEaH~~~~~~~~~----~~~~~-~~~~~l~lSATp~  229 (472)
T 2fwr_A          196 LIFDEVHHLPAESYVQ----IAQMS-IAPFRLGLTATFE  229 (472)
T ss_dssp             EEEETGGGTTSTTTHH----HHHTC-CCSEEEEEESCCC
T ss_pred             EEEECCcCCCChHHHH----HHHhc-CCCeEEEEecCcc
Confidence            9999999998877654    45555 4689999999997

>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=99.26  E-value=4.4e-12  Score=110.80  Aligned_cols=120  Identities=15%  Similarity=0.147  Sum_probs=83.8

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++||||||.|+++.+..+       .+. ..++ ...    .....+-.+-+.|.+.+...+..  ...+++++++
T Consensus       217 ~vLvl~PtreLa~Qi~~~l~~~-------~v~-~~~~-~l~----~~~tp~~~i~~~t~~~l~~~l~~--~~~l~~~~~i  281 (618)
T 2whx_A          217 RTLILAPTRVVAAEMEEALRGL-------PIR-YQTP-AVK----SDHTGREIVDLMCHATFTTRLLS--STRVPNYNLI  281 (618)
T ss_dssp             CEEEEESSHHHHHHHHHHTTTS-------CEE-ECCT-TSS----CCCCSSSCEEEEEHHHHHHHHHH--CSSCCCCSEE
T ss_pred             eEEEEcChHHHHHHHHHHhcCC-------cee-Eecc-cce----eccCCCceEEEEChHHHHHHHhc--cccccCCeEE
Confidence            4899999999999999876532       222 1111 100    00112345667787777766655  2568999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCC-CCCeEEEEeecCChHHHHHHHhhCCCCeEEEEcc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLP-KLRRTGLFSATQTEAVEELSKAGLRNPVRVEVRA  139 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~-~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~~  139 (183)
                      |+||||.+ +.+|...+..+.+.++ +++|+++||||+++.+..+..   .++..+.+..
T Consensus       282 ViDEah~~-~~~~~~~~~~i~~~l~~~~~q~il~SAT~~~~~~~~~~---~~~~~~~v~~  337 (618)
T 2whx_A          282 VMDEAHFT-DPCSVAARGYISTRVEMGEAAAIFMTATPPGSTDPFPQ---SNSPIEDIER  337 (618)
T ss_dssp             EEESTTCC-SHHHHHHHHHHHHHHHHTSCEEEEECSSCTTCCCSSCC---CSSCEEEEEC
T ss_pred             EEECCCCC-CccHHHHHHHHHHHhcccCccEEEEECCCchhhhhhhc---cCCceeeecc
Confidence            99999998 7778888888888875 689999999999988654433   3666666544

>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=99.24  E-value=7.7e-13  Score=111.22  Aligned_cols=102  Identities=23%  Similarity=0.304  Sum_probs=68.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcE-EEeCcHHHHHHHHh-------cCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANL-LIGTPGRLYDIMER-------MDVL   72 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~I-iV~TP~~l~~~l~~-------~~~~   72 (183)
                      +++|++|||+||.|+++.+..+     ++.  ...+                .+ .|+||+++.+++..       ....
T Consensus        39 ~~lil~Ptr~La~Q~~~~l~~~-----~v~--~~~~----------------~~~~v~Tp~~l~~~l~~~~l~~~~~~~~   95 (440)
T 1yks_A           39 RTLVLAPTRVVLSEMKEAFHGL-----DVK--FHTQ----------------AFSAHGSGREVIDAMCHATLTYRMLEPT   95 (440)
T ss_dssp             CEEEEESSHHHHHHHHHHTTTS-----CEE--EESS----------------CCCCCCCSSCCEEEEEHHHHHHHHTSSS
T ss_pred             eEEEEcchHHHHHHHHHHHhcC-----CeE--Eecc----------------cceeccCCccceeeecccchhHhhhCcc
Confidence            4899999999999999877644     222  1111                11 37888777654433       0123


Q ss_pred             CCCCceEEEEcccchhhccchHHHHHHHHHhC-CCCCeEEEEeecCChHHHHHHH
Q 030094           73 DFRNLEILVLDEADRLLDMGFQKQISYIISRL-PKLRRTGLFSATQTEAVEELSK  126 (183)
Q Consensus        73 ~l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l-~~~~Q~v~~SAT~~~~v~~~~~  126 (183)
                      .+++++++|+||||.+ +.++...+..+.+.. ++++|+++||||+++.+..+..
T Consensus        96 ~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~~~~~~l~~SAT~~~~~~~~~~  149 (440)
T 1yks_A           96 RVVNWEVIIMDEAHFL-DPASIAARGWAAHRARANESATILMTATPPGTSDEFPH  149 (440)
T ss_dssp             CCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCC
T ss_pred             cccCccEEEEECcccc-CcchHHHHHHHHHHhccCCceEEEEeCCCCchhhhhhh
Confidence            4899999999999998 444443333333333 3679999999999988655444

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.23  E-value=6.6e-12  Score=108.75  Aligned_cols=103  Identities=12%  Similarity=0.067  Sum_probs=56.2

Q ss_pred             EEEEeCcHHHHHHHH-HHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhc---CCcCCCCc
Q 030094            2 GMIISPTRELSSQIY-HVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM---DVLDFRNL   77 (183)
Q Consensus         2 alIl~PtreLa~Qi~-~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~---~~~~l~~l   77 (183)
                      +|||+||++|+.|++ +.++.+.     ..+..+.++.         ...+.+|+|+||+++.......   ..+...++
T Consensus       238 vlil~P~~~L~~Q~~~~~~~~~~-----~~~~~~~~~~---------~~~~~~I~v~T~~~l~~~~~~~~~~~~~~~~~~  303 (590)
T 3h1t_A          238 ILFLADRNVLVDDPKDKTFTPFG-----DARHKIEGGK---------VVKSREIYFAIYQSIASDERRPGLYKEFPQDFF  303 (590)
T ss_dssp             EEEEEC-----------CCTTTC-----SSEEECCC-----------CCSSCSEEEEEGGGC------CCGGGGSCTTSC
T ss_pred             EEEEeCCHHHHHHHHHHHHHhcc-----hhhhhhhccC---------CCCCCcEEEEEhhhhccccccccccccCCCCcc
Confidence            799999999999998 7666553     2233333221         1457899999999999886521   34567789


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChH
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~  120 (183)
                      +++|+||||++...+ ...+..+++.++ ..+++++|||....
T Consensus       304 ~lvIiDEaH~~~~~~-~~~~~~il~~~~-~~~~l~lTATP~~~  344 (590)
T 3h1t_A          304 DLIIIDECHRGSARD-NSNWREILEYFE-PAFQIGMTATPLRE  344 (590)
T ss_dssp             SEEEESCCC----------CHHHHHHST-TSEEEEEESSCSCT
T ss_pred             CEEEEECCccccccc-hHHHHHHHHhCC-cceEEEeccccccc
Confidence            999999999986532 356677778875 57899999997743

>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=99.23  E-value=2e-11  Score=111.81  Aligned_cols=107  Identities=13%  Similarity=0.175  Sum_probs=81.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCc-CCCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL-DFRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~-~l~~l~~l   80 (183)
                      +|||||+++|+.|+.+.+.++....       +.|+.+.......+...+++|+|+||+++..+++....+ .++...++
T Consensus       333 vLvlvpr~eL~~Q~~~~f~~f~~~~-------v~~~~s~~~l~~~L~~~~~~IiVtTiqkl~~~l~~~~~~~~~~~~~lv  405 (1038)
T 2w00_A          333 VFFVVDRKDLDYQTMKEYQRFSPDS-------VNGSENTAGLKRNLDKDDNKIIVTTIQKLNNLMKAESDLPVYNQQVVF  405 (1038)
T ss_dssp             EEEEECGGGCCHHHHHHHHTTSTTC-------SSSSCCCHHHHHHHHCSSCCEEEEEHHHHHHHHHHCCCCGGGGSCEEE
T ss_pred             EEEEeCcHHHHHHHHHHHHHhcccc-------cccccCHHHHHHHhcCCCCCEEEEEHHHHHHHHhcccchhccccccEE
Confidence            7999999999999999998875421       234555555555564567999999999999998762222 45677899


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCCh
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~  119 (183)
                      |+||||++..   ......|.+.+| ++++++||||...
T Consensus       406 IiDEAHrs~~---~~~~~~I~~~~p-~a~~lgfTATP~~  440 (1038)
T 2w00_A          406 IFDECHRSQF---GEAQKNLKKKFK-RYYQFGFTGTPIF  440 (1038)
T ss_dssp             EEESCCTTHH---HHHHHHHHHHCS-SEEEEEEESSCCC
T ss_pred             EEEccchhcc---hHHHHHHHHhCC-cccEEEEeCCccc
Confidence            9999999863   334556777775 5899999999874

>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=99.22  E-value=6.6e-11  Score=91.62  Aligned_cols=96  Identities=20%  Similarity=0.121  Sum_probs=72.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCce-EEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVK-SVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEI   79 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~-~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~   79 (183)
                      .++|++||++|+.|+++.+.++     +++ +..+.|+..          ...+|+|+||+.+......    ..+++++
T Consensus       135 ~~liv~P~~~L~~q~~~~~~~~-----~~~~v~~~~g~~~----------~~~~i~v~T~~~l~~~~~~----~~~~~~l  195 (237)
T 2fz4_A          135 PTLIVVPTLALAEQWKERLGIF-----GEEYVGEFSGRIK----------ELKPLTVSTYDSAYVNAEK----LGNRFML  195 (237)
T ss_dssp             CEEEEESSHHHHHHHHHHHGGG-----CGGGEEEESSSCB----------CCCSEEEEEHHHHHHTHHH----HTTTCSE
T ss_pred             CEEEEeCCHHHHHHHHHHHHhC-----CCCeEEEEeCCCC----------CcCCEEEEeHHHHHhhHHH----hcccCCE
Confidence            3789999999999999988874     566 666666554          3679999999998776653    1245889


Q ss_pred             EEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChH
Q 030094           80 LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (183)
Q Consensus        80 lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~  120 (183)
                      +|+||||.+.+..+.    .+++.++ ..+++++|||....
T Consensus       196 lIiDEaH~l~~~~~~----~i~~~~~-~~~~l~LSATp~r~  231 (237)
T 2fz4_A          196 LIFDEVHHLPAESYV----QIAQMSI-APFRLGLTATFERE  231 (237)
T ss_dssp             EEEECSSCCCTTTHH----HHHHTCC-CSEEEEEEESCC--
T ss_pred             EEEECCccCCChHHH----HHHHhcc-CCEEEEEecCCCCC
Confidence            999999999776554    3555554 68899999998754

>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=99.22  E-value=2.3e-11  Score=102.47  Aligned_cols=119  Identities=13%  Similarity=0.082  Sum_probs=79.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++|||+||.|+++.+..+       .+....+....      ....+..|.++||+.+...+.+  ...+++++++
T Consensus        50 ~~lvl~Ptr~La~Q~~~~l~g~-------~v~~~~~~~~~------~~~~~~~i~~~t~~~l~~~l~~--~~~l~~~~~i  114 (451)
T 2jlq_A           50 RTLILAPTRVVAAEMEEALRGL-------PIRYQTPAVKS------DHTGREIVDLMCHATFTTRLLS--STRVPNYNLI  114 (451)
T ss_dssp             CEEEEESSHHHHHHHHHHTTTS-------CEEECCTTCSC------CCCSSCCEEEEEHHHHHHHHHH--CSCCCCCSEE
T ss_pred             cEEEECCCHHHHHHHHHHhcCc-------eeeeeeccccc------cCCCCceEEEEChHHHHHHhhC--cccccCCCEE
Confidence            4799999999999999876422       22211111110      0123567999999999888876  3568899999


Q ss_pred             EEcccchhhccchHHHHHHHHH-hCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEc
Q 030094           81 VLDEADRLLDMGFQKQISYIIS-RLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVR  138 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~-~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~  138 (183)
                      |+||||.+ +.++...+..+.. ..++++|+++||||+++++..   .+..++..+...
T Consensus       115 ViDEah~~-~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~---~~~~~~~~~~~~  169 (451)
T 2jlq_A          115 VMDEAHFT-DPCSVAARGYISTRVEMGEAAAIFMTATPPGSTDP---FPQSNSPIEDIE  169 (451)
T ss_dssp             EEETTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCS---SCCCSSCEEEEE
T ss_pred             EEeCCccC-CcchHHHHHHHHHhhcCCCceEEEEccCCCccchh---hhcCCCceEecC
Confidence            99999987 4444443333332 235689999999999876443   244566666554

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.17  E-value=1.1e-10  Score=97.83  Aligned_cols=108  Identities=18%  Similarity=0.187  Sum_probs=72.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +++|++||++||.|+++.+.       ++.+....|+...      ....+.-+.+.|.+.+...+..  ...+++++++
T Consensus        33 ~~lvl~Pt~~La~Q~~~~~~-------~~~v~~~~~~~~~------~~~~~~~~~~~~~~~l~~~l~~--~~~~~~l~~v   97 (431)
T 2v6i_A           33 RTVILAPTRVVASEMYEALR-------GEPIRYMTPAVQS------ERTGNEIVDFMCHSTFTMKLLQ--GVRVPNYNLY   97 (431)
T ss_dssp             CEEEEESSHHHHHHHHHHTT-------TSCEEEC---------------CCCSEEEEEHHHHHHHHHH--TCCCCCCSEE
T ss_pred             CEEEECcHHHHHHHHHHHhC-------CCeEEEEecCccc------cCCCCceEEEEchHHHHHHHhc--CccccCCCEE
Confidence            58999999999999987654       3344444443211      1122455667788888776655  4568899999


Q ss_pred             EEcccchhhccchHHHHHHHHHhC-CCCCeEEEEeecCChHHHHH
Q 030094           81 VLDEADRLLDMGFQKQISYIISRL-PKLRRTGLFSATQTEAVEEL  124 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l-~~~~Q~v~~SAT~~~~v~~~  124 (183)
                      |+||||.+ +.++......+.+.. ++++|++++|||+++.+..+
T Consensus        98 ViDEaH~~-~~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~~~~~  141 (431)
T 2v6i_A           98 IMDEAHFL-DPASVAARGYIETRVSMGDAGAIFMTATPPGTTEAF  141 (431)
T ss_dssp             EEESTTCC-SHHHHHHHHHHHHHHHTTSCEEEEEESSCTTCCCSS
T ss_pred             EEeCCccC-CccHHHHHHHHHHHhhCCCCcEEEEeCCCCcchhhh
Confidence            99999997 544444444444432 56899999999999875443

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.12  E-value=4.1e-11  Score=105.52  Aligned_cols=115  Identities=19%  Similarity=0.116  Sum_probs=83.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      ++|++|||+||.|+++.+.++     ++++..++|+...-..   -.....+++++|++.+.         ..+.++++|
T Consensus       182 gl~l~PtR~LA~Qi~~~l~~~-----g~~v~lltG~~~~iv~---TpGr~~~il~~T~e~~~---------l~~~v~lvV  244 (677)
T 3rc3_A          182 GVYCGPLKLLAHEIFEKSNAA-----GVPCDLVTGEERVTVQ---PNGKQASHVSCTVEMCS---------VTTPYEVAV  244 (677)
T ss_dssp             EEEEESSHHHHHHHHHHHHHT-----TCCEEEECSSCEECCS---TTCCCCSEEEEEGGGCC---------SSSCEEEEE
T ss_pred             eEEEeCHHHHHHHHHHHHHhc-----CCcEEEEECCeeEEec---CCCcccceeEecHhHhh---------hcccCCEEE
Confidence            589999999999999998775     5678888887654000   00012567777763221         246779999


Q ss_pred             EcccchhhccchHHHHHHHHHhCC-CCCeEEEEeecCChHHHHHHHhhCCCCeEE
Q 030094           82 LDEADRLLDMGFQKQISYIISRLP-KLRRTGLFSATQTEAVEELSKAGLRNPVRV  135 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~-~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i  135 (183)
                      +||||.+++.++...+..++..++ +..|++++|||. +.+..++... ..+..+
T Consensus       245 IDEaH~l~d~~~g~~~~~~l~~l~~~~i~il~~SAT~-~~i~~l~~~~-~~~~~v  297 (677)
T 3rc3_A          245 IDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAI-DLVMELMYTT-GEEVEV  297 (677)
T ss_dssp             ECSGGGGGCTTTHHHHHHHHHHCCEEEEEEEECGGGH-HHHHHHHHHH-TCCEEE
T ss_pred             EecceecCCccchHHHHHHHHccCccceEEEeccchH-HHHHHHHHhc-CCceEE
Confidence            999999999899999999999888 778999999995 4456555543 334333

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.10  E-value=8.1e-12  Score=110.04  Aligned_cols=103  Identities=18%  Similarity=0.276  Sum_probs=64.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhc-------CCcC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM-------DVLD   73 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~-------~~~~   73 (183)
                      ++||++|||+||.|+++.+..+     ++.  ...+  .       + .     .++||+++.+++...       ....
T Consensus       272 ~~lilaPTr~La~Q~~~~l~~~-----~i~--~~~~--~-------l-~-----~v~tp~~ll~~l~~~~l~~~l~~~~~  329 (673)
T 2wv9_A          272 RTAVLAPTRVVAAEMAEALRGL-----PVR--YLTP--A-------V-Q-----REHSGNEIVDVMCHATLTHRLMSPLR  329 (673)
T ss_dssp             CEEEEESSHHHHHHHHHHTTTS-----CCE--ECCC------------------CCCCSCCCEEEEEHHHHHHHHHSSSC
T ss_pred             cEEEEccHHHHHHHHHHHHhcC-----Cee--eecc--c-------c-c-----ccCCHHHHHHHHHhhhhHHHHhcccc
Confidence            5899999999999999877654     222  1000  0       0 0     145665543332220       1246


Q ss_pred             CCCceEEEEcccchhhccchHHHHHHHHHhC-CCCCeEEEEeecCChHHHHHHH
Q 030094           74 FRNLEILVLDEADRLLDMGFQKQISYIISRL-PKLRRTGLFSATQTEAVEELSK  126 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l-~~~~Q~v~~SAT~~~~v~~~~~  126 (183)
                      +++++++|+||||.+ +..+...+..+.+.+ ++.+|+++||||+++.+..+..
T Consensus       330 l~~l~lvViDEaH~~-~~~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~~~~~  382 (673)
T 2wv9_A          330 VPNYNLFVMDEAHFT-DPASIAARGYIATRVEAGEAAAIFMTATPPGTSDPFPD  382 (673)
T ss_dssp             CCCCSEEEEESTTCC-CHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCSSCC
T ss_pred             cccceEEEEeCCccc-CccHHHHHHHHHHhccccCCcEEEEcCCCChhhhhhcc
Confidence            899999999999998 333333444444433 3689999999999988654433

>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=99.08  E-value=8.9e-11  Score=99.09  Aligned_cols=113  Identities=12%  Similarity=0.159  Sum_probs=71.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++|||+||.|+++.+..+       .+....+....     . ...+..+.+.|.+.+...+..  ...+++++++
T Consensus        52 ~~lvl~Ptr~La~Q~~~~l~g~-------~v~~~~~~~~~-----~-~t~~~~i~~~~~~~l~~~l~~--~~~l~~~~~i  116 (459)
T 2z83_A           52 RTAVLAPTRVVAAEMAEALRGL-------PVRYQTSAVQR-----E-HQGNEIVDVMCHATLTHRLMS--PNRVPNYNLF  116 (459)
T ss_dssp             CEEEEECSHHHHHHHHHHTTTS-------CEEECC--------------CCCSEEEEEHHHHHHHHHS--CC-CCCCSEE
T ss_pred             cEEEECchHHHHHHHHHHhcCc-------eEeEEeccccc-----C-CCCCcEEEEEchHHHHHHhhc--cccccCCcEE
Confidence            3799999999999999877622       22211111110     0 122445778888887776654  4678999999


Q ss_pred             EEcccch-----hhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEE
Q 030094           81 VLDEADR-----LLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRV  135 (183)
Q Consensus        81 VvDEad~-----ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i  135 (183)
                      |+||||.     ++..++...+.     .++.+|+++||||++.++..+...  ..|+..
T Consensus       117 ViDEaH~~~~~~~~~~~~~~~~~-----~~~~~~~il~SAT~~~~~~~~~~~--~~pi~~  169 (459)
T 2z83_A          117 VMDEAHFTDPASIAARGYIATKV-----ELGEAAAIFMTATPPGTTDPFPDS--NAPIHD  169 (459)
T ss_dssp             EESSTTCCSHHHHHHHHHHHHHH-----HTTSCEEEEECSSCTTCCCSSCCC--SSCEEE
T ss_pred             EEECCccCCchhhHHHHHHHHHh-----ccCCccEEEEEcCCCcchhhhccC--CCCeEE
Confidence            9999998     44444433322     136899999999999876544332  345443

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.73  E-value=1.7e-08  Score=86.94  Aligned_cols=87  Identities=21%  Similarity=0.151  Sum_probs=65.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcch---------------------------------HHHHHH--
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEV---------------------------------KADVKK--   46 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~---------------------------------~~~~~~--   46 (183)
                      ++|++||++|+.|+.+.+.++.+.. ++++..+.|+...                                 ......  
T Consensus        50 v~i~~pt~~l~~q~~~~~~~l~~~~-~~~~~~l~gr~~~c~~~~~~~~~~~~~c~~c~~~~~~~~~g~~~~~~~~~~~~~  128 (551)
T 3crv_A           50 VLFVVRTHNEFYPIYRDLTKIREKR-NITFSFLVGKPSSCLYAEKGAESEDIPCKYCELKGSIVEVKTDDSPLSLVKKLK  128 (551)
T ss_dssp             EEEEESSGGGHHHHHHHHTTCCCSS-CCCEEECCCHHHHCTTBCTTCCGGGCCGGGCTTTTCCCCCCCCSCHHHHHHHHH
T ss_pred             EEEEcCCHHHHHHHHHHHHHHhhhc-CccEEEEccccccCcCchhcCCCcccccCCCCCccccccccccCCHHHHHHHHH
Confidence            7999999999999999999997665 7888887774321                                 111111  


Q ss_pred             ---------------HHhcCCcEEEeCcHHHHHHHHhcCCcCC-CCceEEEEcccchhhc
Q 030094           47 ---------------IEEEGANLLIGTPGRLYDIMERMDVLDF-RNLEILVLDEADRLLD   90 (183)
Q Consensus        47 ---------------l~~~~~~IiV~TP~~l~~~l~~~~~~~l-~~l~~lVvDEad~ll~   90 (183)
                                     ....++||||+||+.|.+...+ ..+.+ ....++|+||||.|.+
T Consensus       129 ~~G~~~~~Cpy~~ar~~~~~adIVV~~~~~l~~~~~~-~~~~~~~~~~~vIiDEAHnl~d  187 (551)
T 3crv_A          129 KDGLQDKFCPYYSLLNSLYKADVIALTYPYFFIDRYR-EFIDIDLREYMIVIDEAHNLDK  187 (551)
T ss_dssp             HHHHHHTCCHHHHHHHHGGGCSEEEEETHHHHCHHHH-TTSCCCSTTEEEEETTGGGGGG
T ss_pred             HcCCcCCcCccHHHHhhhhcCCEEEeCchHhcCHHHH-HhcCCCcCCeEEEEecccchHH
Confidence                           1124789999999999988655 33433 4678999999999987

>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=98.62  E-value=2.4e-08  Score=84.49  Aligned_cols=100  Identities=17%  Similarity=0.213  Sum_probs=71.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||+||+ .|+.|..+.++++.   |+.++....|+...      ....+++|+|+||+++.....    +......++|
T Consensus        89 ~LIv~P~-~l~~qw~~e~~~~~---~~~~v~~~~g~~~~------~~~~~~~ivi~t~~~l~~~~~----l~~~~~~~vI  154 (500)
T 1z63_A           89 SLVICPL-SVLKNWEEELSKFA---PHLRFAVFHEDRSK------IKLEDYDIILTTYAVLLRDTR----LKEVEWKYIV  154 (500)
T ss_dssp             EEEEECS-TTHHHHHHHHHHHC---TTSCEEECSSSTTS------CCGGGSSEEEEEHHHHTTCHH----HHTCCEEEEE
T ss_pred             EEEEccH-HHHHHHHHHHHHHC---CCceEEEEecCchh------ccccCCcEEEeeHHHHhccch----hcCCCcCEEE
Confidence            6999995 58899999888875   46677766665532      112468999999998865433    3345678999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      +||||.+-+.+  ......+..+ +..+.+++|||..
T Consensus       155 vDEaH~~kn~~--~~~~~~l~~l-~~~~~l~LTaTP~  188 (500)
T 1z63_A          155 IDEAQNIKNPQ--TKIFKAVKEL-KSKYRIALTGTPI  188 (500)
T ss_dssp             EETGGGGSCTT--SHHHHHHHTS-CEEEEEEECSSCS
T ss_pred             EeCccccCCHh--HHHHHHHHhh-ccCcEEEEecCCC
Confidence            99999996543  2344455556 3567899999984

>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=98.42  E-value=1.8e-06  Score=75.65  Aligned_cols=108  Identities=19%  Similarity=0.277  Sum_probs=71.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHH--HHHHHHh-----cCCcEEEeCcHHHHHHHHhcCCcCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKA--DVKKIEE-----EGANLLIGTPGRLYDIMERMDVLDF   74 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~--~~~~l~~-----~~~~IiV~TP~~l~~~l~~~~~~~l   74 (183)
                      +||+||+ .|+.|..+.+.++...  .+.+..+.||.....  .......     ...+|+|+|++.+....   ..+..
T Consensus       117 ~LiV~P~-sll~qW~~E~~~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~vvi~ty~~l~~~~---~~l~~  190 (644)
T 1z3i_X          117 VIVVSPS-SLVRNWYNEVGKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHA---EVLHK  190 (644)
T ss_dssp             EEEEECH-HHHHHHHHHHHHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHT---TTTTT
T ss_pred             EEEEecH-HHHHHHHHHHHHHcCC--CeeEEEEeCCCHHHHHHHHHHHHHhcCCCCCCcEEEeeHHHHHhhH---HHhhc
Confidence            6899997 8889999999988654  356666666654322  2222211     14789999999887643   33445


Q ss_pred             CCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC
Q 030094           75 RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      ....++|+||||++-+..  ......+..+ +....+++|||.-
T Consensus       191 ~~~~~vI~DEaH~ikn~~--~~~~~al~~l-~~~~rl~LTgTPi  231 (644)
T 1z3i_X          191 GKVGLVICDEGHRLKNSD--NQTYLALNSM-NAQRRVLISGTPI  231 (644)
T ss_dssp             SCCCEEEETTGGGCCTTC--HHHHHHHHHH-CCSEEEEECSSCS
T ss_pred             CCccEEEEECceecCChh--hHHHHHHHhc-ccCcEEEEecCcc
Confidence            677899999999985432  2233334444 3567899999973

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.41  E-value=7e-07  Score=80.09  Aligned_cols=119  Identities=15%  Similarity=0.243  Sum_probs=79.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHH-----------HhcCCcEEEeCcHHHHHHHHhcC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKI-----------EEEGANLLIGTPGRLYDIMERMD   70 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l-----------~~~~~~IiV~TP~~l~~~l~~~~   70 (183)
                      +||||| ..++.|..+.+.+++   |++++....|+..........           ....++|+|+|++.+......  
T Consensus       289 ~LIV~P-~sll~qW~~E~~~~~---p~~~v~~~~g~~~~r~~~~~~~~~~~~~~~~~~~~~~dvvitTy~~l~~~~~~--  362 (800)
T 3mwy_W          289 HIIVVP-LSTMPAWLDTFEKWA---PDLNCICYMGNQKSRDTIREYEFYTNPRAKGKKTMKFNVLLTTYEYILKDRAE--  362 (800)
T ss_dssp             EEEECC-TTTHHHHHHHHHHHS---TTCCEEECCCSSHHHHHHHHHHSCSCC-----CCCCCSEEEECTTHHHHTHHH--
T ss_pred             EEEEEC-chHHHHHHHHHHHHC---CCceEEEEeCCHHHHHHHHHHHhhccccccccccccCCEEEecHHHHHhhHHH--
Confidence            699999 677888888887764   578888888876655443332           124578999999998765433  


Q ss_pred             CcCCCCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecC----ChHHHHHHHhhCC
Q 030094           71 VLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ----TEAVEELSKAGLR  130 (183)
Q Consensus        71 ~~~l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~----~~~v~~~~~~~~~  130 (183)
                       +......++|+||||++-+.  .......+..+ +....+++|||.    ..++..+.+...+
T Consensus       363 -l~~~~w~~vIvDEaH~lkn~--~s~~~~~l~~l-~~~~rl~LTgTPiqN~l~el~~ll~fL~p  422 (800)
T 3mwy_W          363 -LGSIKWQFMAVDEAHRLKNA--ESSLYESLNSF-KVANRMLITGTPLQNNIKELAALVNFLMP  422 (800)
T ss_dssp             -HHTSEEEEEEETTGGGGCCS--SSHHHHHHTTS-EEEEEEEECSCCCSSCSHHHHHHHHHHCS
T ss_pred             -HhcCCcceeehhhhhhhcCc--hhHHHHHHHHh-hhccEEEeeCCcCCCCHHHHHHHHHHhCc
Confidence             33345789999999998432  23444455555 456678899997    2334444444433

>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=98.30  E-value=1.7e-07  Score=85.69  Aligned_cols=108  Identities=19%  Similarity=0.137  Sum_probs=66.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHH--HhcCCcEEEeCcHHHHHHHHhcCCcCCCCceE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKI--EEEGANLLIGTPGRLYDIMERMDVLDFRNLEI   79 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l--~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~   79 (183)
                      +|||||+ .|+.|..+.+.+..    ++++..+.|+... ......  .....+|+|+|++.+.........+...++.+
T Consensus       203 vLIVvP~-sLl~Qw~~E~~~~f----~l~v~v~~~~~~~-~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dl  276 (968)
T 3dmq_A          203 VLIIVPE-TLQHQWLVEMLRRF----NLRFALFDDERYA-EAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDL  276 (968)
T ss_dssp             EEEECCT-TTHHHHHHHHHHHS----CCCCEECCHHHHH-HHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCE
T ss_pred             EEEEeCH-HHHHHHHHHHHHHh----CCCEEEEccchhh-hhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCE
Confidence            7999999 99999988886543    4444444443222 111110  01256999999987754221111234567889


Q ss_pred             EEEcccchhhccch-----HHHHHHHHHhCCCCCeEEEEeecCC
Q 030094           80 LVLDEADRLLDMGF-----QKQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        80 lVvDEad~ll~~~~-----~~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      +|+||||++-..+.     ...+..+.   .+.++++++|||..
T Consensus       277 VIvDEAH~~kn~~~~~s~~~~~l~~L~---~~~~~~L~LTATPi  317 (968)
T 3dmq_A          277 LVVDEAHHLVWSEDAPSREYQAIEQLA---EHVPGVLLLTATPE  317 (968)
T ss_dssp             EEECCSSCCCCBTTBCCHHHHHHHHHH---TTCSSEEESCSSCS
T ss_pred             EEehhhHhhcCCCCcchHHHHHHHHHh---hcCCcEEEEEcCCc
Confidence            99999999964332     22333332   24567999999974

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.17  E-value=1.4e-06  Score=74.94  Aligned_cols=81  Identities=21%  Similarity=0.259  Sum_probs=52.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcch--------H-H--------------------------H---
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEV--------K-A--------------------------D---   43 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~--------~-~--------------------------~---   43 (183)
                      ++|++||++|+.|+.+.+.++     ++++..+.|....        . +                          +   
T Consensus        54 ~~~~~~t~~l~~q~~~~~~~l-----~~~~~~l~gr~~lC~~~~~~~~~~~~~c~~c~~~~~~~~~gd~~~~~~~~~~~~  128 (540)
T 2vl7_A           54 VLIFTRTHSQLDSIYKNAKLL-----GLKTGFLIGKSASCIYAQGDEEPDEINCSKCRLKDKIKTIEDKEPSKLIEEFKD  128 (540)
T ss_dssp             EEEEESCHHHHHHHHHHHGGG-----TCCEEEC-----------------------------------------------
T ss_pred             EEEEcCCHHHHHHHHHHHHhc-----CCcEEEecCCccccCCchhcccccccCCCCCCchhcccccccCCcHHHHHHHhh
Confidence            789999999999999887775     3444444443210        0 0                          0   


Q ss_pred             ---------HHHHHhcCCcEEEeCcHHHHHHHHhcCCcC-------CCCceEEEEcccchhh
Q 030094           44 ---------VKKIEEEGANLLIGTPGRLYDIMERMDVLD-------FRNLEILVLDEADRLL   89 (183)
Q Consensus        44 ---------~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~-------l~~l~~lVvDEad~ll   89 (183)
                               .+.. ..++||+|+|+..+.+.... +.+.       +....++|+||||.+.
T Consensus       129 ~~~~Cpy~~~r~~-~~~adiVV~n~~~l~~~~~~-~~~~~~~~~~~~~~~~~vIiDEAHnl~  188 (540)
T 2vl7_A          129 AVDYCPYYSLRAN-LKDKDVIAMTYPYLFQKPIR-NSVFCNKDDCLKLEDYLIVIDEAHNLL  188 (540)
T ss_dssp             ----------CTT-GGGCSEEEEETHHHHSHHHH-HHHSCSSTTSCCGGGEEEEETTGGGGG
T ss_pred             hcCCChHHHHHHH-hhcCCEEEEChHHhcCHHHH-HhhCcccccccCcCCCEEEEEccccHH
Confidence                     0000 13579999999999886544 2222       3567899999999994

>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=97.53  E-value=0.0003  Score=62.38  Aligned_cols=85  Identities=15%  Similarity=0.051  Sum_probs=62.8

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcC-------------------------------------------
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGG-------------------------------------------   37 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~-------------------------------------------   37 (183)
                      .+.|++||++||.|-.+.+..+..++ ++++.+++..                                           
T Consensus       118 ~vhVvT~ndyLA~rdae~m~~l~~~L-glsvg~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~  196 (822)
T 3jux_A          118 GVHLVTVNDYLARRDALWMGPVYLFL-GLRVGVINSLGKSYEVVWKNPDLARKAIEENWSVWPDGFNGEVLKEESMNKEA  196 (822)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHHHHHT-TCCEEEEETTTEEEEEEESSHHHHHHHHHTTCCSSCTTCCSSSCCGGGSCHHH
T ss_pred             ceEEEeccHHHHHhHHHHHHHHHHHh-CCEEEEEcCCCcccccccccchhhhhhhccccccccccccccccccccccccc
Confidence            37899999999999999999999998 9999999872                                           


Q ss_pred             -------cchHHHHHHHHhcCCcEEEeCcHHHH-HHHHhcC-----CcCCCCceEEEEcccchhh
Q 030094           38 -------VEVKADVKKIEEEGANLLIGTPGRLY-DIMERMD-----VLDFRNLEILVLDEADRLL   89 (183)
Q Consensus        38 -------~~~~~~~~~l~~~~~~IiV~TP~~l~-~~l~~~~-----~~~l~~l~~lVvDEad~ll   89 (183)
                             .+..+ .+.  ...|||.=||...+- ++++.+=     ..-.+...+.|+||+|.+|
T Consensus       197 ~~~~~~~~~~~e-rr~--aY~~DItYgTn~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiL  258 (822)
T 3jux_A          197 VEAFQVELKEIT-RKE--AYLCDVTYGTNNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVL  258 (822)
T ss_dssp             HTTTCEECCBCC-HHH--HHHSSEEEEEHHHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHH
T ss_pred             chhccccCCHHH-HHH--HhcCCCEEccCcchhhHhHHhhccCCHHHhccCCCCeEEEeccccee
Confidence                   11111 112  135899999998863 3444311     1224667899999999986

>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=97.25  E-value=0.00047  Score=59.99  Aligned_cols=98  Identities=20%  Similarity=0.319  Sum_probs=56.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEe-CcHHHHHHHHhcCCcCCCCceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIG-TPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~-TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +++++||+++|.++.+.+....... +++.... .+..  .+     ....|-+++ +|+.. . +.. ...+..+++++
T Consensus       199 vll~APTg~AA~~L~e~~~~~~~~l-~l~~~~~-~~~~--~~-----~~Tih~ll~~~~~~~-~-~~~-~~~~~l~~d~l  266 (608)
T 1w36_D          199 IRLAAPTGKAAARLTESLGKALRQL-PLTDEQK-KRIP--ED-----ASTLHRLLGAQPGSQ-R-LRH-HAGNPLHLDVL  266 (608)
T ss_dssp             EEEEBSSHHHHHHHHHHHTHHHHHS-SCCSCCC-CSCS--CC-----CBTTTSCC--------------CTTSCCSCSEE
T ss_pred             EEEEeCChhHHHHHHHHHHHHHhcC-CCCHHHH-hccc--hh-----hhhhHhhhccCCCch-H-HHh-ccCCCCCCCEE
Confidence            6789999999999999888776654 3321100 0000  00     011222222 33221 1 122 22233478999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEee
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSA  115 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SA  115 (183)
                      |+|||+ |++   ...+..+++.++..+|+++++=
T Consensus       267 IIDEAs-ml~---~~~~~~Ll~~l~~~~~liLvGD  297 (608)
T 1w36_D          267 VVDEAS-MID---LPMMSRLIDALPDHARVIFLGD  297 (608)
T ss_dssp             EECSGG-GCB---HHHHHHHHHTCCTTCEEEEEEC
T ss_pred             EEechh-hCC---HHHHHHHHHhCCCCCEEEEEcc
Confidence            999999 554   5678889999999999999864

>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=96.14  E-value=0.0024  Score=56.11  Aligned_cols=74  Identities=19%  Similarity=0.184  Sum_probs=45.7

Q ss_pred             EEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccchhhcc--chHHHHH----HHHHh----
Q 030094           34 LVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDM--GFQKQIS----YIISR----  103 (183)
Q Consensus        34 ~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~ll~~--~~~~~l~----~i~~~----  103 (183)
                      +.|+.+...+..... .|     +||++|.+++.. +       .++|+||+|.+++.  ++.....    .+.+.    
T Consensus       303 ~~G~e~~~~~~~~~~-~g-----~tpg~LlDyl~~-~-------~llVlDEa~~~l~~~~~~~~~~~~~~~~l~~~G~~l  368 (661)
T 2d7d_A          303 CSGIENYSRHLTLRP-PG-----STPYTLLDYFPD-D-------FMIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRL  368 (661)
T ss_dssp             CTTGGGGHHHHTTCC-TT-----CCCBCGGGGSCS-S-------CEEEEETHHHHHHHHHHHHHHHHHHHHHHHHTTSSC
T ss_pred             eccchhHHHHHcccc-CC-----CCccHHHHHccc-C-------cEEEEecHHHHHHHHHHHHHHHHHHHHHHHHccccc
Confidence            345555555544432 23     999999999854 2       28999999998742  1222111    11111    


Q ss_pred             --------------CCCCCeEEEEeecCChHH
Q 030094          104 --------------LPKLRRTGLFSATQTEAV  121 (183)
Q Consensus       104 --------------l~~~~Q~v~~SAT~~~~v  121 (183)
                                    .++.+|+++||||.++..
T Consensus       369 p~~l~~~~l~~~e~~~~~~q~i~~SAT~~~~~  400 (661)
T 2d7d_A          369 PSALDNRPLRFEEFEKHMHNIVYVSATPGPYE  400 (661)
T ss_dssp             GGGGGSCCCCHHHHHHTCSEEEEECSSCCHHH
T ss_pred             hhhhhcccccHHHHhccCCCEEEEecCCChhH
Confidence                          124689999999998664

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=96.08  E-value=0.062  Score=39.42  Aligned_cols=71  Identities=18%  Similarity=0.263  Sum_probs=54.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-+..+.+.+...     ++.+..+.|+.+..++..   ...++..+|+|+|.     .+.  .++|+.++.
T Consensus        57 ~lVF~~~~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~-----~~~--~Gldi~~v~  124 (191)
T 2p6n_A           57 VLIFAEKKADVDAIHEYLLLK-----GVEAVAIHGGKDQEERTKAIEAFREGKKDVLVATD-----VAS--KGLDFPAIQ  124 (191)
T ss_dssp             EEEECSCHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHHTSCSEEEECH-----HHH--TTCCCCCCS
T ss_pred             EEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCEEEEEcC-----chh--cCCCcccCC
Confidence            799999999999998888765     567888888876544433   34456789999993     443  478999999


Q ss_pred             EEEEcc
Q 030094           79 ILVLDE   84 (183)
Q Consensus        79 ~lVvDE   84 (183)
                      ++|.-+
T Consensus       125 ~VI~~d  130 (191)
T 2p6n_A          125 HVINYD  130 (191)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            888643

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=95.97  E-value=0.06  Score=38.20  Aligned_cols=73  Identities=14%  Similarity=0.216  Sum_probs=54.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|+|++-+..+.+.+...     ++.+..+.|+.+..+...   ...++..+|+|+|.     .+.  .++|+.++
T Consensus        37 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~--~Gld~~~~  104 (163)
T 2hjv_A           37 SCIIFCRTKEHVNQLTDELDDL-----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD-----VAA--RGIDIENI  104 (163)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----GGT--TTCCCSCC
T ss_pred             cEEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECC-----hhh--cCCchhcC
Confidence            3799999999999998887765     567888888876544433   34456789999994     332  57899999


Q ss_pred             eEEEEccc
Q 030094           78 EILVLDEA   85 (183)
Q Consensus        78 ~~lVvDEa   85 (183)
                      .++|.-+.
T Consensus       105 ~~Vi~~~~  112 (163)
T 2hjv_A          105 SLVINYDL  112 (163)
T ss_dssp             SEEEESSC
T ss_pred             CEEEEeCC
Confidence            99886443

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=95.75  E-value=0.083  Score=37.49  Aligned_cols=73  Identities=10%  Similarity=0.173  Sum_probs=54.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|+|++-+..+.+.+...     ++.+..+.|+.+..+...   ....+..+|+|+|.     .+.  .++|+.++
T Consensus        32 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~--~G~d~~~~   99 (165)
T 1fuk_A           32 QAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----LLA--RGIDVQQV   99 (165)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----GGT--TTCCCCSC
T ss_pred             CEEEEECCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcC-----hhh--cCCCcccC
Confidence            3799999999999988877764     567888888876544433   34456789999994     332  57899999


Q ss_pred             eEEEEccc
Q 030094           78 EILVLDEA   85 (183)
Q Consensus        78 ~~lVvDEa   85 (183)
                      .++|.-+.
T Consensus       100 ~~Vi~~~~  107 (165)
T 1fuk_A          100 SLVINYDL  107 (165)
T ss_dssp             SEEEESSC
T ss_pred             CEEEEeCC
Confidence            98886443

>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=95.71  E-value=0.069  Score=39.75  Aligned_cols=70  Identities=14%  Similarity=0.226  Sum_probs=53.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|||++-+..+++.+.+.     ++.+..+.|+.+..++..   ...++..+|+|+|.     .+ . .++|+..+
T Consensus        33 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~-----~~-~-~Gidi~~v  100 (212)
T 3eaq_A           33 RAMVFTRTKAETEEIAQGLLRL-----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATD-----VA-A-RGLDIPQV  100 (212)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHH-----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECT-----TT-T-CSSSCCCB
T ss_pred             eEEEEeCCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecC-----hh-h-cCCCCccC
Confidence            3799999999999998887765     567888999877655443   33456789999995     33 3 57999999


Q ss_pred             eEEEE
Q 030094           78 EILVL   82 (183)
Q Consensus        78 ~~lVv   82 (183)
                      .++|.
T Consensus       101 ~~Vi~  105 (212)
T 3eaq_A          101 DLVVH  105 (212)
T ss_dssp             SEEEE
T ss_pred             cEEEE
Confidence            98874

>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=95.63  E-value=0.062  Score=38.56  Aligned_cols=71  Identities=18%  Similarity=0.228  Sum_probs=53.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-|..+++.+.+.     +..+..+.|+.+..+...   ....+..+|+|+|.     .+ . .++|+..+.
T Consensus        37 ~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~-----~~-~-~Gid~~~~~  104 (175)
T 2rb4_A           37 AIIFCQTRRNAKWLTVEMIQD-----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTN-----VC-A-RGIDVKQVT  104 (175)
T ss_dssp             EEEECSCHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECC-----SC-C-TTTCCTTEE
T ss_pred             EEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEec-----ch-h-cCCCcccCC
Confidence            799999999999988877764     567888888877554433   34456789999995     22 2 578999999


Q ss_pred             EEEEcc
Q 030094           79 ILVLDE   84 (183)
Q Consensus        79 ~lVvDE   84 (183)
                      ++|.-+
T Consensus       105 ~Vi~~d  110 (175)
T 2rb4_A          105 IVVNFD  110 (175)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            988533

>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=95.48  E-value=0.0038  Score=54.89  Aligned_cols=57  Identities=21%  Similarity=0.263  Sum_probs=36.5

Q ss_pred             eCcHHHHHHHHhcCCcCCCCceEEEEcccchhhcc--chHHHH----HHHHHh------------------CCCCCeEEE
Q 030094           57 GTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDM--GFQKQI----SYIISR------------------LPKLRRTGL  112 (183)
Q Consensus        57 ~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~ll~~--~~~~~l----~~i~~~------------------l~~~~Q~v~  112 (183)
                      +||++|.+++.. +       .++|+||+|.+++.  ++....    ..+.+.                  .++.+|+++
T Consensus       314 ~tp~~LlDyl~~-~-------~llVlDEah~~~~~~~~~~~~~~~~~~~l~~~G~~lp~~l~~~~l~~~e~~~~~~q~i~  385 (664)
T 1c4o_A          314 EPPYTLLDYFPE-D-------FLVFLDESHVTVPQLQGMYRGDYARKKTLVDYGFRLPSALDNRPLRFEEFLERVSQVVF  385 (664)
T ss_dssp             SCCCCGGGGSCT-T-------CEEEEETHHHHHHHHHHHHHHHHHHHHHHHHTTSSCGGGGGSSCCCHHHHHHTCSEEEE
T ss_pred             CCchHHHHHHhh-c-------cEEEEecccccHHHHHHHHHHHHHHHHHHHHccccchhhhhcCcccHHHHHhhcCCEEE
Confidence            789988888754 2       28999999998742  111111    111110                  124689999


Q ss_pred             EeecCChHH
Q 030094          113 FSATQTEAV  121 (183)
Q Consensus       113 ~SAT~~~~v  121 (183)
                      ||||.++..
T Consensus       386 ~SAT~~~~~  394 (664)
T 1c4o_A          386 VSATPGPFE  394 (664)
T ss_dssp             EESSCCHHH
T ss_pred             EecCCCHHH
Confidence            999998654

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=95.13  E-value=0.16  Score=41.00  Aligned_cols=69  Identities=10%  Similarity=0.159  Sum_probs=53.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-|..+++.+.+.     ++.+..+.|+.+.+++..   ...++..+|+|+|.     .+.  .++|+.++.
T Consensus       279 ~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlvaT~-----~~~--~Gidip~v~  346 (417)
T 2i4i_A          279 TLVFVETKKGADSLEDFLYHE-----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-----VAA--RGLDISNVK  346 (417)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHHTSSCEEEECH-----HHH--TTSCCCCEE
T ss_pred             EEEEECCHHHHHHHHHHHHHC-----CCCeeEecCCCCHHHHHHHHHHHHcCCCCEEEECC-----hhh--cCCCcccCC
Confidence            799999999999998887764     567888888877554433   34456789999994     454  479999999


Q ss_pred             EEEE
Q 030094           79 ILVL   82 (183)
Q Consensus        79 ~lVv   82 (183)
                      ++|.
T Consensus       347 ~Vi~  350 (417)
T 2i4i_A          347 HVIN  350 (417)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8885

>1t5i_A C_terminal domain of A probable ATP-dependent RNA helicase; RECA-like fold, PRE-mRNA processing protein; 1.90A {Homo sapiens} SCOP: c.37.1.19

Probab=95.09  E-value=0.35  Score=34.56  Aligned_cols=73  Identities=8%  Similarity=0.153  Sum_probs=54.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|+|++-+..+++.+...     ++.+..+.|+.+..+...   ...++..+|+|+|.     .+ . .++|+..+
T Consensus        33 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~-~-~Gldi~~~  100 (172)
T 1t5i_A           33 QVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN-----LF-G-RGMDIERV  100 (172)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESS-----CC-S-TTCCGGGC
T ss_pred             cEEEEECCHHHHHHHHHHHHhc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECC-----ch-h-cCcchhhC
Confidence            3799999999999998887764     567888888876554433   34456789999996     22 2 57899999


Q ss_pred             eEEEEccc
Q 030094           78 EILVLDEA   85 (183)
Q Consensus        78 ~~lVvDEa   85 (183)
                      .++|.-+.
T Consensus       101 ~~Vi~~d~  108 (172)
T 1t5i_A          101 NIAFNYDM  108 (172)
T ss_dssp             SEEEESSC
T ss_pred             CEEEEECC
Confidence            99886443

>2jgn_A DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosphorylation, nucleotide-binding, hydrolase, RNA-binding, ATP-binding, DNA-binding, nuclear protein; 1.91A {Homo sapiens}

Probab=95.02  E-value=0.12  Score=37.52  Aligned_cols=71  Identities=10%  Similarity=0.161  Sum_probs=45.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHH---HHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKA---DVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~---~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|+|++-|..+.+.+...     ++.+..+.|+.+..+   .......+..+|+|+|.     .+.  .++|+.++
T Consensus        48 k~lVF~~~~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~--~Gldi~~~  115 (185)
T 2jgn_A           48 LTLVFVETKKGADSLEDFLYHE-----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-----VAA--RGLDISNV  115 (185)
T ss_dssp             CEEEEESCHHHHHHHHHHHHHT-----TCCEEEEC--------CHHHHHHHHTSSSEEEEEC-------------CCCSB
T ss_pred             eEEEEECCHHHHHHHHHHHHHc-----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcC-----hhh--cCCCcccC
Confidence            3799999999999998887764     567888888765433   23344457789999995     333  47888899


Q ss_pred             eEEEEc
Q 030094           78 EILVLD   83 (183)
Q Consensus        78 ~~lVvD   83 (183)
                      .++|.-
T Consensus       116 ~~VI~~  121 (185)
T 2jgn_A          116 KHVINF  121 (185)
T ss_dssp             SEEEES
T ss_pred             CEEEEe
Confidence            988863

>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=94.69  E-value=0.89  Score=36.00  Aligned_cols=75  Identities=16%  Similarity=0.289  Sum_probs=56.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|++++-|..+++.+++.     +..+..+.|+.+..++..   ...++..+|+|+|.     .+ . .++|+.++.
T Consensus       246 ~lvf~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~-~-~Gidip~~~  313 (395)
T 3pey_A          246 SIIFVATKKTANVLYGKLKSE-----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTN-----VL-A-RGIDIPTVS  313 (395)
T ss_dssp             EEEECSCHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECG-----GG-S-SSCCCTTEE
T ss_pred             EEEEeCCHHHHHHHHHHHHhc-----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECC-----hh-h-cCCCcccCC
Confidence            689999999999998888765     567788888876544433   34456789999995     33 2 689999999


Q ss_pred             EEEEcccchh
Q 030094           79 ILVLDEADRL   88 (183)
Q Consensus        79 ~lVvDEad~l   88 (183)
                      ++|.-+...+
T Consensus       314 ~Vi~~~~p~~  323 (395)
T 3pey_A          314 MVVNYDLPTL  323 (395)
T ss_dssp             EEEESSCCBC
T ss_pred             EEEEcCCCCC
Confidence            9997666543

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=94.30  E-value=0.2  Score=39.52  Aligned_cols=70  Identities=14%  Similarity=0.225  Sum_probs=52.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|+|++-+..+++.+...     ++.+..++|+.+..++..   ...++..+|+|||.     .. . .++|+..+
T Consensus        30 ~~LVF~~t~~~~~~l~~~L~~~-----g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~-----va-~-~Gidi~~v   97 (300)
T 3i32_A           30 RAMVFTRTKAETEEIAQGLLRL-----GHPAQALHGDMSQGERERVMGAFRQGEVRVLVATD-----VA-A-RGLDIPQV   97 (300)
T ss_dssp             SEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECS-----TT-T-CSTTCCCC
T ss_pred             CEEEEECCHHHHHHHHHHHHhC-----CCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEec-----hh-h-cCccccce
Confidence            3799999999999888776653     677888999876554443   33456789999995     33 2 57899999


Q ss_pred             eEEEE
Q 030094           78 EILVL   82 (183)
Q Consensus        78 ~~lVv   82 (183)
                      .++|.
T Consensus        98 ~~VI~  102 (300)
T 3i32_A           98 DLVVH  102 (300)
T ss_dssp             SEEEE
T ss_pred             eEEEE
Confidence            98874

>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=94.27  E-value=0.95  Score=39.60  Aligned_cols=75  Identities=13%  Similarity=0.297  Sum_probs=58.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHH---HHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~---l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|+.-|..+.+.+...     ++++..+.|+.+..++...   ...+..+|+|||-     .+.  .++|+..++
T Consensus       448 vlVf~~t~~~ae~L~~~L~~~-----gi~~~~lh~~~~~~~R~~~l~~f~~g~~~VLVaT~-----~l~--~GlDip~v~  515 (661)
T 2d7d_A          448 VLVTTLTKKMSEDLTDYLKEI-----GIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGIN-----LLR--EGLDIPEVS  515 (661)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESC-----CCS--TTCCCTTEE
T ss_pred             EEEEECCHHHHHHHHHHHHhc-----CCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecc-----hhh--CCcccCCCC
Confidence            789999999999988877765     5677778887665444433   4456789999995     333  589999999


Q ss_pred             EEEEcccchh
Q 030094           79 ILVLDEADRL   88 (183)
Q Consensus        79 ~lVvDEad~l   88 (183)
                      ++|+-++|..
T Consensus       516 lVi~~d~d~~  525 (661)
T 2d7d_A          516 LVAILDADKE  525 (661)
T ss_dssp             EEEETTTTCC
T ss_pred             EEEEeCcccc
Confidence            9999999874

>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=94.17  E-value=0.26  Score=38.78  Aligned_cols=72  Identities=17%  Similarity=0.303  Sum_probs=53.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-+..+++.+++.     +..+..+.|+.+..++..   ...++..+|+|+|.     .+..  ++|+.++.
T Consensus       241 ~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-----~~~~--Gid~~~~~  308 (367)
T 1hv8_A          241 GLVFCKTKRDTKELASMLRDI-----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-----VMSR--GIDVNDLN  308 (367)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-----THHH--HCCCSCCS
T ss_pred             EEEEECCHHHHHHHHHHHHhc-----CCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECC-----hhhc--CCCcccCC
Confidence            689999999999998888775     567888888876544433   34456789999995     4443  68888899


Q ss_pred             EEEEccc
Q 030094           79 ILVLDEA   85 (183)
Q Consensus        79 ~lVvDEa   85 (183)
                      ++|.-+.
T Consensus       309 ~Vi~~~~  315 (367)
T 1hv8_A          309 CVINYHL  315 (367)
T ss_dssp             EEEESSC
T ss_pred             EEEEecC
Confidence            8886443

>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=94.11  E-value=0.27  Score=41.67  Aligned_cols=75  Identities=15%  Similarity=0.283  Sum_probs=57.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|+.-|..+++.+.+....  ++.+..+.|+.+..++..   ...++..+|+|||.     .+.  .++|+.++.
T Consensus       342 ~iVF~~s~~~~~~l~~~L~~~~~~--~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~-----~~~--~GiDip~v~  412 (563)
T 3i5x_A          342 AIIFAPTVKFTSFLCSILKNEFKK--DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----VGA--RGMDFPNVH  412 (563)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHTT--TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----GGT--SSCCCTTCC
T ss_pred             EEEEcCcHHHHHHHHHHHHHhccC--CceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcc-----hhh--cCCCcccCC
Confidence            799999999999999998886432  677888888876544433   34457799999996     333  589999999


Q ss_pred             EEEEccc
Q 030094           79 ILVLDEA   85 (183)
Q Consensus        79 ~lVvDEa   85 (183)
                      ++|.-..
T Consensus       413 ~VI~~~~  419 (563)
T 3i5x_A          413 EVLQIGV  419 (563)
T ss_dssp             EEEEESC
T ss_pred             EEEEECC
Confidence            9886554

>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=94.08  E-value=0.23  Score=39.85  Aligned_cols=71  Identities=18%  Similarity=0.247  Sum_probs=54.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-|..+++.+.+.     +..+..+.|+.+..++..   ...++..+|+|||.     .+.  .++|+.++.
T Consensus       269 ~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~--~Gidip~~~  336 (412)
T 3fht_A          269 AMIFCHTRKTASWLAAELSKE-----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTN-----VCA--RGIDVEQVS  336 (412)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-----GGT--SSCCCTTEE
T ss_pred             EEEEeCCHHHHHHHHHHHHhC-----CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcC-----ccc--cCCCccCCC
Confidence            689999999999999888775     567788888876554433   34456789999995     333  589999999


Q ss_pred             EEEEcc
Q 030094           79 ILVLDE   84 (183)
Q Consensus        79 ~lVvDE   84 (183)
                      ++|.-.
T Consensus       337 ~Vi~~~  342 (412)
T 3fht_A          337 VVINFD  342 (412)
T ss_dssp             EEEESS
T ss_pred             EEEEEC
Confidence            988533

>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=94.03  E-value=0.26  Score=40.55  Aligned_cols=70  Identities=11%  Similarity=0.164  Sum_probs=53.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-|..+++.+.+.     ++.+..+.|+....++..   ...++..+|+|||.     .+ . .++|+.++.
T Consensus       303 ~lVF~~t~~~a~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~-----v~-~-rGlDi~~v~  370 (434)
T 2db3_A          303 TIVFVETKRGADFLASFLSEK-----EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATS-----VA-S-RGLDIKNIK  370 (434)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECG-----GG-T-SSCCCTTCC
T ss_pred             EEEEEeCcHHHHHHHHHHHhC-----CCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEch-----hh-h-CCCCcccCC
Confidence            689999999999998877764     567888888876554433   34456789999996     33 3 589999999


Q ss_pred             EEEEc
Q 030094           79 ILVLD   83 (183)
Q Consensus        79 ~lVvD   83 (183)
                      ++|.-
T Consensus       371 ~VI~~  375 (434)
T 2db3_A          371 HVINY  375 (434)
T ss_dssp             EEEES
T ss_pred             EEEEE
Confidence            98853

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=93.92  E-value=0.3  Score=41.72  Aligned_cols=76  Identities=16%  Similarity=0.287  Sum_probs=57.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-|..+++.+.+...  .++.+..+.|+.+..++.   .....+..+|+|||.     .+.  .++|+.++.
T Consensus       291 ~iVF~~t~~~~~~l~~~L~~~~~--~~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~-----~~~--~GiDip~v~  361 (579)
T 3sqw_A          291 AIIFAPTVKFTSFLCSILKNEFK--KDLPILEFHGKITQNKRTSLVKRFKKDESGILVCTD-----VGA--RGMDFPNVH  361 (579)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHT--TTSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECG-----GGT--SSCCCTTCC
T ss_pred             EEEECCcHHHHHHHHHHHHHhhc--CCCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcc-----hhh--cCCCcccCC
Confidence            79999999999999999888643  267788888887655443   344457799999995     333  589999999


Q ss_pred             EEEEcccc
Q 030094           79 ILVLDEAD   86 (183)
Q Consensus        79 ~lVvDEad   86 (183)
                      ++|.-..-
T Consensus       362 ~VI~~~~p  369 (579)
T 3sqw_A          362 EVLQIGVP  369 (579)
T ss_dssp             EEEEESCC
T ss_pred             EEEEcCCC
Confidence            98865543

>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=93.85  E-value=0.098  Score=43.43  Aligned_cols=67  Identities=12%  Similarity=0.135  Sum_probs=46.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +++|+|||++-|..+++.+++.     ++++..+.|. ...+......++..+|+|||.     .+.  .++|+. +.++
T Consensus       179 ~~lVF~~s~~~a~~l~~~L~~~-----~~~v~~lhg~-~R~~~~~~F~~g~~~vLVaT~-----v~e--~GiDip-v~~V  244 (440)
T 1yks_A          179 PTAWFLPSIRAANVMAASLRKA-----GKSVVVLNRK-TFEREYPTIKQKKPDFILATD-----IAE--MGANLC-VERV  244 (440)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHT-----TCCEEECCSS-SCC--------CCCSEEEESS-----STT--CCTTCC-CSEE
T ss_pred             CEEEEeCCHHHHHHHHHHHHHc-----CCCEEEecch-hHHHHHhhhcCCCceEEEECC-----hhh--eeeccC-ceEE
Confidence            4799999999999998887775     5678888873 344444555567899999996     343  578888 8887


Q ss_pred             E
Q 030094           81 V   81 (183)
Q Consensus        81 V   81 (183)
                      |
T Consensus       245 I  245 (440)
T 1yks_A          245 L  245 (440)
T ss_dssp             E
T ss_pred             E
Confidence            6

>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=93.62  E-value=1.4  Score=38.58  Aligned_cols=75  Identities=11%  Similarity=0.205  Sum_probs=57.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHH---HHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~---l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|+.-|..+.+.+...     ++++..+.|+.+..++...   ...+..+|+|||-     .+.  .++|+..++
T Consensus       442 vlVf~~t~~~ae~L~~~L~~~-----gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~-----~l~--~GlDip~v~  509 (664)
T 1c4o_A          442 TLVTVLTVRMAEELTSFLVEH-----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN-----LLR--EGLDIPEVS  509 (664)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC-----CCC--TTCCCTTEE
T ss_pred             EEEEECCHHHHHHHHHHHHhc-----CCCceeecCCCCHHHHHHHHHHhhcCCceEEEccC-----hhh--cCccCCCCC
Confidence            789999999999988877765     5677778887665444433   4456789999995     333  589999999


Q ss_pred             EEEEcccchh
Q 030094           79 ILVLDEADRL   88 (183)
Q Consensus        79 ~lVvDEad~l   88 (183)
                      ++|+=++|..
T Consensus       510 lVI~~d~d~~  519 (664)
T 1c4o_A          510 LVAILDADKE  519 (664)
T ss_dssp             EEEETTTTSC
T ss_pred             EEEEeCCccc
Confidence            9999888764

>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=93.38  E-value=0.4  Score=38.19  Aligned_cols=73  Identities=8%  Similarity=0.155  Sum_probs=54.9

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-|..+++.+.+.     ++.+..+.|+.+..++..   ...++..+|+|+|.     .+.  .++|+..+.
T Consensus       253 ~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-----~~~--~Gidi~~~~  320 (391)
T 1xti_A          253 VVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN-----LFG--RGMDIERVN  320 (391)
T ss_dssp             EEEECSCHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESC-----CCS--SCBCCTTEE
T ss_pred             EEEEeCcHHHHHHHHHHHHhC-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECC-----hhh--cCCCcccCC
Confidence            689999999999998887764     567888888876544433   34456789999995     232  579999999


Q ss_pred             EEEEcccc
Q 030094           79 ILVLDEAD   86 (183)
Q Consensus        79 ~lVvDEad   86 (183)
                      ++|.-+..
T Consensus       321 ~Vi~~~~p  328 (391)
T 1xti_A          321 IAFNYDMP  328 (391)
T ss_dssp             EEEESSCC
T ss_pred             EEEEeCCC
Confidence            99875543

>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=93.34  E-value=0.38  Score=38.75  Aligned_cols=71  Identities=13%  Similarity=0.196  Sum_probs=53.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-+..+++.+...     ++.+..+.|+.+..++..   ...++..+|+|+|.     .+.  .++|+.++.
T Consensus       279 ~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~--~Gidi~~v~  346 (410)
T 2j0s_A          279 AVIFCNTKRKVDWLTEKMREA-----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD-----VWA--RGLDVPQVS  346 (410)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG-----GGS--SSCCCTTEE
T ss_pred             EEEEEcCHHHHHHHHHHHHhC-----CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECC-----hhh--CcCCcccCC
Confidence            689999999999988877764     567888888876544333   34456789999996     332  589999999


Q ss_pred             EEEEcc
Q 030094           79 ILVLDE   84 (183)
Q Consensus        79 ~lVvDE   84 (183)
                      ++|.-+
T Consensus       347 ~Vi~~~  352 (410)
T 2j0s_A          347 LIINYD  352 (410)
T ss_dssp             EEEESS
T ss_pred             EEEEEC
Confidence            988533

>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=93.33  E-value=0.39  Score=38.49  Aligned_cols=71  Identities=6%  Similarity=0.127  Sum_probs=53.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-+..+++.+...     +..+..+.|+.+..++..   ...++..+|+|+|.     .+.  .++|+..+.
T Consensus       261 ~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vLv~T~-----~~~--~Gidip~~~  328 (400)
T 1s2m_A          261 AIIFCNSTNRVELLAKKITDL-----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSD-----LLT--RGIDIQAVN  328 (400)
T ss_dssp             EEEECSSHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESS-----CSS--SSCCCTTEE
T ss_pred             EEEEEecHHHHHHHHHHHHhc-----CCCeEEecCCCCHHHHHHHHHHHhcCCCcEEEEcC-----ccc--cCCCccCCC
Confidence            689999999999998888775     567888888876554433   34456789999995     332  579999999


Q ss_pred             EEEEcc
Q 030094           79 ILVLDE   84 (183)
Q Consensus        79 ~lVvDE   84 (183)
                      ++|.-+
T Consensus       329 ~Vi~~~  334 (400)
T 1s2m_A          329 VVINFD  334 (400)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            888543

>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=93.09  E-value=0.37  Score=40.85  Aligned_cols=71  Identities=14%  Similarity=0.202  Sum_probs=54.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-+.++++.+.+.     ++.+....|+.+.++..   .....+..+|+|||.     .+ . .++|+.+++
T Consensus       239 ~IVf~~sr~~~e~l~~~L~~~-----g~~~~~~h~~l~~~~R~~~~~~f~~g~~~vlVaT~-----a~-~-~GiD~p~v~  306 (523)
T 1oyw_A          239 GIIYCNSRAKVEDTAARLQSK-----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV-----AF-G-MGINKPNVR  306 (523)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT-----TS-C-TTTCCTTCC
T ss_pred             EEEEeCCHHHHHHHHHHHHHC-----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEec-----hh-h-CCCCccCcc
Confidence            689999999999998888764     56788888887754433   344456799999996     23 2 578999999


Q ss_pred             EEEEcc
Q 030094           79 ILVLDE   84 (183)
Q Consensus        79 ~lVvDE   84 (183)
                      ++|.-.
T Consensus       307 ~VI~~~  312 (523)
T 1oyw_A          307 FVVHFD  312 (523)
T ss_dssp             EEEESS
T ss_pred             EEEEEC
Confidence            988543

>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=92.93  E-value=0.39  Score=44.80  Aligned_cols=92  Identities=15%  Similarity=0.268  Sum_probs=65.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +++|+||+++-+..+++.+++.   .|+.++..+.|+.+..+...   ...++..+|+|||.     .+.  .++|+.++
T Consensus       814 qvlvf~~~v~~~~~l~~~L~~~---~p~~~v~~lhg~~~~~eR~~il~~F~~g~~~VLVaT~-----v~e--~GiDip~v  883 (1151)
T 2eyq_A          814 QVYYLYNDVENIQKAAERLAEL---VPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----IIE--TGIDIPTA  883 (1151)
T ss_dssp             EEEEECCCSSCHHHHHHHHHHH---CTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS-----TTG--GGSCCTTE
T ss_pred             eEEEEECCHHHHHHHHHHHHHh---CCCCeEEEEeCCCCHHHHHHHHHHHHcCCCcEEEECC-----cce--eeecccCC
Confidence            3789999999998888877765   46788999999876544433   34456799999995     444  48999999


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCC
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPK  106 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~  106 (183)
                      .++|+..+|..   +.. .+.....+.++
T Consensus       884 ~~VIi~~~~~~---~l~-~l~Qr~GRvgR  908 (1151)
T 2eyq_A          884 NTIIIERADHF---GLA-QLHQLRGRVGR  908 (1151)
T ss_dssp             EEEEETTTTSS---CHH-HHHHHHTTCCB
T ss_pred             cEEEEeCCCCC---CHH-HHHHHHhccCc
Confidence            99999888763   222 33344445443

>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=92.88  E-value=0.41  Score=41.36  Aligned_cols=71  Identities=13%  Similarity=0.164  Sum_probs=54.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|+.-|.++++.+...     ++.+..+.|+.+..++..   ....+..+|+|+|-     .+ . .++|..+++
T Consensus       270 ~IVf~~sr~~~e~la~~L~~~-----g~~~~~~h~~l~~~~R~~~~~~F~~g~~~VlVAT~-----a~-~-~GID~p~V~  337 (591)
T 2v1x_A          270 GIIYCFSQKDSEQVTVSLQNL-----GIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATV-----AF-G-MGIDKPDVR  337 (591)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECT-----TS-C-TTCCCSCEE
T ss_pred             eEEEeCcHHHHHHHHHHHHHC-----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEec-----hh-h-cCCCccccc
Confidence            689999999999999888764     677888899877554433   34456789999995     23 2 578999999


Q ss_pred             EEEEcc
Q 030094           79 ILVLDE   84 (183)
Q Consensus        79 ~lVvDE   84 (183)
                      ++|.-.
T Consensus       338 ~VI~~~  343 (591)
T 2v1x_A          338 FVIHHS  343 (591)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            988433

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=92.43  E-value=0.21  Score=43.86  Aligned_cols=67  Identities=15%  Similarity=0.145  Sum_probs=49.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||+|||++-+..+++.+++.     ++++..+.|+ ..........++..+|+|||-     .+.  .++|+. +.++
T Consensus       412 ~~lVF~~s~~~~e~la~~L~~~-----g~~v~~lHg~-eR~~v~~~F~~g~~~VLVaTd-----v~e--~GIDip-v~~V  477 (673)
T 2wv9_A          412 KTVWFVASVKMSNEIAQCLQRA-----GKRVIQLNRK-SYDTEYPKCKNGDWDFVITTD-----ISE--MGANFG-ASRV  477 (673)
T ss_dssp             CEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSS-SHHHHGGGGGTCCCSEEEECG-----GGG--TTCCCC-CSEE
T ss_pred             CEEEEECCHHHHHHHHHHHHhC-----CCeEEEeChH-HHHHHHHHHHCCCceEEEECc-----hhh--cceeeC-CcEE
Confidence            4799999999999888877664     5678888884 333334444456789999995     444  478887 8776


Q ss_pred             E
Q 030094           81 V   81 (183)
Q Consensus        81 V   81 (183)
                      |
T Consensus       478 I  478 (673)
T 2wv9_A          478 I  478 (673)
T ss_dssp             E
T ss_pred             E
Confidence            6

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=92.39  E-value=0.28  Score=40.53  Aligned_cols=66  Identities=17%  Similarity=0.134  Sum_probs=48.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +++|+|||++-|..+++.+++.     +.++..+.|+ ...+......++..+|+|||-     .+.  .++|+. +..+
T Consensus       173 ~~lVF~~~~~~~~~l~~~L~~~-----~~~v~~lhg~-~r~~~~~~f~~g~~~vLVaT~-----v~e--~GiDip-~~~V  238 (431)
T 2v6i_A          173 RTVWFVHSIKQGAEIGTCLQKA-----GKKVLYLNRK-TFESEYPKCKSEKWDFVITTD-----ISE--MGANFK-ADRV  238 (431)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHT-----TCCEEEESTT-THHHHTTHHHHSCCSEEEECG-----GGG--TSCCCC-CSEE
T ss_pred             CEEEEeCCHHHHHHHHHHHHHc-----CCeEEEeCCc-cHHHHHHhhcCCCCeEEEECc-----hHH--cCcccC-CcEE
Confidence            4799999999999998887775     5678888876 334444455567899999995     444  467775 5554

>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=91.37  E-value=0.45  Score=42.49  Aligned_cols=74  Identities=14%  Similarity=0.094  Sum_probs=55.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhh------hCCCceEEEEEcCcchHHHHHHHH--------hcCCcEEEeCcHHHHHHHH
Q 030094            2 GMIISPTRELSSQIYHVAQPFIS------TLPDVKSVLLVGGVEVKADVKKIE--------EEGANLLIGTPGRLYDIME   67 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~------~~~~~~~~~~~g~~~~~~~~~~l~--------~~~~~IiV~TP~~l~~~l~   67 (183)
                      +||.+|+++-+.++++.+.+...      ..+++.+..++|+.+..++...+.        .+...|||||.     .+.
T Consensus       306 iLVF~~~~~~i~~l~~~L~~~~~~l~~~~~~~~~~v~~lhg~l~~~eR~~v~~~f~~~~~~~g~~kVlVAT~-----iae  380 (773)
T 2xau_A          306 ILLFLTGEDEIEDAVRKISLEGDQLVREEGCGPLSVYPLYGSLPPHQQQRIFEPAPESHNGRPGRKVVISTN-----IAE  380 (773)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECTTCCHHHHGGGGSCCCCCSSSSCCEEEEEECT-----HHH
T ss_pred             EEEECCCHHHHHHHHHHHHHHHHhhcccccCCCeEEEEeCCCCCHHHHHHHHhhcccccCCCCceEEEEeCc-----HHH
Confidence            69999999999999998876332      224788999999988766654432        23568999995     454


Q ss_pred             hcCCcCCCCceEEEE
Q 030094           68 RMDVLDFRNLEILVL   82 (183)
Q Consensus        68 ~~~~~~l~~l~~lVv   82 (183)
                      .  ++|+..+.++|-
T Consensus       381 ~--GidIp~v~~VId  393 (773)
T 2xau_A          381 T--SLTIDGIVYVVD  393 (773)
T ss_dssp             H--TCCCTTEEEEEE
T ss_pred             h--CcCcCCeEEEEe
Confidence            4  789999987773

>2yjt_D ATP-dependent RNA helicase SRMB, regulator of ribonuclease activity A; hydrolase inhibitor-hydrolase complex, DEAD box RNA helicase; 2.90A {Escherichia coli}

Probab=90.65  E-value=0.037  Score=39.60  Aligned_cols=71  Identities=14%  Similarity=0.220  Sum_probs=49.9

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-|..+.+.+...     ++.+..+.|+.+..+..   .....+..+|+|+|.     .+.  .++|+..+.
T Consensus        33 ~iVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~--~Gid~~~~~  100 (170)
T 2yjt_D           33 SIVFVRKRERVHELANWLREA-----GINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATD-----VAA--RGIDIPDVS  100 (170)
Confidence            689999999999888877764     56677777776543332   233345688999994     333  478888888


Q ss_pred             EEEEcc
Q 030094           79 ILVLDE   84 (183)
Q Consensus        79 ~lVvDE   84 (183)
                      ++|.-+
T Consensus       101 ~Vi~~~  106 (170)
T 2yjt_D          101 HVFNFD  106 (170)
Confidence            877533

>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=90.68  E-value=0.42  Score=39.64  Aligned_cols=67  Identities=13%  Similarity=0.141  Sum_probs=48.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||.|||++-|.++++.+++.     ++++..+.|... ........++..+|+|||.     .+.  .++|+.. .++
T Consensus       190 ~~lVF~~s~~~a~~l~~~L~~~-----g~~~~~lh~~~~-~~~~~~f~~g~~~vLVaT~-----v~~--~GiDip~-~~V  255 (451)
T 2jlq_A          190 KTVWFVPSIKAGNDIANCLRKS-----GKRVIQLSRKTF-DTEYPKTKLTDWDFVVTTD-----ISE--MGANFRA-GRV  255 (451)
T ss_dssp             CEEEECSSHHHHHHHHHHHHTT-----TCCEEEECTTTH-HHHGGGGGSSCCSEEEECG-----GGG--SSCCCCC-SEE
T ss_pred             CEEEEcCCHHHHHHHHHHHHHc-----CCeEEECCHHHH-HHHHHhhccCCceEEEECC-----HHH--hCcCCCC-CEE
Confidence            3799999999999988887664     566777776544 3333344456789999995     443  5788888 666


Q ss_pred             E
Q 030094           81 V   81 (183)
Q Consensus        81 V   81 (183)
                      |
T Consensus       256 I  256 (451)
T 2jlq_A          256 I  256 (451)
T ss_dssp             E
T ss_pred             E
Confidence            5

>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=90.56  E-value=1.2  Score=36.02  Aligned_cols=73  Identities=21%  Similarity=0.332  Sum_probs=51.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEc--------CcchHHH---HHHHHhcCCcEEEeCcHHHHHHHHhcC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVG--------GVEVKAD---VKKIEEEGANLLIGTPGRLYDIMERMD   70 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g--------~~~~~~~---~~~l~~~~~~IiV~TP~~l~~~l~~~~   70 (183)
                      +||.|++++-+..+++.+...     ++++..+.|        +.+.+++   .+....+.++|+|+|.     .+.  .
T Consensus       364 ~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~-----~~~--~  431 (494)
T 1wp9_A          364 IIVFTNYRETAKKIVNELVKD-----GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATS-----VGE--E  431 (494)
T ss_dssp             EEEECSCHHHHHHHHHHHHHT-----TCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECG-----GGG--G
T ss_pred             EEEEEccHHHHHHHHHHHHHc-----CCCcEEEeccccccccccCCHHHHHHHHHHHhcCCceEEEECC-----ccc--c
Confidence            799999999999998888775     567788888        4443322   3344456789999994     233  5


Q ss_pred             CcCCCCceEEEEcccc
Q 030094           71 VLDFRNLEILVLDEAD   86 (183)
Q Consensus        71 ~~~l~~l~~lVvDEad   86 (183)
                      ++|+..+.++|.-+..
T Consensus       432 Gldl~~~~~Vi~~d~~  447 (494)
T 1wp9_A          432 GLDVPEVDLVVFYEPV  447 (494)
T ss_dssp             GGGSTTCCEEEESSCC
T ss_pred             CCCchhCCEEEEeCCC
Confidence            7999999999865543

>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=90.36  E-value=0.78  Score=39.83  Aligned_cols=67  Identities=13%  Similarity=0.156  Sum_probs=49.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||.|+|++-|..+++.+++.     ++++..+.|. ...+..+...++..+|+|||.     .+.  .++|+. +.++
T Consensus       357 ~~LVF~~s~~~a~~l~~~L~~~-----g~~v~~lhg~-~R~~~l~~F~~g~~~VLVaTd-----v~~--rGiDi~-v~~V  422 (618)
T 2whx_A          357 KTVWFVPSIKAGNDIANCLRKS-----GKRVIQLSRK-TFDTEYPKTKLTDWDFVVTTD-----ISE--MGANFR-AGRV  422 (618)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTT-THHHHTTHHHHSCCSEEEECG-----GGG--TTCCCC-CSEE
T ss_pred             CEEEEECChhHHHHHHHHHHHc-----CCcEEEEChH-HHHHHHHhhcCCCcEEEEECc-----HHH--cCcccC-ceEE
Confidence            3799999999999998888775     5677777774 333444455567899999996     444  478885 7776


Q ss_pred             E
Q 030094           81 V   81 (183)
Q Consensus        81 V   81 (183)
                      |
T Consensus       423 I  423 (618)
T 2whx_A          423 I  423 (618)
T ss_dssp             E
T ss_pred             E
Confidence            3

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=90.23  E-value=0.84  Score=40.14  Aligned_cols=74  Identities=12%  Similarity=0.200  Sum_probs=54.9

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchH---HHHHHHHh--cCCcEEEeCcHHHHHHHHhcCCcCCCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVK---ADVKKIEE--EGANLLIGTPGRLYDIMERMDVLDFRN   76 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~---~~~~~l~~--~~~~IiV~TP~~l~~~l~~~~~~~l~~   76 (183)
                      .+|+|+|++-+.++.+.+.+.     +..+..++|+.+..   +..+...+  +..+|+|||-     .+.  .++|+ +
T Consensus       323 ~iIf~~s~~~ie~la~~L~~~-----g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATd-----i~e--~GlDi-~  389 (677)
T 3rc3_A          323 DCIVCFSKNDIYSVSRQIEIR-----GLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATD-----AIG--MGLNL-S  389 (677)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECG-----GGG--SSCCC-C
T ss_pred             CEEEEcCHHHHHHHHHHHHhc-----CCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCc-----HHH--CCcCc-C
Confidence            467899999888777777663     67889999998765   34444444  5589999995     443  57999 8


Q ss_pred             ceEEEEcccchh
Q 030094           77 LEILVLDEADRL   88 (183)
Q Consensus        77 l~~lVvDEad~l   88 (183)
                      ++.+|.-.....
T Consensus       390 v~~VI~~~~~k~  401 (677)
T 3rc3_A          390 IRRIIFYSLIKP  401 (677)
T ss_dssp             BSEEEESCSBC-
T ss_pred             ccEEEECCcccc
Confidence            999998887654

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=89.34  E-value=6.2  Score=32.69  Aligned_cols=74  Identities=14%  Similarity=0.225  Sum_probs=50.4

Q ss_pred             EEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceE
Q 030094            3 MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEI   79 (183)
Q Consensus         3 lIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~   79 (183)
                      +|++.+.+-+..+.+.+.+.     +.++..+.|+.+..+..   ....++..+|+|||+.    .+..  ++|+.++..
T Consensus       351 ~ivf~~~~~~~~l~~~L~~~-----~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~----~~~~--GiDip~v~~  419 (510)
T 2oca_A          351 FVMFKHVSHGKAIFDLIKNE-----YDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYG----VFST--GISVKNLHH  419 (510)
T ss_dssp             EEEESSHHHHHHHHHHHHTT-----CSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHH----HHHH--SCCCCSEEE
T ss_pred             EEEEecHHHHHHHHHHHHHc-----CCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcC----hhhc--ccccccCcE
Confidence            45666666666665555543     23788888877654432   3344567899999963    4544  789999999


Q ss_pred             EEEcccch
Q 030094           80 LVLDEADR   87 (183)
Q Consensus        80 lVvDEad~   87 (183)
                      +|+..++.
T Consensus       420 vi~~~~~~  427 (510)
T 2oca_A          420 VVLAHGVK  427 (510)
T ss_dssp             EEESSCCC
T ss_pred             EEEeCCCC
Confidence            99988874

>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=89.23  E-value=1.1  Score=34.58  Aligned_cols=68  Identities=18%  Similarity=0.236  Sum_probs=47.3

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.++|++-+..+++.+.         ++..+.|+.+..++..   ...++..+|+|+|.     .+.  .++|+..+.
T Consensus       223 ~lvf~~~~~~~~~l~~~l~---------~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-----~~~--~Gid~~~~~  286 (337)
T 2z0m_A          223 VIVFVRTRNRVAKLVRLFD---------NAIELRGDLPQSVRNRNIDAFREGEYDMLITTD-----VAS--RGLDIPLVE  286 (337)
T ss_dssp             EEEECSCHHHHHHHHTTCT---------TEEEECTTSCHHHHHHHHHHHHTTSCSEEEECH-----HHH--TTCCCCCBS
T ss_pred             EEEEEcCHHHHHHHHHHhh---------hhhhhcCCCCHHHHHHHHHHHHcCCCcEEEEcC-----ccc--cCCCccCCC
Confidence            6899999998887655332         3556677765444333   34456789999994     454  579999999


Q ss_pred             EEEEccc
Q 030094           79 ILVLDEA   85 (183)
Q Consensus        79 ~lVvDEa   85 (183)
                      ++|.-..
T Consensus       287 ~Vi~~~~  293 (337)
T 2z0m_A          287 KVINFDA  293 (337)
T ss_dssp             EEEESSC
T ss_pred             EEEEecC
Confidence            9886544

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=88.24  E-value=1.2  Score=35.90  Aligned_cols=70  Identities=16%  Similarity=0.192  Sum_probs=50.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEE-EEEcCcchHHHHHHHHhcCCcEEEe----CcHHHHHHHHhcCCcCCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSV-LLVGGVEVKADVKKIEEEGANLLIG----TPGRLYDIMERMDVLDFR   75 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~-~~~g~~~~~~~~~~l~~~~~~IiV~----TP~~l~~~l~~~~~~~l~   75 (183)
                      .+||.|+|++-|..+++.+.+.     ++++. .+.|. .. + .....++..+|+||    |.     .+.  .++|+.
T Consensus       254 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~h~~-~r-~-~~~f~~g~~~vLvat~s~T~-----~~~--~GiDip  318 (414)
T 3oiy_A          254 GILIFAQTEEEGKELYEYLKRF-----KFNVGETWSEF-EK-N-FEDFKVGKINILIGVQAYYG-----KLT--RGVDLP  318 (414)
T ss_dssp             SEEEEESSHHHHHHHHHHHHHT-----TCCEEESSSCH-HH-H-HHHHHTTSCSEEEEECCTTC-----CCC--CCCCCT
T ss_pred             CEEEEECCHHHHHHHHHHHHHc-----CCceehhhcCc-ch-H-HHHHhCCCCeEEEEecCcCc-----hhh--ccCccc
Confidence            3799999999999998888774     55665 44443 22 2 56666678999999    74     232  579999


Q ss_pred             C-ceEEEEccc
Q 030094           76 N-LEILVLDEA   85 (183)
Q Consensus        76 ~-l~~lVvDEa   85 (183)
                      + +.++|.-+.
T Consensus       319 ~~v~~VI~~~~  329 (414)
T 3oiy_A          319 ERIKYVIFWGT  329 (414)
T ss_dssp             TTCCEEEEESC
T ss_pred             cccCEEEEECC
Confidence            8 999885444

>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=88.08  E-value=0.66  Score=40.75  Aligned_cols=63  Identities=10%  Similarity=0.178  Sum_probs=48.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||.|||++-+.++++.+++.     ++++..+.|+.+..+.    .+.+.+|+|+|.     .+..  ++|+. ++++|
T Consensus       399 vLVFv~Tr~~ae~la~~L~~~-----g~~v~~lHG~l~q~er----~~~~~~VLVATd-----Vaer--GIDId-V~~VI  461 (666)
T 3o8b_A          399 HLIFCHSKKKCDELAAKLSGL-----GINAVAYYRGLDVSVI----PTIGDVVVVATD-----ALMT--GYTGD-FDSVI  461 (666)
T ss_dssp             EEEECSCHHHHHHHHHHHHTT-----TCCEEEECTTSCGGGS----CSSSCEEEEECT-----THHH--HCCCC-BSEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHhC-----CCcEEEecCCCCHHHH----HhCCCcEEEECC-----hHHc--cCCCC-CcEEE
Confidence            789999999999998877764     6788889988765432    245679999995     4554  67775 88776

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=87.85  E-value=0.37  Score=41.85  Aligned_cols=36  Identities=17%  Similarity=0.300  Sum_probs=31.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCc
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGV   38 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~   38 (183)
                      ++|++||++++.|+.+.+..+.... ++++..+.|+.
T Consensus        54 vli~t~T~~l~~Qi~~el~~l~~~~-~~~~~~l~gr~   89 (620)
T 4a15_A           54 VLYLVRTNSQEEQVIKELRSLSSTM-KIRAIPMQGRV   89 (620)
T ss_dssp             EEEEESSHHHHHHHHHHHHHHHHHS-CCCEEECCCHH
T ss_pred             EEEECCCHHHHHHHHHHHHHHhhcc-CeEEEEEECCC
Confidence            6899999999999999999998776 78888877754

>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=87.68  E-value=0.47  Score=38.07  Aligned_cols=70  Identities=14%  Similarity=0.212  Sum_probs=45.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-+..+++.+.+.     ++.+..+.|+.+..++..   ...++..+|+|+|.     .+.  .++|+.++.
T Consensus       283 ~lvf~~~~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~-----~~~--~Gidip~v~  350 (414)
T 3eiq_A          283 AVIFINTRRKVDWLTEKMHAR-----DFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTD-----LLA--RGIDVQQVS  350 (414)
T ss_dssp             CEEECSCHHHHHHHHHHHHTT-----TCCCEEC---CHHHHHHHHHHHHSCC---CEEECS-----SCC----CCGGGCS
T ss_pred             EEEEeCCHHHHHHHHHHHHhc-----CCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECC-----ccc--cCCCccCCC
Confidence            689999999999888877654     567788888876554433   33345688999996     232  578888888


Q ss_pred             EEEEc
Q 030094           79 ILVLD   83 (183)
Q Consensus        79 ~lVvD   83 (183)
                      ++|.-
T Consensus       351 ~Vi~~  355 (414)
T 3eiq_A          351 LVINY  355 (414)
T ss_dssp             CEEES
T ss_pred             EEEEe
Confidence            88753

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=86.55  E-value=2.2  Score=35.58  Aligned_cols=18  Identities=28%  Similarity=0.444  Sum_probs=14.4

Q ss_pred             EEEEeCcHHHHHHHHHHH
Q 030094            2 GMIISPTRELSSQIYHVA   19 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~   19 (183)
                      .+|++||++++..+.+.+
T Consensus       187 ~lVlTpT~~aa~~l~~kl  204 (446)
T 3vkw_A          187 DLILVPGRQAAEMIRRRA  204 (446)
T ss_dssp             CEEEESCHHHHHHHHHHH
T ss_pred             eEEEeCCHHHHHHHHHHh
Confidence            378999999998776654

>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=85.87  E-value=0.15  Score=42.37  Aligned_cols=68  Identities=19%  Similarity=0.281  Sum_probs=0.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|||+.-|..+++.+...     +..+..+.|+.+..++..   ....+..+|+|||.     .+.  .++|+.++.
T Consensus       336 ~lvF~~s~~~~~~l~~~L~~~-----~~~v~~lh~~~~~~~R~~~~~~f~~g~~~iLv~T~-----~~~--~GlDip~v~  403 (479)
T 3fmp_B          336 AMIFCHTRKTASWLAAELSKE-----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTN-----VCA--RGIDVEQVS  403 (479)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             eEEEeCcHHHHHHHHHHHHhC-----CccEEEecCCCCHHHHHHHHHHHHcCCCcEEEEcc-----ccc--cCCccccCC
Confidence            689999999999888877765     456777777765443322   33346789999994     444  478988888


Q ss_pred             EEE
Q 030094           79 ILV   81 (183)
Q Consensus        79 ~lV   81 (183)
                      ++|
T Consensus       404 ~VI  406 (479)
T 3fmp_B          404 VVI  406 (479)
T ss_dssp             ---
T ss_pred             EEE
Confidence            886

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=85.14  E-value=1.7  Score=36.18  Aligned_cols=76  Identities=20%  Similarity=0.303  Sum_probs=47.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEc--------CcchHHHH---HHHHh-cCCcEEEeCcHHHHHHHHhc
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVG--------GVEVKADV---KKIEE-EGANLLIGTPGRLYDIMERM   69 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g--------~~~~~~~~---~~l~~-~~~~IiV~TP~~l~~~l~~~   69 (183)
                      +||.|++++-+..+.+.+...... +.+++..+.|        +.+.+++.   ..... +..+|+|||.     .+ . 
T Consensus       392 ~lVF~~~~~~~~~l~~~L~~~~~~-~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~-----~~-~-  463 (555)
T 3tbk_A          392 TILFVKTRALVDALKKWIEENPAL-SFLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATS-----VA-D-  463 (555)
T ss_dssp             EEEECSSHHHHHHHHHHHHHCGGG-TTCCEEECCC--------------------------CCSEEEECC-----CT-T-
T ss_pred             EEEEeCcHHHHHHHHHHHhhCcCc-CceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcc-----hh-h-
Confidence            799999999999999999886432 2456666655        33322222   23333 5689999996     33 2 


Q ss_pred             CCcCCCCceEEEEccc
Q 030094           70 DVLDFRNLEILVLDEA   85 (183)
Q Consensus        70 ~~~~l~~l~~lVvDEa   85 (183)
                      .++|+..+.++|.=+.
T Consensus       464 ~GlDlp~v~~VI~~d~  479 (555)
T 3tbk_A          464 EGIDIAECNLVILYEY  479 (555)
T ss_dssp             CCEETTSCSEEEEESC
T ss_pred             cCCccccCCEEEEeCC
Confidence            5799999999886433

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=84.27  E-value=1.6  Score=40.54  Aligned_cols=72  Identities=15%  Similarity=0.188  Sum_probs=53.3

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEE-EEEcCcchHHHHHHHHhcCCcEEEe----CcHHHHHHHHhcCCcCCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSV-LLVGGVEVKADVKKIEEEGANLLIG----TPGRLYDIMERMDVLDFR   75 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~-~~~g~~~~~~~~~~l~~~~~~IiV~----TP~~l~~~l~~~~~~~l~   75 (183)
                      .+||.|||++-|..+++.+...     ++++. .+.|.  ..+ .....++..+|+||    |     +.+.  .++|+.
T Consensus       311 ~~LVF~~s~~~a~~l~~~L~~~-----g~~~~~~lhg~--rr~-l~~F~~G~~~VLVatas~T-----dvla--rGIDip  375 (1104)
T 4ddu_A          311 GILIFAQTEEEGKELYEYLKRF-----KFNVGETWSEF--EKN-FEDFKVGKINILIGVQAYY-----GKLT--RGVDLP  375 (1104)
T ss_dssp             SEEEEESSSHHHHHHHHHHHHT-----TCCEEESSSSH--HHH-HHHHHHTSCSEEEEETTTH-----HHHC--CSCCCT
T ss_pred             CEEEEECcHHHHHHHHHHHHhC-----CCCeeeEecCc--HHH-HHHHHCCCCCEEEEecCCC-----CeeE--ecCcCC
Confidence            4799999999999998888775     55665 55552  333 56666778999999    6     3454  589999


Q ss_pred             C-ceEEEEcccch
Q 030094           76 N-LEILVLDEADR   87 (183)
Q Consensus        76 ~-l~~lVvDEad~   87 (183)
                      + ++++|.=+.-.
T Consensus       376 ~~V~~VI~~d~P~  388 (1104)
T 4ddu_A          376 ERIKYVIFWGTPS  388 (1104)
T ss_dssp             TTCCEEEEESCCE
T ss_pred             CCCCEEEEECCCC
Confidence            9 99988766554

>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=83.60  E-value=6.1  Score=36.51  Aligned_cols=117  Identities=10%  Similarity=0.107  Sum_probs=70.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhh-------hCCCceEEEEEcCcc-----------------------------------
Q 030094            2 GMIISPTRELSSQIYHVAQPFIS-------TLPDVKSVLLVGGVE-----------------------------------   39 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~-------~~~~~~~~~~~g~~~-----------------------------------   39 (183)
                      |+|+|+|++-|...++.+.++..       ..++++++.+..+..                                   
T Consensus       540 amVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~~~~~~~~~~G~~~~e~~~~~~~~~~~r~~l~~~I~dy  619 (1038)
T 2w00_A          540 AMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSFAANEEQNAIGEISDETFDTSAMDSSAKEFLDAAIREY  619 (1038)
T ss_dssp             EEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCCCC------CCCCCCCCSCGGGSCHHHHHHHHHHHHHH
T ss_pred             EEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEEEeCCCccccccccccccccccccccchhHHHHHHHHHHHH
Confidence            79999999999999999999862       223466655544321                                   


Q ss_pred             ------------------hHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEEcccchhhccchHHHHHHHH
Q 030094           40 ------------------VKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYII  101 (183)
Q Consensus        40 ------------------~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvDEad~ll~~~~~~~l~~i~  101 (183)
                                        .++-.....++..+|+|+|-     ++ . .++|...+..+.+|=-   ++  ...-++.+-
T Consensus       620 n~~f~~~~~~~~~~~~~~R~~i~~~Fk~g~i~ILIvvd-----~l-l-tGfDiP~l~tlylDkp---l~--~~~liQaIG  687 (1038)
T 2w00_A          620 NSHFKTNFSTDSNGFQNYYRDLAQRVKNQDIDLLIVVG-----MF-L-TGFDAPTLNTLFVDKN---LR--YHGLMQAFS  687 (1038)
T ss_dssp             HHHHTCCCCSSHHHHHHHHHHHHHHHHTTSSSEEEESS-----TT-S-SSCCCTTEEEEEEESC---CC--HHHHHHHHH
T ss_pred             HHHhcccccccchhhhHHHHHHHHHHHcCCCeEEEEcc-----hH-H-hCcCcccccEEEEccC---CC--ccceeehhh
Confidence                              00111233456789999995     33 2 6899999998888743   21  233344444


Q ss_pred             HhCC---C-C--CeEEEEeecCChHHHHHHHhhCCC
Q 030094          102 SRLP---K-L--RRTGLFSATQTEAVEELSKAGLRN  131 (183)
Q Consensus       102 ~~l~---~-~--~Q~v~~SAT~~~~v~~~~~~~~~~  131 (183)
                      +...   . +  ..++-| .....++......|...
T Consensus       688 RtnR~~~~~K~~G~IVdf-~~~~~~l~~Al~~y~~~  722 (1038)
T 2w00_A          688 RTNRIYDATKTFGNIVTF-RDLERSTIDAITLFGDK  722 (1038)
T ss_dssp             TTCCCCCTTCCSEEEEES-SCCHHHHHHHHHHTSCS
T ss_pred             ccCcCCCCCCCcEEEEEc-cccHHHHHHHHHHHhCC
Confidence            3332   1 1  224444 34666677777766553

>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=83.57  E-value=3.9  Score=35.77  Aligned_cols=74  Identities=9%  Similarity=0.149  Sum_probs=51.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhC-------------C---------------CceEEEEEcCcchHHHHH---HHHh
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTL-------------P---------------DVKSVLLVGGVEVKADVK---KIEE   49 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~-------------~---------------~~~~~~~~g~~~~~~~~~---~l~~   49 (183)
                      .+||.||||+-+..+++.+.+.....             .               ...+...+|+.+..++..   ...+
T Consensus       239 ~~LVF~~sr~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~l~~~~~~~v~~~h~~l~~~~R~~v~~~f~~  318 (720)
T 2zj8_A          239 GALIFVNMRRKAERVALELSKKVKSLLTKPEIRALNELADSLEENPTNEKLAKAIRGGVAFHHAGLGRDERVLVEENFRK  318 (720)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHHGGGSCHHHHHHHHHHHHTSCSCHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHHHHT
T ss_pred             CEEEEecCHHHHHHHHHHHHHHHHHhcChhhHHHHHHHHHHHhcccchHHHHHHHhcCeeeecCCCCHHHHHHHHHHHHC
Confidence            47999999999999988887643210             0               123778888877655543   3334


Q ss_pred             cCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094           50 EGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus        50 ~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +..+|+|||.     .+.  .++|+..+.++|
T Consensus       319 g~~~vlvaT~-----~l~--~Gvdip~~~~VI  343 (720)
T 2zj8_A          319 GIIKAVVATP-----TLS--AGINTPAFRVII  343 (720)
T ss_dssp             TSSCEEEECS-----TTG--GGCCCCBSEEEE
T ss_pred             CCCeEEEECc-----Hhh--ccCCCCceEEEE
Confidence            6789999996     333  478888887654

>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=83.10  E-value=0.47  Score=41.22  Aligned_cols=74  Identities=23%  Similarity=0.308  Sum_probs=47.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhh-CCCceEEEEEcC--------cchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhc
Q 030094            2 GMIISPTRELSSQIYHVAQPFIST-LPDVKSVLLVGG--------VEVKADVK---KIEEEGANLLIGTPGRLYDIMERM   69 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~-~~~~~~~~~~g~--------~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~   69 (183)
                      +||.|+|+..+..+.+.+...... ..++++..+.|+        .+..++..   ....+..+|+|||-     .+ . 
T Consensus       403 ~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~-----~~-~-  475 (699)
T 4gl2_A          403 GIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATT-----VA-E-  475 (699)
T ss_dssp             EEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEEC-----SC-C-
T ss_pred             EEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEcc-----cc-c-
Confidence            799999999999999988764110 115777888887        55444433   33345689999995     33 2 


Q ss_pred             CCcCCCCceEEEE
Q 030094           70 DVLDFRNLEILVL   82 (183)
Q Consensus        70 ~~~~l~~l~~lVv   82 (183)
                      .++|+..+.++|.
T Consensus       476 ~GIDip~v~~VI~  488 (699)
T 4gl2_A          476 EGLDIKECNIVIR  488 (699)
T ss_dssp             TTSCCCSCCCCEE
T ss_pred             cCCccccCCEEEE
Confidence            5788888888873

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=82.41  E-value=4.8  Score=35.10  Aligned_cols=75  Identities=7%  Similarity=0.145  Sum_probs=52.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhh--CC-----------------------------CceEEEEEcCcchHHHHHH---
Q 030094            1 MGMIISPTRELSSQIYHVAQPFIST--LP-----------------------------DVKSVLLVGGVEVKADVKK---   46 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~--~~-----------------------------~~~~~~~~g~~~~~~~~~~---   46 (183)
                      .+||.||||+-+..+.+.+.+....  ++                             ...+..++|+.+..++...   
T Consensus       254 ~~LVF~~s~~~~~~~a~~L~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~l~~~~~~~v~~~h~~l~~~~r~~v~~~  333 (715)
T 2va8_A          254 QVLVFRNSRKMAESTALKIANYMNFVSLDENALSEILKQLDDIEEGGSDEKELLKSLISKGVAYHHAGLSKALRDLIEEG  333 (715)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHTTTSSCCCHHHHHHHHHHHHTCCSSCHHHHHHHHHHHTTTEEEECTTSCHHHHHHHHHH
T ss_pred             CEEEEECCHHHHHHHHHHHHHHHhhccCChHHHHHHHHHHHHhhhccccccHHHHHHHhcCEEEECCCCCHHHHHHHHHH
Confidence            4799999999999998888764321  00                             1247788888776555442   


Q ss_pred             HHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEEE
Q 030094           47 IEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILVL   82 (183)
Q Consensus        47 l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lVv   82 (183)
                      ..++..+|+|||.     .+.  .++|+..+.++|-
T Consensus       334 f~~g~~~vlvaT~-----~l~--~Gidip~~~~VI~  362 (715)
T 2va8_A          334 FRQRKIKVIVATP-----TLA--AGVNLPARTVIIG  362 (715)
T ss_dssp             HHTTCSCEEEECG-----GGG--GSSCCCBSEEEEC
T ss_pred             HHcCCCeEEEECh-----HHh--cccCCCceEEEEe
Confidence            3346789999995     343  4789888887663

>3kta_B Chromosome segregation protein SMC; structural maintenance of chromosomes, ABC ATPase, CFTR adenylate kinase, AP5A, transferase; HET: AP5; 1.63A {Pyrococcus furiosus} PDB: 1xew_Y 1xex_B*

Probab=82.04  E-value=1.3  Score=31.99  Aligned_cols=40  Identities=20%  Similarity=0.196  Sum_probs=33.0

Q ss_pred             CceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEee
Q 030094           76 NLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSA  115 (183)
Q Consensus        76 ~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SA  115 (183)
                      .-.++++||.+.-+|......+..+++.+.+..|+++.|-
T Consensus        86 ~~~~llLDEp~a~LD~~~~~~~~~~l~~~~~~~~~ivith  125 (173)
T 3kta_B           86 PAPFYLFDEIDAHLDDANVKRVADLIKESSKESQFIVITL  125 (173)
T ss_dssp             CCSEEEEESTTTTCCHHHHHHHHHHHHHHTTTSEEEEECS
T ss_pred             CCCEEEECCCccCCCHHHHHHHHHHHHHhccCCEEEEEEe
Confidence            3479999999999998888888888888777788877764

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=81.93  E-value=4.5  Score=34.37  Aligned_cols=77  Identities=10%  Similarity=0.125  Sum_probs=50.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhh---CCCceEEEEEcCcch--HHHHHHHHhcCCc---EEEeCcHHHHHHHHhcCCcC
Q 030094            2 GMIISPTRELSSQIYHVAQPFIST---LPDVKSVLLVGGVEV--KADVKKIEEEGAN---LLIGTPGRLYDIMERMDVLD   73 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~---~~~~~~~~~~g~~~~--~~~~~~l~~~~~~---IiV~TP~~l~~~l~~~~~~~   73 (183)
                      +||+|+|++-|..+++.+.+....   ..+-.+..+.|....  ++......+...+   |+|+|-     ++.  .++|
T Consensus       442 ~lVF~~~~~~a~~l~~~L~~~~~~~~~~~~~~~~~i~g~~~~~r~~~l~~F~~~~~~~~~ilvtt~-----~l~--~GiD  514 (590)
T 3h1t_A          442 TIVFCVDQEHADEMRRALNNLNSDLSRKHPDYVARVTSEEGKIGKGHLSRFQELETSTPVILTTSQ-----LLT--TGVD  514 (590)
T ss_dssp             EEEEESSHHHHHHHHHHHHHHTHHHHTTCTTSEEECSSTTHHHHHHHHHHHHCTTCCCCCEEEESS-----TTT--TTCC
T ss_pred             EEEEECCHHHHHHHHHHHHHhhhhhhccCCCeEEEEeCCChHHHHHHHHHHhCCCCCCCEEEEECC-----hhh--cCcc
Confidence            799999999999999999876431   112235555665442  2223333332233   888874     343  5799


Q ss_pred             CCCceEEEEccc
Q 030094           74 FRNLEILVLDEA   85 (183)
Q Consensus        74 l~~l~~lVvDEa   85 (183)
                      +..+..+|++..
T Consensus       515 ip~v~~Vi~~~~  526 (590)
T 3h1t_A          515 APTCKNVVLARV  526 (590)
T ss_dssp             CTTEEEEEEESC
T ss_pred             chheeEEEEEec
Confidence            999999998655

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=80.80  E-value=1.2  Score=38.73  Aligned_cols=77  Identities=21%  Similarity=0.286  Sum_probs=43.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEc--------CcchHHHHH---HHHh-cCCcEEEeCcHHHHHHHHhc
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVG--------GVEVKADVK---KIEE-EGANLLIGTPGRLYDIMERM   69 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g--------~~~~~~~~~---~l~~-~~~~IiV~TP~~l~~~l~~~   69 (183)
                      +||.|+|++-|..+++.+.... ..+.+++..+.|        +.+.+++..   .... +..+|+|||-     .. . 
T Consensus       401 ~IIF~~~~~~~~~l~~~L~~~~-~~~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~-----v~-~-  472 (696)
T 2ykg_A          401 TILFVKTRALVDALKNWIEGNP-KLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATS-----VA-D-  472 (696)
T ss_dssp             EEEECSCHHHHHHHHHHHHHCT-TCCSCCEEC-----------------------------CCSCSEEEE-----SS-C-
T ss_pred             EEEEeCcHHHHHHHHHHHHhCC-CccccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEec-----hh-h-
Confidence            7999999999999999888863 223477777765        444333332   3333 5689999995     22 2 


Q ss_pred             CCcCCCCceEEEEcccc
Q 030094           70 DVLDFRNLEILVLDEAD   86 (183)
Q Consensus        70 ~~~~l~~l~~lVvDEad   86 (183)
                      .++|+.++.++|.-+..
T Consensus       473 ~GiDip~v~~VI~~d~p  489 (696)
T 2ykg_A          473 EGIDIAQCNLVILYEYV  489 (696)
T ss_dssp             CC---CCCSEEEEESCC
T ss_pred             cCCcCccCCEEEEeCCC
Confidence            57999999998864443

>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=80.19  E-value=1  Score=37.36  Aligned_cols=67  Identities=15%  Similarity=0.117  Sum_probs=45.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||.|||++-|..+++.+++.     ++++..+.|... ........++..+|+|||-     .+.  .++|+.. .++
T Consensus       192 ~~LVF~~s~~~~~~l~~~L~~~-----g~~v~~lh~~~R-~~~~~~f~~g~~~iLVaT~-----v~~--~GiDip~-~~V  257 (459)
T 2z83_A          192 KTVWFVASVKMGNEIAMCLQRA-----GKKVIQLNRKSY-DTEYPKCKNGDWDFVITTD-----ISE--MGANFGA-SRV  257 (459)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHT-----TCCEEEESTTCC-CCCGGGSSSCCCSEEEESS-----CC-----CCCSC-SEE
T ss_pred             CEEEEeCChHHHHHHHHHHHhc-----CCcEEecCHHHH-HHHHhhccCCCceEEEECC-----hHH--hCeecCC-CEE
Confidence            3799999999999998888775     567777777432 2222233346789999995     333  4688777 655


Q ss_pred             E
Q 030094           81 V   81 (183)
Q Consensus        81 V   81 (183)
                      |
T Consensus       258 I  258 (459)
T 2z83_A          258 I  258 (459)
T ss_dssp             E
T ss_pred             E
Confidence            5

>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=80.06  E-value=2  Score=35.81  Aligned_cols=76  Identities=22%  Similarity=0.354  Sum_probs=35.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEc--------CcchHHHH---HHHHh-cCCcEEEeCcHHHHHHHHhc
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVG--------GVEVKADV---KKIEE-EGANLLIGTPGRLYDIMERM   69 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g--------~~~~~~~~---~~l~~-~~~~IiV~TP~~l~~~l~~~   69 (183)
                      +||.|++++-+..+.+.+.+... .+.+++..+.|        +.+.+++.   ..... +..+|+|||.     .+.  
T Consensus       393 ~lVF~~~~~~~~~l~~~L~~~~~-~~~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~-----~~~--  464 (556)
T 4a2p_A          393 TLLFAKTRALVSALKKCMEENPI-LNYIKPGVLMGRGRRDQTTGMTLPSQKGVLDAFKTSKDNRLLIATS-----VAD--  464 (556)
T ss_dssp             EEEEESSHHHHHHHHHHHTTCSG-GGSCCEEC------------------------------CCEEEEEC----------
T ss_pred             EEEEEccHHHHHHHHHHHHhCCC-cceeeeeEEEccCCcccccccCHHHHHHHHHHhcccCceEEEEEcC-----chh--
Confidence            79999999999999998877521 12445554444        33332222   23334 5689999995     333  


Q ss_pred             CCcCCCCceEEEEccc
Q 030094           70 DVLDFRNLEILVLDEA   85 (183)
Q Consensus        70 ~~~~l~~l~~lVvDEa   85 (183)
                      .++|+..+.++|.=+.
T Consensus       465 ~GiDip~v~~VI~~d~  480 (556)
T 4a2p_A          465 EGIDIVQCNLVVLYEY  480 (556)
T ss_dssp             --------CEEEEETC
T ss_pred             cCCCchhCCEEEEeCC
Confidence            5799999999886444

---

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	183
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	1e-33
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	2e-24
d1qdea_	212	c.37.1.19 (A:) Initiation factor 4a {Baker's yeast	3e-23
d2g9na1	218	c.37.1.19 (A:21-238) Initiation factor 4a {Human (	7e-22
d2j0sa1	222	c.37.1.19 (A:22-243) Probable ATP-dependent RNA he	1e-20
d1veca_	206	c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Huma	2e-17
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	3e-16
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	1e-15
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	7e-14
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	4e-11
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	4e-08
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	2e-07
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	2e-06
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	9e-06

>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 =  116 bits (292), Expect = 1e-33
 Identities = 37/138 (26%), Positives = 70/138 (50%), Gaps = 3/138 (2%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +  II       +         +    ++K   + GG  +   +K ++   AN+++GTPG
Sbjct: 73  IEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK--NANIVVGTPG 130

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           R+ D + R   L+ +N++  +LDEAD +L+MGF K +  I++   K +R  LFSAT    
Sbjct: 131 RILDHINR-GTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPRE 189

Query: 121 VEELSKAGLRNPVRVEVR 138
           +  L+K  + +   ++ +
Sbjct: 190 ILNLAKKYMGDYSFIKAK 207

>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 = 93.0 bits (230), Expect = 2e-24
 Identities = 33/136 (24%), Positives = 79/136 (58%), Gaps = 2/136 (1%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR+
Sbjct: 73  LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 132

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
             +      L+ ++++  +LDE D++L+ +  ++ +  I    P  ++  +FSAT ++ +
Sbjct: 133 LALARNK-SLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEI 191

Query: 122 EELSKAGLRNPVRVEV 137
             + +  +++P+ + V
Sbjct: 192 RPVCRKFMQDPMEIFV 207

>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 = 89.9 bits (222), Expect = 3e-23
 Identities = 33/88 (37%), Positives = 53/88 (60%), Gaps = 1/88 (1%)

Query: 50  EGANLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRR 109
             A +++GTPGR++D ++R        +++ +LDEAD +L  GF++QI  I + LP   +
Sbjct: 126 RDAQIVVGTPGRVFDNIQRR-RFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQ 184

Query: 110 TGLFSATQTEAVEELSKAGLRNPVRVEV 137
             L SAT    V E++   +RNPVR+ V
Sbjct: 185 VVLLSATMPNDVLEVTTKFMRNPVRILV 212

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]} Length = 218

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 86.4 bits (213), Expect = 7e-22
 Identities = 47/137 (34%), Positives = 81/137 (59%), Gaps = 2/137 (1%)

Query: 2   GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V                +GG  V+A+V+K++ E  ++++GTPGR
Sbjct: 83  ALVLAPTRELAQQIQKVVMALGDY-MGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGR 141

Query: 62  LYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           ++D++ R   L  + +++ VLDEAD +L  GF+ QI  I  +L    +  L SAT    V
Sbjct: 142 VFDMLNRRY-LSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDV 200

Query: 122 EELSKAGLRNPVRVEVR 138
            E++K  +R+P+R+ V+
Sbjct: 201 LEVTKKFMRDPIRILVK 217

>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 = 83.4 bits (205), Expect = 1e-20
 Identities = 47/138 (34%), Positives = 80/138 (57%), Gaps = 3/138 (2%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             +I++PTREL+ QI            +V+    +GG  V  D++K++  G +++ GTPG
Sbjct: 87  QALILAPTRELAVQIQKGLLAL-GDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGTPG 144

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           R++D M R   L  R +++LVLDEAD +L+ GF++QI  +   LP   +  L SAT    
Sbjct: 145 RVFD-MIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHE 203

Query: 121 VEELSKAGLRNPVRVEVR 138
           + E++   + +P+R+ V+
Sbjct: 204 ILEMTNKFMTDPIRILVK 221

>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 = 74.2 bits (181), Expect = 2e-17
 Identities = 40/135 (29%), Positives = 74/135 (54%), Gaps = 2/135 (1%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             M+I PTREL+ Q+  +       +   K +   GG  ++ D+ ++++    + I TPG
Sbjct: 73  QAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVV-IATPG 131

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           R+ D++++       +++++VLDEAD+LL   F + +  II  LPK R+  L+SAT   +
Sbjct: 132 RILDLIKKGV-AKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLS 190

Query: 121 VEELSKAGLRNPVRV 135
           V++   + L  P  +
Sbjct: 191 VQKFMNSHLEKPYEI 205

>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 = 71.9 bits (175), Expect = 3e-16
 Identities = 50/139 (35%), Positives = 84/139 (60%), Gaps = 7/139 (5%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTREL+ QI   +Q F    P ++S ++ GG +  + +++++  G +LL+ TPGRL
Sbjct: 102 LILAPTRELAIQILSESQKFSLNTP-LRSCVVYGGADTHSQIREVQM-GCHLLVATPGRL 159

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRL----PKLRRTGLFSATQT 118
            D +E+   +     + +VLDEADR+LDMGF+ QI  II          R+T +FSAT  
Sbjct: 160 VDFIEKN-KISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFP 218

Query: 119 EAVEELSKAGLRNPVRVEV 137
           + +++L+   L N + + V
Sbjct: 219 KEIQKLAADFLYNYIFMTV 237

>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 = 69.2 bits (168), Expect = 1e-15
 Identities = 28/85 (32%), Positives = 45/85 (52%), Gaps = 1/85 (1%)

Query: 53  NLLIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGL 112
           ++L+GTPGR    +    V D  +  + ++DEAD++L   F+  I  I+S LP   ++ L
Sbjct: 121 HILVGTPGR-VLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLL 179

Query: 113 FSATQTEAVEELSKAGLRNPVRVEV 137
           FSAT    V+E     L  P  + +
Sbjct: 180 FSATFPLTVKEFMVKHLHKPYEINL 204

>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 = 64.7 bits (156), Expect = 7e-14
 Identities = 29/83 (34%), Positives = 42/83 (50%)

Query: 55  LIGTPGRLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFS 114
           ++       +   R   LD     ILV+DEAD +LDMGF   +  I +R+PK  +  +FS
Sbjct: 126 IVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFS 185

Query: 115 ATQTEAVEELSKAGLRNPVRVEV 137
           AT  E ++   K  + NP  V V
Sbjct: 186 ATIPEKLKPFLKKYMENPTFVHV 208

>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 = 57.6 bits (138), Expect = 4e-11
 Identities = 15/137 (10%), Positives = 38/137 (27%), Gaps = 20/137 (14%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLP----DVKSVLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I PT  L  Q     + +         ++         + + +          ++I T
Sbjct: 90  YVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITT 149

Query: 59  PGRLYDIMERMDVLDFRNLEILVLDEADRLLD-----------MGFQKQISYIISRLPKL 107
              L          +  + + + +D+ D +L            +GF   +          
Sbjct: 150 TQFLSK-----HYRELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEAR 204

Query: 108 RRTGLFSATQTEAVEEL 124
               + +AT  +  +  
Sbjct: 205 GCLMVSTATAKKGKKAE 221

>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 = 49.5 bits (117), Expect = 4e-08
 Identities = 10/123 (8%), Positives = 36/123 (29%), Gaps = 15/123 (12%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTR +++++              +++  +        ++        + +      
Sbjct: 42  LILAPTRVVAAEME-------------EALRGLPIRYQTPAIRAEHTGREIVDLMCHATF 88

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
              +     +   N  ++++DEA          +                 +AT   + +
Sbjct: 89  TMRLLSP--IRVPNYNLIIMDEAHFTDPASIAARGYISTRVEMGEAAGIFMTATPPGSRD 146

Query: 123 ELS 125
              
Sbjct: 147 PFP 149

>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 = 46.9 bits (110), Expect = 2e-07
 Identities = 25/138 (18%), Positives = 44/138 (31%), Gaps = 11/138 (7%)

Query: 3   MIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +++SP   L        Q        + S       +    +         LL   P RL
Sbjct: 69  VVVSPLISLMKDQVDQLQANGVAAACLNSTQTRE--QQLEVMTGCRTGQIRLLYIAPERL 126

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISY-----IISRLPKLRRTGLFSATQ 117
                 ++ L   N  +L +DEA  +   G   +  Y     +  R P        +AT 
Sbjct: 127 ML-DNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPT-LPFMALTATA 184

Query: 118 TEAVEE--LSKAGLRNPV 133
            +   +  +   GL +P+
Sbjct: 185 DDTTRQDIVRLLGLNDPL 202

>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 = 44.0 bits (102), Expect = 2e-06
 Identities = 13/81 (16%), Positives = 29/81 (35%), Gaps = 1/81 (1%)

Query: 63  YDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            +       +   ++ ++V DEA R +       I+    R  K       +A+     E
Sbjct: 112 IENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPE 171

Query: 123 ELSK-AGLRNPVRVEVRAESK 142
           ++ +         +E R+E+ 
Sbjct: 172 KIMEVINNLGIEHIEYRSENS 192

>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 = 42.3 bits (98), Expect = 9e-06
 Identities = 18/129 (13%), Positives = 48/129 (37%), Gaps = 11/129 (8%)

Query: 1   MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             + + P R L+ + Y   + +       K  L +G      + +       ++++ T  
Sbjct: 70  KSLYVVPLRALAGEKYESFKKWE------KIGLRIGISTGDYESRDEHLGDCDIIVTTSE 123

Query: 61  RLYDIMERMDVLDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKL---RRTGLFSATQ 117
           +   ++        + +  LV+DE   L        +  +++++ ++    R    SAT 
Sbjct: 124 KADSLIRNRA-SWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATA 182

Query: 118 TEAVEELSK 126
                E+++
Sbjct: 183 PNV-TEIAE 190

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	183
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	100.0
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	100.0
d2g9na1	218	Initiation factor 4a {Human (Homo sapiens) [TaxId:	99.97
d1hv8a1	208	Putative DEAD box RNA helicase {Archaeon Methanoco	99.97
d1qdea_	212	Initiation factor 4a {Baker's yeast (Saccharomyces	99.97
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.97
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.96
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.92
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.66
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.65
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.63
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.55
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.37
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.33
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.3
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.05
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.02
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.92
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.73
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	97.93
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	97.19
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	96.78
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	96.78
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	96.51
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	96.5
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	96.48
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	96.32
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	96.09
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	95.71
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	95.71
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	95.52
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	95.42
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	94.99
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	93.17
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	92.82
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	91.9
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	90.83
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	90.59
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	90.53
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	89.26
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	87.22
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	85.87
d1w36d1	359	Exodeoxyribonuclease V alpha chain (RecD) {Escheri	85.14
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	80.36

>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=2.9e-34  Score=220.17  Aligned_cols=135  Identities=34%  Similarity=0.601  Sum_probs=127.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +|+|++||||||.|+++.+.+++++. ++++..++||....++...+ +.++||+||||+|+.+++.. +.+++++++++
T Consensus        87 ~~lil~PtreLa~Qi~~~~~~l~~~~-~i~~~~~~g~~~~~~~~~~l-~~~~~Ilv~TPgrl~~~~~~-~~~~~~~l~~l  163 (222)
T d2j0sa1          87 QALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKL-DYGQHVVAGTPGRVFDMIRR-RSLRTRAIKML  163 (222)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHH-HHCCSEEEECHHHHHHHHHT-TSSCCTTCCEE
T ss_pred             eeEEecchHHHHHHHHHHHHHHhCcc-ceeEEEEeecccchhhHHHh-ccCCeEEeCCCCcHHhcccc-cccccccceee
Confidence            58999999999999999999998876 89999999999988888887 46899999999999999988 88999999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVR  138 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~  138 (183)
                      |+||||.|++.+|.+++..|++.+|+++|+++||||++++++++++.++++|+.|.+.
T Consensus       164 VlDEaD~ll~~~f~~~i~~I~~~l~~~~Q~ilfSAT~~~~v~~l~~~~l~~Pv~I~V~  221 (222)
T d2j0sa1         164 VLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEILEMTNKFMTDPIRILVK  221 (222)
T ss_dssp             EEETHHHHTSTTTHHHHHHHHTTSCTTCEEEEEESCCCHHHHTTGGGTCSSCEEECCC
T ss_pred             eecchhHhhhcCcHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEEe
Confidence            9999999999999999999999999999999999999999999999999999998764

>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=1.7e-32  Score=208.24  Aligned_cols=136  Identities=24%  Similarity=0.527  Sum_probs=127.7

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +++|++||||||.|+++.++.++.+.+.+++..+.|+.....+...+...+|||+||||+++.+++++ +.+++++++++
T Consensus        71 ~~lil~PtreL~~qi~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~ilI~TP~rl~~~~~~-~~~~l~~l~~l  149 (207)
T d1t6na_          71 SVLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRILALARN-KSLNLKHIKHF  149 (207)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHTTTSTTCCEEEESCCSCHHHHHHHHHHSCCSEEEECHHHHHHHHHT-TSSCCTTCCEE
T ss_pred             eEEEEeccchhhHHHHHHHHHHHhhCCCceeEEEeccccHHHHHHHHHhcCCCEEEeCcchhhhhccC-Cceecccccee
Confidence            48999999999999999999999888778899999999988888888778999999999999999998 88999999999


Q ss_pred             EEcccchhhcc-chHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEE
Q 030094           81 VLDEADRLLDM-GFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEV  137 (183)
Q Consensus        81 VvDEad~ll~~-~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~  137 (183)
                      |+||||.|++. +|.++++.|++.+|+++|+++||||++++++++++.+++||+.|.+
T Consensus       150 VlDEaD~ll~~~~~~~~i~~I~~~~~~~~Q~il~SAT~~~~v~~l~~~~l~~P~~I~V  207 (207)
T d1t6na_         150 ILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEIRPVCRKFMQDPMEIFV  207 (207)
T ss_dssp             EEESHHHHHSSHHHHHHHHHHHHTSCSSSEEEEEESCCCTTTHHHHHTTCSSCEEEEC
T ss_pred             ehhhhhhhhhcCCcHHHHHHHHHhCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEeC
Confidence            99999999984 8999999999999999999999999999999999999999998864

>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=2.1e-32  Score=207.50  Aligned_cols=133  Identities=31%  Similarity=0.564  Sum_probs=124.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +++|++||||||.|+++++.++.+...++.+....|+.....+...+ ..++||+||||+++.+++.. +.+++++++++
T Consensus        73 ~~lil~pt~el~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~l-~~~~~ivv~TPgrl~~~~~~-~~~~~~~l~~l  150 (206)
T d1veca_          73 QAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRL-DDTVHVVIATPGRILDLIKK-GVAKVDHVQMI  150 (206)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHT-TSCCSEEEECHHHHHHHHHT-TCSCCTTCCEE
T ss_pred             ceEEEeecchhhHHHHHHHHHHhhcccCcccccccCCccHHHHHHHH-HhccCeEEeCCccccccccc-hhccccccceE
Confidence            48999999999999999999998877778888888888888777776 57899999999999999988 88999999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEE
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRV  135 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i  135 (183)
                      |+||||.|++.+|.+++..|++.+|+++|+++||||++++++++++.+|++|+.|
T Consensus       151 VlDEaD~ll~~~f~~~i~~I~~~~~~~~Q~~l~SAT~~~~v~~l~~~~l~~P~~I  205 (206)
T d1veca_         151 VLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             EEETHHHHTSTTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             EEeccccccccchHHHHHHHHHhCCCCCEEEEEEecCCHHHHHHHHHHCCCCEEE
Confidence            9999999999999999999999999999999999999999999999999999887

>d2g9na1 c.37.1.19 (A:21-238) Initiation factor 4a {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=2.8e-32  Score=208.59  Aligned_cols=136  Identities=35%  Similarity=0.613  Sum_probs=123.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +|||++||||||.|+++.+.++.+.. +.+...+.++....++.......++||+||||+++.+++.+ +...+++++++
T Consensus        82 ~alil~Pt~eL~~Q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~IvV~TP~rl~~~l~~-~~~~~~~l~~l  159 (218)
T d2g9na1          82 QALVLAPTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGRVFDMLNR-RYLSPKYIKMF  159 (218)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHTTT-TCCEEEECC--CCCSTTTSSSSCCCSEEEECHHHHHHHHHT-TSSCSTTCCEE
T ss_pred             cEEEEcccchhhhhHHHHHhhhcccc-ceeEEeeecccchhHHHHHHhcCCCEEEEeCChhHHHHHhc-CCcccccceEE
Confidence            58999999999999999999999887 78888888877766655555456899999999999999988 88899999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVR  138 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~  138 (183)
                      |+||||.|++.+|.+++..|++.+|+++|+++||||++++++++++.|+++|+.|.+.
T Consensus       160 VlDEaD~ll~~~f~~~~~~Il~~~~~~~Q~il~SAT~~~~v~~~~~~~l~~pv~i~v~  217 (218)
T d2g9na1         160 VLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDVLEVTKKFMRDPIRILVK  217 (218)
T ss_dssp             EEESHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEEECC
T ss_pred             EeeecchhhcCchHHHHHHHHHhCCCCCeEEEEEecCCHHHHHHHHHHCCCCEEEEEe
Confidence            9999999999999999999999999999999999999999999999999999999875

>d1hv8a1 c.37.1.19 (A:3-210) Putative DEAD box RNA helicase {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative DEAD box RNA helicase
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=99.97  E-value=2.2e-31  Score=202.10  Aligned_cols=133  Identities=32%  Similarity=0.552  Sum_probs=124.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      ++||++||++||.|+++.++++..+. +.++....|+.+..++.+.+  .+|||+||||+++.+++++ +.+++++++++
T Consensus        74 ~~lil~pt~~l~~q~~~~~~~~~~~~-~~~v~~~~g~~~~~~~~~~l--~~~~IlV~TP~~l~~~l~~-~~~~~~~l~~l  149 (208)
T d1hv8a1          74 EAIILTPTRELAIQVADEIESLKGNK-NLKIAKIYGGKAIYPQIKAL--KNANIVVGTPGRILDHINR-GTLNLKNVKYF  149 (208)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHHCSS-CCCEEEECTTSCHHHHHHHH--HTCSEEEECHHHHHHHHHT-TCSCTTSCCEE
T ss_pred             ceEEEeeccccchhhhhhhhhhcccC-CeEEEEeeCCCChHHHHHhc--CCCCEEEEChHHHHHHHHc-CCCCcccCcEE
Confidence            58999999999999999999998776 88999999999888887766  3799999999999999988 88999999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEE
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEV  137 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~  137 (183)
                      |+||||.|++.++.+++..|++.+++++|+++||||+++++.+++++|++||..|.+
T Consensus       150 ViDEad~l~~~~~~~~i~~I~~~~~~~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~~  206 (208)
T d1hv8a1         150 ILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKA  206 (208)
T ss_dssp             EEETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEEC
T ss_pred             EEEChHHhhcCCChHHHHHHHHhCCCCCeEEEEEccCCHHHHHHHHHHCCCCeEEEE
Confidence            999999999999999999999999999999999999999999999999999999875

>d1qdea_ c.37.1.19 (A:) Initiation factor 4a {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Initiation factor 4a
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.97  E-value=9e-31  Score=199.31  Aligned_cols=133  Identities=35%  Similarity=0.592  Sum_probs=115.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +++|++||||||.|++..+..+.... .+++....|+....++...+  .+|||+||||+++.+++.. +.+++++++++
T Consensus        80 ~~lil~pt~el~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~--~~~~IvI~TP~~l~~~~~~-~~~~l~~l~~l  155 (212)
T d1qdea_          80 QALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGL--RDAQIVVGTPGRVFDNIQR-RRFRTDKIKMF  155 (212)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTS-CCCEEEECC----------C--TTCSEEEECHHHHHHHHHT-TSSCCTTCCEE
T ss_pred             ceEEEcccHHHhhhhhhhhccccccc-ccceeeEeeccchhHHHHHh--cCCcEEEECCCcccccccc-CceecCcceEE
Confidence            58999999999999999999998776 78888888888877776665  4799999999999999988 88999999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEE
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEV  137 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~  137 (183)
                      |+||||.|++.+|.+++..|++.+++++|+++||||++++++++++.+++||+.|.+
T Consensus       156 VlDEad~lld~~f~~~v~~I~~~~~~~~Q~vl~SAT~~~~v~~l~~~~l~~Pv~i~v  212 (212)
T d1qdea_         156 ILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDVLEVTTKFMRNPVRILV  212 (212)
T ss_dssp             EEETHHHHHHTTCHHHHHHHHHHSCTTCEEEEEESSCCHHHHHHHHHHCSSCEEEC-
T ss_pred             eehhhhhhcccchHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHHCCCCEEEeC
Confidence            999999999999999999999999999999999999999999999999999998854

>d1wrba1 c.37.1.19 (A:164-401) putative ATP-dependent RNA helicase VlgB {Flatworm (Dugesia japonica) [TaxId: 6161]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase VlgB
species: Flatworm (Dugesia japonica) [TaxId: 6161]

Probab=99.97  E-value=2.3e-30  Score=200.23  Aligned_cols=135  Identities=36%  Similarity=0.579  Sum_probs=124.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      +|||++||||||.|+++.+..++.+. ++++..+.|+.....+.+.. ..++||+||||++|.++++. +.+++++++++
T Consensus       100 ~alil~pt~el~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~-~~~~~ivV~TP~~l~~~~~~-~~~~l~~v~~l  176 (238)
T d1wrba1         100 KCLILAPTRELAIQILSESQKFSLNT-PLRSCVVYGGADTHSQIREV-QMGCHLLVATPGRLVDFIEK-NKISLEFCKYI  176 (238)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHHHTTS-SCCEEEECSSSCSHHHHHHH-SSCCSEEEECHHHHHHHHHT-TSBCCTTCCEE
T ss_pred             eEEEeccchhhhcchheeeeecccCC-CcEEEEEeccchhhHHHhhc-ccCCceeecCHHHHHhHHcc-Cceecccccee
Confidence            58999999999999999999998887 79999999999888887766 56899999999999999988 88999999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCC----CCCeEEEEeecCChHHHHHHHhhCCCCeEEEEc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLP----KLRRTGLFSATQTEAVEELSKAGLRNPVRVEVR  138 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~----~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~  138 (183)
                      |+||||.|++.+|.+++..|++.+.    .++|+++||||++++++++++.||++|++|.++
T Consensus       177 ViDEaD~ll~~~f~~~i~~Il~~~~~~~~~~~Q~il~SAT~~~~v~~l~~~~~~~p~~i~vg  238 (238)
T d1wrba1         177 VLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVG  238 (238)
T ss_dssp             EEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC
T ss_pred             eeehhhhhhhhccHHHHHHHHHHhcCCCCCCCEEEEEeeeCCHHHHHHHHHHCCCCEEEEeC
Confidence            9999999999999999999999764    367999999999999999999999999999764

>d1s2ma1 c.37.1.19 (A:46-251) Putative ATP-dependent RNA helicase DHH1 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Putative ATP-dependent RNA helicase DHH1
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.96  E-value=2.3e-29  Score=190.48  Aligned_cols=135  Identities=31%  Similarity=0.559  Sum_probs=126.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+++++|+++++.|.+..+..+.... ++++....|+.....+...+ ..+|||+||||++|.++++. +.+++++++++
T Consensus        71 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~l-~~~~~Ili~TP~~l~~~l~~-~~~~l~~l~~l  147 (206)
T d1s2ma1          71 QALIMVPTRELALQTSQVVRTLGKHC-GISCMVTTGGTNLRDDILRL-NETVHILVGTPGRVLDLASR-KVADLSDCSLF  147 (206)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECSSSCHHHHHHHT-TSCCSEEEECHHHHHHHHHT-TCSCCTTCCEE
T ss_pred             cceeeccchhhhhhhhhhhhhccccc-CeeEEeecCccchhhHHHHh-cccceEEEECCccccccccc-ceeecccceEE
Confidence            47899999999999999999997765 89999999999988887776 57899999999999999998 88999999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEEc
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEVR  138 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~~  138 (183)
                      |+||||.|++.+|.+++..|++.+++++|+++||||+++++.+++++|+++|+.|.+.
T Consensus       148 V~DEaD~l~~~~f~~~v~~I~~~l~~~~Q~il~SATl~~~v~~~~~~~l~~P~~I~~~  205 (206)
T d1s2ma1         148 IMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTVKEFMVKHLHKPYEINLM  205 (206)
T ss_dssp             EEESHHHHSSHHHHHHHHHHHTTSCSSCEEEEEESCCCHHHHHHHHHHCSSCEEESCC
T ss_pred             EeechhhhhhhhhHHHHHHHHHhCCCCCEEEEEEEeCCHHHHHHHHHHCCCCEEEEee
Confidence            9999999999999999999999999999999999999999999999999999998764

>d1q0ua_ c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR {Bacillus stearothermophilus [TaxId: 1422]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Probable DEAD box RNA helicase YqfR
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=99.92  E-value=4.5e-25  Score=166.59  Aligned_cols=134  Identities=37%  Similarity=0.585  Sum_probs=117.5

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhC---CCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTL---PDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~---~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      .++++|+++++.+.+..+....+..   ....+..+.|+.+...+.... ..+|||+||||+++..++.+ +...+++++
T Consensus        72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~Ilv~TP~~l~~~~~~-~~~~~~~l~  149 (209)
T d1q0ua_          72 AVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKL-NVQPHIVIGTPGRINDFIRE-QALDVHTAH  149 (209)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHTTSCGGGCCCEEEECCCSHHHHTTCCC-SSCCSEEEECHHHHHHHHHT-TCCCGGGCC
T ss_pred             ccccccccchhHHHHHHHHhhhccccccccccccccccchhhHHHHHHh-ccCceEEEecCchhhhhhhh-hccccccce
Confidence            5789999999999999888876643   235666667776666554444 46899999999999999988 788899999


Q ss_pred             EEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEEEE
Q 030094           79 ILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRVEV  137 (183)
Q Consensus        79 ~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i~~  137 (183)
                      ++|+||||.+++.+|.+++..|++.+++++|+++||||++++++++++.++++|+.|.+
T Consensus       150 ~lViDEad~ll~~~f~~~v~~I~~~~~~~~Q~il~SATl~~~v~~l~~~~l~~p~~i~V  208 (209)
T d1q0ua_         150 ILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSATIPEKLKPFLKKYMENPTFVHV  208 (209)
T ss_dssp             EEEECSHHHHHHTTCHHHHHHHHHTSCTTCEEEEEESCCCGGGHHHHHHHCSSCEEEEC
T ss_pred             EEEEeecccccccccHHHHHHHHHHCCCCCEEEEEEccCCHHHHHHHHHHCCCCEEEEe
Confidence            99999999999999999999999999999999999999999999999999999999875

>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=99.66  E-value=8.5e-16  Score=113.85  Aligned_cols=136  Identities=18%  Similarity=0.165  Sum_probs=101.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+++++||++|+.|.++.+.++.... +.++....++.........+  ..++++++||+++...+.. ..+.+++++++
T Consensus        54 ~il~i~P~~~L~~q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~--~~~~i~i~t~~~~~~~~~~-~~~~~~~~~~v  129 (200)
T d1wp9a1          54 KVLMLAPTKPLVLQHAESFRRLFNLP-PEKIVALTGEKSPEERSKAW--ARAKVIVATPQTIENDLLA-GRISLEDVSLI  129 (200)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHBCSC-GGGEEEECSCSCHHHHHHHH--HHCSEEEECHHHHHHHHHT-TSCCTTSCSEE
T ss_pred             cEEEEcCchHHHHHHHHHHHHhhccc-ccceeeeecccchhHHHHhh--hcccccccccchhHHHHhh-hhhhccccceE
Confidence            37899999999999999999997654 78887777766665554444  3479999999999999887 77889999999


Q ss_pred             EEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhC-CCCeEEEEccC
Q 030094           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGL-RNPVRVEVRAE  140 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~-~~~~~i~~~~~  140 (183)
                      |+||||.+.+......+...+....+.++.+++|||+......+....- .+...|.+..+
T Consensus       130 IiDE~H~~~~~~~~~~~~~~~~~~~~~~~~l~~SATp~~~~~~~~~~~~~l~~~~i~~~~~  190 (200)
T d1wp9a1         130 VFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSE  190 (200)
T ss_dssp             EEETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEESCSCSSHHHHHHHHHHTTCCEEEECCT
T ss_pred             EEEehhhhhcchhHHHHHHHHHhcCCCCcEEEEEecCCCcHHHHHHHHhcCCceEEEeCCC
Confidence            9999999876554444444444445678999999998765555443321 13456665555

>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=99.65  E-value=1.8e-17  Score=126.68  Aligned_cols=115  Identities=13%  Similarity=0.128  Sum_probs=79.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCce----EEEEEcCcchHHHHHHHH-hcCCcEEEeCcHHHHHHHHhcCCcCCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVK----SVLLVGGVEVKADVKKIE-EEGANLLIGTPGRLYDIMERMDVLDFR   75 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~----~~~~~g~~~~~~~~~~l~-~~~~~IiV~TP~~l~~~l~~~~~~~l~   75 (183)
                      .+||++||++|+.|+++.++++.++. +++    .....++.....+.+.+. ..+++|+|+||++|.+.     ..+++
T Consensus        88 rvliv~Pt~~La~Q~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~~-----~~~~~  161 (237)
T d1gkub1          88 RCYVIFPTSLLVIQAAETIRKYAEKA-GVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSKH-----YRELG  161 (237)
T ss_dssp             CEEEEESCHHHHHHHHHHHHHHHTTT-CCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHHC-----STTSC
T ss_pred             eEEEEeccHHHHHHHHHHHHHHHHHc-CCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHHh-----hhhcC
Confidence            37999999999999999999998765 433    333334444443333332 34689999999987543     33567


Q ss_pred             CceEEEEcccchhhccchHHHHHHHHHh-------------CCCCCeEEEEeecCChHHHH
Q 030094           76 NLEILVLDEADRLLDMGFQKQISYIISR-------------LPKLRRTGLFSATQTEAVEE  123 (183)
Q Consensus        76 ~l~~lVvDEad~ll~~~~~~~l~~i~~~-------------l~~~~Q~v~~SAT~~~~v~~  123 (183)
                      +++++|+||+|.+++.+..  +..+...             .+...|++++|||+++..+.
T Consensus       162 ~~~~vVvDE~d~~l~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~  220 (237)
T d1gkub1         162 HFDFIFVDDVDAILKASKN--VDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAKKGKKA  220 (237)
T ss_dssp             CCSEEEESCHHHHHTSTHH--HHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSCCCTTH
T ss_pred             CCCEEEEEChhhhhhcccc--hhHHHHhcCChHHHHHHHhhCCCCCeEEEEeCCCCcccHH
Confidence            8999999999999875422  2222222             24567999999999876544

>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=99.63  E-value=8.2e-16  Score=114.56  Aligned_cols=125  Identities=18%  Similarity=0.244  Sum_probs=93.0

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +|+++||++|+.|.++.++++...  ..++....|+......    ...+++|+++||..+..++.+ ....+.+++++|
T Consensus        71 vl~l~P~~~L~~q~~~~~~~~~~~--~~~v~~~~~~~~~~~~----~~~~~~ii~~~~~~~~~~~~~-~~~~~~~~~~ii  143 (202)
T d2p6ra3          71 SLYVVPLRALAGEKYESFKKWEKI--GLRIGISTGDYESRDE----HLGDCDIIVTTSEKADSLIRN-RASWIKAVSCLV  143 (202)
T ss_dssp             EEEEESSHHHHHHHHHHHTTTTTT--TCCEEEECSSCBCCSS----CSTTCSEEEEEHHHHHHHHHT-TCSGGGGCCEEE
T ss_pred             ceeecccHHHHHHHHHHHHHHhhc--cccceeeccCcccccc----cccccceeeeccHHHHHHHhc-cchhhhhhhhcc
Confidence            799999999999999999888654  3455556665443221    125789999999999999887 667788999999


Q ss_pred             EcccchhhccchHHHHHHHH---HhCCCCCeEEEEeecCChHHHHHHHhhCCCCeEE
Q 030094           82 LDEADRLLDMGFQKQISYII---SRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRV  135 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~---~~l~~~~Q~v~~SAT~~~~v~~~~~~~~~~~~~i  135 (183)
                      +||+|.+.+..+......++   +..++..|++++|||+++ .+++++ |+..+.++
T Consensus       144 ~DE~h~~~~~~r~~~~~~~l~~i~~~~~~~~~l~lSATl~n-~~~~~~-~l~~~~~~  198 (202)
T d2p6ra3         144 VDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAE-WLDADYYV  198 (202)
T ss_dssp             ETTGGGGGCTTTHHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHHH-HTTCEEEE
T ss_pred             ccHHHHhcccccchHHHHHHHHHHhcCCCCcEEEEcCCCCc-HHHHHH-HcCCCeee
Confidence            99999998765544444443   444678999999999976 477764 45444433

>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=99.55  E-value=1.8e-15  Score=112.92  Aligned_cols=125  Identities=18%  Similarity=0.168  Sum_probs=87.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcc---hHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVE---VKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~---~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +++++|+++|+.|..+.++....     ......+...   ............++|+++||.++...... .....++++
T Consensus        68 ~~~v~P~~~L~~q~~~~l~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~t~~~~~~~~~~-~~~~~~~v~  141 (206)
T d1oywa2          68 TVVVSPLISLMKDQVDQLQANGV-----AAACLNSTQTREQQLEVMTGCRTGQIRLLYIAPERLMLDNFL-EHLAHWNPV  141 (206)
T ss_dssp             EEEECSCHHHHHHHHHHHHHTTC-----CEEEECTTSCHHHHHHHHHHHHHTCCSEEEECHHHHTSTTHH-HHHTTSCEE
T ss_pred             eEEeccchhhhhhHHHHHHhhcc-----cccccccccccccchhHHHHHhcCCceEEEEechhhhchhhc-ccchhheee
Confidence            68999999999999998887742     2222222222   22222233346799999999988665544 456678899


Q ss_pred             EEEEcccchhhccch--H---HHHHHHHHhCCCCCeEEEEeecCChHHHH-HHHh-hCCCCe
Q 030094           79 ILVLDEADRLLDMGF--Q---KQISYIISRLPKLRRTGLFSATQTEAVEE-LSKA-GLRNPV  133 (183)
Q Consensus        79 ~lVvDEad~ll~~~~--~---~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~-~~~~-~~~~~~  133 (183)
                      ++|+||||.+.+.++  .   ..+..+.+.+ +++|++++|||+++++.+ +++. .+.+|+
T Consensus       142 ~lviDEaH~~~~~~~~~~~~~~~~~~l~~~~-~~~~ii~lSATl~~~v~~di~~~L~l~~p~  202 (206)
T d1oywa2         142 LLAVDEAHCISQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPL  202 (206)
T ss_dssp             EEEESSGGGGCTTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCE
T ss_pred             eeeeeeeeeeeccccchHHHHHHHHHHHHhC-CCCceEEEEeCCCHHHHHHHHHHcCCCCCc
Confidence            999999999876542  1   2334455555 479999999999999865 5555 488995

>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=99.37  E-value=2.1e-12  Score=99.70  Aligned_cols=116  Identities=23%  Similarity=0.371  Sum_probs=87.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      ||++++||..||.|.++.++++...+ ++++..+.|+.+.++...   .+.++.++|+|||..    ++..  .+.++++
T Consensus       134 q~~~m~Pt~~La~Qh~~~~~~~f~~~-~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThs----l~~~--~~~f~~L  206 (264)
T d1gm5a3         134 QTAFMVPTSILAIQHYRRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHA----LIQE--DVHFKNL  206 (264)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTT----HHHH--CCCCSCC
T ss_pred             ceeEEeehHhhhHHHHHHHHHhhhhc-cccceeeccccchHHHHHHHHHHHCCCCCEEEeehH----HhcC--CCCcccc
Confidence            68999999999999999999998776 789999999887654433   455678999999983    4443  5677899


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhh
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAG  128 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~  128 (183)
                      .++|+||-|+.   |+...  ..+..-.++..++++|||..++...++..-
T Consensus       207 glviiDEqH~f---gv~Qr--~~l~~~~~~~~~l~~SATPiprtl~~~~~g  252 (264)
T d1gm5a3         207 GLVIIDEQHRF---GVKQR--EALMNKGKMVDTLVMSATPIPRSMALAFYG  252 (264)
T ss_dssp             CEEEEESCCCC----------CCCCSSSSCCCEEEEESSCCCHHHHHHHTC
T ss_pred             ceeeecccccc---chhhH--HHHHHhCcCCCEEEEECCCCHHHHHHHHcC
Confidence            99999999995   33322  122333456889999999988876666543

>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=99.33  E-value=7.5e-12  Score=94.89  Aligned_cols=116  Identities=20%  Similarity=0.322  Sum_probs=90.2

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      |+++++||-.||.|.++.++++...+ ++++..+.|+.+..+...   .+.++.++|+|||..    ++.  ..+.++++
T Consensus       106 qv~~l~Pt~~La~Q~~~~~~~~~~~~-~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths----~l~--~~~~f~~L  178 (233)
T d2eyqa3         106 QVAVLVPTTLLAQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHK----LLQ--SDVKFKDL  178 (233)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTH----HHH--SCCCCSSE
T ss_pred             ceEEEccHHHhHHHHHHHHHHHHhhC-CCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehh----hhc--cCCccccc
Confidence            58999999999999999999988777 789999999887655433   455678999999973    343  46778999


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhh
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAG  128 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~  128 (183)
                      .++|+||-|..   |+.+. +. ++....+..++++|||..++...++..-
T Consensus       179 gLiIiDEeH~f---g~kQ~-~~-l~~~~~~~~~l~~SATPiprtl~~~~~g  224 (233)
T d2eyqa3         179 GLLIVDEEHRF---GVRHK-ER-IKAMRANVDILTLTATPIPRTLNMAMSG  224 (233)
T ss_dssp             EEEEEESGGGS---CHHHH-HH-HHHHHTTSEEEEEESSCCCHHHHHHHTT
T ss_pred             cceeeechhhh---hhHHH-HH-HHhhCCCCCEEEEecchhHHHHHHHHHh
Confidence            99999999984   44332 22 3333467899999999999877766643

>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=99.30  E-value=2.2e-12  Score=100.52  Aligned_cols=103  Identities=12%  Similarity=0.061  Sum_probs=69.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEE
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEIL   80 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~l   80 (183)
                      .+||++|||+||.|+++.++.+.........             .........++++||+.+..+...  ...+.+++++
T Consensus        40 ~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~-------------~~~~~~~~~i~~~t~~~l~~~~~~--~~~~~~~~~v  104 (305)
T d2bmfa2          40 RTLILAPTRVVAAEMEEALRGLPIRYQTPAI-------------RAEHTGREIVDLMCHATFTMRLLS--PIRVPNYNLI  104 (305)
T ss_dssp             CEEEEESSHHHHHHHHHHTTTSCCBCCC---------------------CCCSEEEEEHHHHHHHHTS--SSCCCCCSEE
T ss_pred             EEEEEccHHHHHHHHHHHHhcCCcceeeeEE-------------eecccCccccccCCcHHHHHHHhc--CccccceeEE
Confidence            3799999999999998877665433211111             011134678999999988877644  4567899999


Q ss_pred             EEcccchhhccchHHHHHHHHHhC--CCCCeEEEEeecCChH
Q 030094           81 VLDEADRLLDMGFQKQISYIISRL--PKLRRTGLFSATQTEA  120 (183)
Q Consensus        81 VvDEad~ll~~~~~~~l~~i~~~l--~~~~Q~v~~SAT~~~~  120 (183)
                      |+||+|.+...++  ....++..+  ....|++++|||.+..
T Consensus       105 ViDE~H~~~~~~~--~~~~~l~~~~~~~~~~~v~~SAT~~~~  144 (305)
T d2bmfa2         105 IMDEAHFTDPASI--AARGYISTRVEMGEAAGIFMTATPPGS  144 (305)
T ss_dssp             EEESTTCCSHHHH--HHHHHHHHHHHHTSCEEEEECSSCTTC
T ss_pred             EeeeeeecchhhH--HHHHHHHHhhccccceEEEeecCCCcc
Confidence            9999999865442  122222222  3578999999999865

>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=99.05  E-value=8.3e-11  Score=91.58  Aligned_cols=106  Identities=21%  Similarity=0.153  Sum_probs=75.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||+||+++|+.|.++.+.++.... ...+..+.+|......    .....+++|+|++.+...    ....+++..++|
T Consensus       160 ~Liivp~~~Lv~Q~~~~f~~~~~~~-~~~~~~~~~g~~~~~~----~~~~~~i~i~t~qs~~~~----~~~~~~~f~~VI  230 (282)
T d1rifa_         160 ILIIVPTTALTTQMADDFVDYRLFS-HAMIKKIGGGASKDDK----YKNDAPVVVGTWQTVVKQ----PKEWFSQFGMMM  230 (282)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTSCC-GGGEEECSTTCSSTTC----CCTTCSEEEECHHHHTTS----CGGGGGGEEEEE
T ss_pred             EEEEEcCchhHHHHHHHHHHhhccc-cccceeecceeccccc----ccccceEEEEeeehhhhh----cccccCCCCEEE
Confidence            6999999999999999999885432 4455555555443211    123578999999876543    233467889999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCChH
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~~~  120 (183)
                      +||||++-    ......++..+.+....+++|||+++.
T Consensus       231 vDEaH~~~----a~~~~~il~~~~~~~~rlGlTaT~~~~  265 (282)
T d1rifa_         231 NDECHLAT----GKSISSIISGLNNCMFKFGLSGSLRDG  265 (282)
T ss_dssp             EETGGGCC----HHHHHHHTTTCTTCCEEEEECSSCCTT
T ss_pred             EECCCCCC----chhHHHHHHhccCCCeEEEEEeecCCC
Confidence            99999974    345567777775555579999998654

>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=99.02  E-value=3.6e-10  Score=77.49  Aligned_cols=100  Identities=20%  Similarity=0.137  Sum_probs=64.3

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +++++|+++++.|.++.+...     ...+....+...        ......+.+.|...+.....  ....+.+++++|
T Consensus        39 vli~~p~~~l~~q~~~~~~~~-----~~~~~~~~~~~~--------~~~~~~~~~~~~~~l~~~~~--~~~~~~~~~lvI  103 (140)
T d1yksa1          39 TLVLAPTRVVLSEMKEAFHGL-----DVKFHTQAFSAH--------GSGREVIDAMCHATLTYRML--EPTRVVNWEVII  103 (140)
T ss_dssp             EEEEESSHHHHHHHHHHTTTS-----CEEEESSCCCCC--------CCSSCCEEEEEHHHHHHHHT--SSSCCCCCSEEE
T ss_pred             eeeeecchhHHHHHHHHhhhh-----hhhhcccccccc--------cccccchhhhhHHHHHHHHh--ccccccceeEEE
Confidence            689999999999998765433     222221111111        02345678888887766543  456788999999


Q ss_pred             EcccchhhccchH--HHHHHHHHhCCCCCeEEEEeecCC
Q 030094           82 LDEADRLLDMGFQ--KQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        82 vDEad~ll~~~~~--~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      +||||.+-..++.  ..+.. +.. .++++++++|||.|
T Consensus       104 iDEaH~~~~~~~~~~~~~~~-~~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1         104 MDEAHFLDPASIAARGWAAH-RAR-ANESATILMTATPP  140 (140)
T ss_dssp             ETTTTCCSHHHHHHHHHHHH-HHH-TTSCEEEEECSSCT
T ss_pred             EccccccChhhHHHHHHHHH-Hhh-CCCCCEEEEEcCCC
Confidence            9999987433221  22222 222 46799999999986

>d1a1va1 c.37.1.14 (A:190-325) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=98.92  E-value=4.1e-09  Score=72.63  Aligned_cols=99  Identities=13%  Similarity=0.076  Sum_probs=66.9

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      ++|++|+++|+.|..+.+.+.....    .....++...        .....+.++|.+.....    ....+++++++|
T Consensus        36 vli~~P~~~l~~q~~~~~~~~~~~~----~~~~~~~~~~--------~~~~~~~~~~~~~~~~~----~~~~~~~~~~vI   99 (136)
T d1a1va1          36 VLVLNPSVAATLGFGAYMSKAHGVD----PNIRTGVRTI--------TTGSPITYSTYGKFLAD----GGCSGGAYDIII   99 (136)
T ss_dssp             EEEEESCHHHHHHHHHHHHHHHSCC----CEEECSSCEE--------CCCCSEEEEEHHHHHHT----TGGGGCCCSEEE
T ss_pred             EEEEcChHHHHHHHHHHHHHHhhcc----cccccccccc--------ccccceEEEeeeeeccc----cchhhhcCCEEE
Confidence            7999999999999999988875432    2233333321        23456888998765433    344678899999


Q ss_pred             EcccchhhccchHHHHHHHHHhCC--CCCeEEEEeecC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLP--KLRRTGLFSATQ  117 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~--~~~Q~v~~SAT~  117 (183)
                      +||+|.+- ......+..+++.+.  .+.+.+++|||.
T Consensus       100 iDE~H~~~-~~~~~~~~~~l~~~~~~~~~~~l~~TATP  136 (136)
T d1a1va1         100 CDECHSTD-ATSILGIGTVLDQAETAGARLVVLATATP  136 (136)
T ss_dssp             EETTTCCS-HHHHHHHHHHHHHTTTTTCSEEEEEESSC
T ss_pred             EecccccC-HHHHHHHHHHHHHHHHCCCCcEEEEeCCC
Confidence            99999863 222334555555553  456789999984

>d2fz4a1 c.37.1.19 (A:24-229) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=98.73  E-value=3.3e-08  Score=72.89  Aligned_cols=94  Identities=20%  Similarity=0.085  Sum_probs=65.9

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||+||++.|+.|..+.++++..    -.+....|+..          ...+|+|+|...+....+.    ..++.+++|
T Consensus       113 ~Liv~p~~~L~~q~~~~~~~~~~----~~~~~~~~~~~----------~~~~i~i~t~~~~~~~~~~----~~~~~~lvI  174 (206)
T d2fz4a1         113 TLIVVPTLALAEQWKERLGIFGE----EYVGEFSGRIK----------ELKPLTVSTYDSAYVNAEK----LGNRFMLLI  174 (206)
T ss_dssp             EEEEESSHHHHHHHHHHHGGGCG----GGEEEESSSCB----------CCCSEEEEEHHHHHHTHHH----HTTTCSEEE
T ss_pred             eeEEEcccchHHHHHHHHHhhcc----cchhhcccccc----------cccccccceehhhhhhhHh----hCCcCCEEE
Confidence            69999999999999998877642    23344444322          3567999999887766543    134678999


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      +||||++-...    ...+++.++ ....+++|||+.
T Consensus       175 iDEaH~~~a~~----~~~i~~~~~-~~~~lgLTATl~  206 (206)
T d2fz4a1         175 FDEVHHLPAES----YVQIAQMSI-APFRLGLTATFE  206 (206)
T ss_dssp             EECSSCCCTTT----HHHHHHTCC-CSEEEEEEESCC
T ss_pred             EECCeeCCcHH----HHHHHhccC-CCcEEEEecCCC
Confidence            99999985333    345555553 456788999984

>d1z3ix2 c.37.1.19 (X:92-389) Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxId: 7955]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Rad54-like, Rad54L
species: Zebra fish (Danio rerio) [TaxId: 7955]

Probab=97.93  E-value=6.2e-05  Score=57.70  Aligned_cols=108  Identities=22%  Similarity=0.298  Sum_probs=67.3

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH--HHHh-----cCCcEEEeCcHHHHHHHHhcCCcCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK--KIEE-----EGANLLIGTPGRLYDIMERMDVLDF   74 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~--~l~~-----~~~~IiV~TP~~l~~~l~~~~~~~l   74 (183)
                      +||+||.. |..|..+++.+.+..  ...+....|+...+....  ....     ...+++|+|...+.....   .+.-
T Consensus       117 ~LIV~P~s-l~~qW~~Ei~k~~~~--~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~i~sy~~~~~~~~---~l~~  190 (298)
T d1z3ix2         117 VIVVSPSS-LVRNWYNEVGKWLGG--RVQPVAIDGGSKDEIDSKLVNFISQQGMRIPTPILIISYETFRLHAE---VLHK  190 (298)
T ss_dssp             EEEEECHH-HHHHHHHHHHHHHGG--GCCEEEECSSCHHHHHHHHHHHHCCCSSCCSCCEEEEEHHHHHHHTT---TTTT
T ss_pred             EEEEccch-hhHHHHHHHHhhcCC--ceeEEEEeCchHHHHHHHHHHhhhccCccccceEEEEeecccccchh---cccc
Confidence            69999986 888999999888654  345555555544322211  1111     135799999877665432   3333


Q ss_pred             CCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC
Q 030094           75 RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~  118 (183)
                      .+..++|+||+|.+-+.+  ......+..+ +....+++|||.-
T Consensus       191 ~~~~~vI~DEaH~ikn~~--s~~~~a~~~l-~~~~rllLTGTPi  231 (298)
T d1z3ix2         191 GKVGLVICDEGHRLKNSD--NQTYLALNSM-NAQRRVLISGTPI  231 (298)
T ss_dssp             SCCCEEEETTGGGCCTTC--HHHHHHHHHH-CCSEEEEECSSCS
T ss_pred             cceeeeeccccccccccc--chhhhhhhcc-ccceeeeecchHH
Confidence            456799999999985433  2222333344 4566789999974

>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=97.19  E-value=0.006  Score=42.89  Aligned_cols=113  Identities=12%  Similarity=0.153  Sum_probs=77.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHH---HHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~---~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|+.-|..+.+.+...     ++++..+.|+.+..+..   ..+.++..+|+|+|-     ++.  .++|..++.
T Consensus        34 ~lvfc~t~~~~~~l~~~L~~~-----Gi~a~~~Hg~~~~~eR~~~l~~F~~G~~~vLVaT~-----v~~--~GiDip~V~  101 (174)
T d1c4oa2          34 TLVTVLTVRMAEELTSFLVEH-----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGIN-----LLR--EGLDIPEVS  101 (174)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESC-----CCC--TTCCCTTEE
T ss_pred             EEEEEcchhHHHHHHHHHHhc-----CCceEEEecccchHHHHHHHHHHHCCCeEEEEeee-----eee--eeccCCCCc
Confidence            699999999999888877764     78999999998755443   355567899999995     443  589999999


Q ss_pred             EEEEcccchhhcc-chHHHHHHHHHhCC-CCCeEEEEeecCChHHHHHHH
Q 030094           79 ILVLDEADRLLDM-GFQKQISYIISRLP-KLRRTGLFSATQTEAVEELSK  126 (183)
Q Consensus        79 ~lVvDEad~ll~~-~~~~~l~~i~~~l~-~~~Q~v~~SAT~~~~v~~~~~  126 (183)
                      ++|+=.++...-. +...-+..+-+... .+...+++....++.+.....
T Consensus       102 ~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~g~~~~~~~~~~~~~~~~i~  151 (174)
T d1c4oa2         102 LVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEAMQRAIE  151 (174)
T ss_dssp             EEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCHHHHHHHH
T ss_pred             EEEEeccccccccchhHHHHHHhhhhhhcCCCeeEEeecCCCHHHHHHHH
Confidence            9998777764211 22333433333332 234566666666666655443

>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=96.78  E-value=0.0032  Score=45.69  Aligned_cols=94  Identities=15%  Similarity=0.237  Sum_probs=70.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHH---HHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKAD---VKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~---~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      |+-||||.-+-...+++.+.+   .+|+.++..+.|..+.++.   +....++..+|+|||.     .++.  ++|..+.
T Consensus        33 Qvy~V~p~I~~~e~~~~~l~~---~~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt-----vIEv--GiDvpnA  102 (211)
T d2eyqa5          33 QVYYLYNDVENIQKAAERLAE---LVPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----IIET--GIDIPTA  102 (211)
T ss_dssp             EEEEECCCSSCHHHHHHHHHH---HCTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS-----TTGG--GSCCTTE
T ss_pred             eEEEEEcCccchhhHHHHHHH---hCCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh-----hhhh--ccCCCCC
Confidence            577899987766666555444   5678999999998775443   3445567899999996     5654  7999999


Q ss_pred             eEEEEcccchhhccchHHHHHHHHHhCCCCC
Q 030094           78 EILVLDEADRLLDMGFQKQISYIISRLPKLR  108 (183)
Q Consensus        78 ~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~  108 (183)
                      .++|+..||++   | ..++..+-.+.++..
T Consensus       103 ~~iiI~~a~rf---G-LaQLhQLRGRVGR~~  129 (211)
T d2eyqa5         103 NTIIIERADHF---G-LAQLHQLRGRVGRSH  129 (211)
T ss_dssp             EEEEETTTTSS---C-HHHHHHHHTTCCBTT
T ss_pred             cEEEEecchhc---c-ccccccccceeeecC
Confidence            99999999996   2 556777777776543

>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=96.78  E-value=0.018  Score=40.52  Aligned_cols=93  Identities=12%  Similarity=0.191  Sum_probs=68.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      +++|.|+|++-+..+...+.+.     ++++..+.|+.+..+...   ...++..+|+|||.     .+.  .++|..++
T Consensus        33 ~~iif~~~~~~~~~~~~~l~~~-----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTd-----v~~--rGiDip~v  100 (181)
T d1t5la2          33 RTLVTTLTKKMAEDLTDYLKEA-----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGIN-----LLR--EGLDIPEV  100 (181)
T ss_dssp             EEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESC-----CCS--SSCCCTTE
T ss_pred             eEEEEeehhhhhHHHHHHHHhC-----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEehh-----HHH--ccCCCCCC
Confidence            3799999999999888877654     788999999988655544   45567899999995     343  58999999


Q ss_pred             eEEEEcccchhh-ccchHHHHHHHHHhCC
Q 030094           78 EILVLDEADRLL-DMGFQKQISYIISRLP  105 (183)
Q Consensus        78 ~~lVvDEad~ll-~~~~~~~l~~i~~~l~  105 (183)
                      .++|.-+++... ..++..-+.++-+.-.
T Consensus       101 ~~VI~~d~p~~~~~~s~~~yi~R~GRagR  129 (181)
T d1t5la2         101 SLVAILDADKEGFLRSERSLIQTIGRAAR  129 (181)
T ss_dssp             EEEEETTTTSCSGGGSHHHHHHHHGGGTT
T ss_pred             CEEEEecCCcccccccHHHHHHHHHhhcc
Confidence            999988887631 1234444555555443

>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=96.51  E-value=0.0062  Score=42.10  Aligned_cols=73  Identities=10%  Similarity=0.170  Sum_probs=56.0

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|.|+.-+.++++.+...     ++.+..+.|+.+..++..   ....+...|+|+|-     .+ . .++|+.++
T Consensus        29 k~iIF~~s~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Td-----v~-~-rGiDi~~v   96 (162)
T d1fuka_          29 QAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----LL-A-RGIDVQQV   96 (162)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEG-----GG-T-TTCCCCSC
T ss_pred             cEEEEEEEEchHHHHHHHHhhc-----CceEEEeccCCchhhHHHHHHHHhhcccceeeccc-----cc-c-ccccCCCc
Confidence            4799999999999998866554     677888999887665544   33457789999996     33 3 68999999


Q ss_pred             eEEEEccc
Q 030094           78 EILVLDEA   85 (183)
Q Consensus        78 ~~lVvDEa   85 (183)
                      .++|.=+.
T Consensus        97 ~~VI~~d~  104 (162)
T d1fuka_          97 SLVINYDL  104 (162)
T ss_dssp             SEEEESSC
T ss_pred             eEEEEecc
Confidence            99886443

>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=96.50  E-value=0.009  Score=44.76  Aligned_cols=121  Identities=16%  Similarity=0.151  Sum_probs=85.8

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHH-HHHHHhcC-----CcCCC
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMD-----VLDFR   75 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l-~~~l~~~~-----~~~l~   75 (183)
                      +-|++.+--||..=.+++..+...+ ++++.+...+....+.....   .|||+=||...+ .++++.+-     ..-.+
T Consensus       124 vhvvTvNdyLA~RDae~m~~iy~~l-Glsvg~~~~~~~~~~r~~~Y---~~di~Ygt~~e~~fDyLrd~~~~~~~~~~~r  199 (273)
T d1tf5a3         124 VHVVTVNEYLASRDAEQMGKIFEFL-GLTVGLNLNSMSKDEKREAY---AADITYSTNNELGFDYLRDNMVLYKEQMVQR  199 (273)
T ss_dssp             EEEEESSHHHHHHHHHHHHHHHHHT-TCCEEECCTTSCHHHHHHHH---HSSEEEEEHHHHHHHHHHHTTCSSGGGCCCC
T ss_pred             ceEEecCccccchhhhHHhHHHHHc-CCCccccccccCHHHHHHHh---hCCceecchhhhhhhhcchhhhcChhhhccC
Confidence            4578889999999999999999988 99999888777666554444   689999999886 44454311     12257


Q ss_pred             CceEEEEcccchhhcc---------c----hH-HHHHHHHHhCCCCCeEEEEeecCChHHHHHHHhhC
Q 030094           76 NLEILVLDEADRLLDM---------G----FQ-KQISYIISRLPKLRRTGLFSATQTEAVEELSKAGL  129 (183)
Q Consensus        76 ~l~~lVvDEad~ll~~---------~----~~-~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~~~~  129 (183)
                      .+.+.|+||+|.++=.         |    .. -..+..++..   .+...++.|-..+.++|.+.|-
T Consensus       200 ~~~~aIvDEvDsiliDeartpliisg~~~~~a~it~q~~f~~y---~~l~gmtgta~~~~~e~~~iy~  264 (273)
T d1tf5a3         200 PLHFAVIDEVDSILIDEARTPLIISGQSMTLATITFQNYFRMY---EKLAGMTGTAKTEEEEFRNIYN  264 (273)
T ss_dssp             CCCEEEEETHHHHHTTTTTCEEEEEEEEEEEEEEEHHHHHTTS---SEEEEEESCCGGGHHHHHHHHC
T ss_pred             CCCEEEEEcchhhhhhccCCceEeccCccchhhhhHHHHHHHH---HHHhCCccccHHHHHHHHhccC
Confidence            7889999999998721         1    00 0123334433   4778888888888788877764

>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=96.32  E-value=0.0014  Score=47.84  Aligned_cols=106  Identities=14%  Similarity=0.160  Sum_probs=61.6

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||+|| ..+..|..+.+.+++.   ..++....+.....      ...+.+|+++|.+.+...-..    .--....+|
T Consensus        64 ~LIv~p-~~l~~~W~~e~~~~~~---~~~~~~~~~~~~~~------~~~~~~vvi~~~~~~~~~~~l----~~~~~~~vI  129 (230)
T d1z63a1          64 SLVICP-LSVLKNWEEELSKFAP---HLRFAVFHEDRSKI------KLEDYDIILTTYAVLLRDTRL----KEVEWKYIV  129 (230)
T ss_dssp             EEEEEC-STTHHHHHHHHHHHCT---TSCEEECSSSTTSC------CGGGSSEEEEEHHHHTTCHHH----HTCCEEEEE
T ss_pred             cceecc-hhhhhHHHHHHHhhcc---cccceeeccccchh------hccCcCEEEeeHHHHHhHHHH----hcccceEEE
Confidence            578888 5566778887777753   33333322221111      123568999999776543222    122457899


Q ss_pred             EcccchhhccchHHHHHHHHHhCCCCCeEEEEeecCC-hHHHHH
Q 030094           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT-EAVEEL  124 (183)
Q Consensus        82 vDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~~-~~v~~~  124 (183)
                      +||||.+-+.+.  ........+. ....+++|||.- +...++
T Consensus       130 ~DEah~~k~~~s--~~~~~~~~l~-a~~r~~LTgTPi~n~~~dl  170 (230)
T d1z63a1         130 IDEAQNIKNPQT--KIFKAVKELK-SKYRIALTGTPIENKVDDL  170 (230)
T ss_dssp             EETGGGGSCTTS--HHHHHHHTSC-EEEEEEECSSCSTTCHHHH
T ss_pred             EEhhhcccccch--hhhhhhhhhc-cceEEEEecchHHhHHHHH
Confidence            999999865432  2223344443 445788999974 334443

>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=96.09  E-value=0.018  Score=39.19  Aligned_cols=71  Identities=15%  Similarity=0.287  Sum_probs=53.5

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|+|++-|.++++.+++.     ++.+..+.|+.+..++..   ....+...|+|+|.     .+.  .++|+..+
T Consensus        30 k~IIF~~s~~~~~~l~~~L~~~-----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~-----~~~--~Gid~~~v   97 (155)
T d1hv8a2          30 YGLVFCKTKRDTKELASMLRDI-----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-----VMS--RGIDVNDL   97 (155)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHT-----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-----THH--HHCCCSCC
T ss_pred             CEEEEECchHHHHHHHhhhccc-----ccccccccccchhhhhhhhhhhhhcccceeeeehh-----HHh--hhhhhccC
Confidence            4799999999999888887764     567888888876554433   34456789999995     343  36899999


Q ss_pred             eEEEEc
Q 030094           78 EILVLD   83 (183)
Q Consensus        78 ~~lVvD   83 (183)
                      .++|.=
T Consensus        98 ~~Vi~~  103 (155)
T d1hv8a2          98 NCVINY  103 (155)
T ss_dssp             SEEEES
T ss_pred             cEEEEe
Confidence            988843

>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=95.71  E-value=0.018  Score=41.18  Aligned_cols=69  Identities=14%  Similarity=0.214  Sum_probs=53.1

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|+.-|..++..+...     ++.+..+.|+.+..+...   ....+..+|+|+|-     .+.  .++|..+++
T Consensus        33 ~IIF~~t~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd-----~~~--~GiD~p~v~  100 (200)
T d1oywa3          33 GIIYCNSRAKVEDTAARLQSK-----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATV-----AFG--MGINKPNVR  100 (200)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECT-----TSC--TTTCCTTCC
T ss_pred             EEEEEeeehhhHHhhhhhccC-----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecc-----hhh--hccCCCCCC
Confidence            799999999999888766654     677888898877554433   44457889999996     332  579999999


Q ss_pred             EEEE
Q 030094           79 ILVL   82 (183)
Q Consensus        79 ~lVv   82 (183)
                      ++|-
T Consensus       101 ~VI~  104 (200)
T d1oywa3         101 FVVH  104 (200)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8884

>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=95.71  E-value=0.018  Score=39.82  Aligned_cols=71  Identities=13%  Similarity=0.196  Sum_probs=54.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-|..+++.++..     ++.+..+.|+.+.++...   ....+..+|+|+|-     .+.  .++|+.++.
T Consensus        37 ~iiF~~~~~~~~~~~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td-----~~~--rGiDi~~v~  104 (168)
T d2j0sa2          37 AVIFCNTKRKVDWLTEKMREA-----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTD-----VWA--RGLDVPQVS  104 (168)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECG-----GGS--SSCCCTTEE
T ss_pred             eEEEeeeHHHHHHHHHHhhhc-----ccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccc-----hhc--ccccccCcc
Confidence            789999999999988877765     567788888877665544   33456789999995     343  689999999


Q ss_pred             EEEEcc
Q 030094           79 ILVLDE   84 (183)
Q Consensus        79 ~lVvDE   84 (183)
                      ++|.=+
T Consensus       105 ~VIn~d  110 (168)
T d2j0sa2         105 LIINYD  110 (168)
T ss_dssp             EEEESS
T ss_pred             eEEEec
Confidence            988433

>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=95.52  E-value=0.04  Score=37.98  Aligned_cols=74  Identities=5%  Similarity=0.088  Sum_probs=56.2

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCce
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLE   78 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~   78 (183)
                      +||.|+|++-|..++..+...     ++.+..+.|+.+..+...   ....+..+|+|+|..     + . .++|+.++.
T Consensus        35 ~iVF~~~~~~~~~l~~~L~~~-----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~-----~-~-~Gid~~~v~  102 (171)
T d1s2ma2          35 AIIFCNSTNRVELLAKKITDL-----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDL-----L-T-RGIDIQAVN  102 (171)
T ss_dssp             EEEECSSHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSC-----S-S-SSCCCTTEE
T ss_pred             eEEEEeeeehhhHhHHhhhcc-----cccccccccccchhhhhhhhhhcccCccccccchhH-----h-h-hccccceeE
Confidence            799999999999888877765     667888888877554433   344578999999972     2 2 689999999


Q ss_pred             EEEEcccch
Q 030094           79 ILVLDEADR   87 (183)
Q Consensus        79 ~lVvDEad~   87 (183)
                      ++|.=+...
T Consensus       103 ~VI~~d~p~  111 (171)
T d1s2ma2         103 VVINFDFPK  111 (171)
T ss_dssp             EEEESSCCS
T ss_pred             EEEecCCcc
Confidence            998555543

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.42  E-value=0.033  Score=38.40  Aligned_cols=73  Identities=8%  Similarity=0.153  Sum_probs=54.9

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHH---HHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~---~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l   77 (183)
                      .+||.|+|++-+..+++.+.+.     +.++..+.|+.+..++..   ...++.++|+|+|-     .+ . .++|+..+
T Consensus        29 k~iIF~~~~~~~~~l~~~L~~~-----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~-----~~-~-~Gid~~~~   96 (168)
T d1t5ia_          29 QVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATN-----LF-G-RGMDIERV   96 (168)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESS-----CC-S-TTCCGGGC
T ss_pred             eEEEEEeeeecchhhhhhhccc-----cccccccccccchhhhhhhhhhhccccceeeeccc-----cc-c-chhhcccc
Confidence            4799999999999888877664     567888899877655544   34457799999995     23 2 57898899


Q ss_pred             eEEEEccc
Q 030094           78 EILVLDEA   85 (183)
Q Consensus        78 ~~lVvDEa   85 (183)
                      .++|.=+.
T Consensus        97 ~~vi~~~~  104 (168)
T d1t5ia_          97 NIAFNYDM  104 (168)
T ss_dssp             SEEEESSC
T ss_pred             hhhhhhhc
Confidence            88876554

>d1jr6a_ c.37.1.14 (A:) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=93.17  E-value=0.058  Score=36.01  Aligned_cols=63  Identities=10%  Similarity=0.245  Sum_probs=48.4

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      +||.|+|+.-|.++++.+++.     ++++..+.|+...++.    .+...+++|||-     .+.  .++| .+++.+|
T Consensus        38 ~IVFc~t~~~ae~la~~L~~~-----G~~~~~~H~~~~~~~~----~~~~~~vlvaTd-----~~~--~GiD-~~v~~Vi  100 (138)
T d1jr6a_          38 HLIFCHSKKKCDELAAKLVAL-----GINAVAYYRGLDVSVI----PTNGDVVVVATD-----ALM--TGFT-GDFDSVI  100 (138)
T ss_dssp             EEEECSCHHHHHHHHHHHHHH-----TCEEEEECTTCCSCCC----TTSSCEEEEESS-----SSC--SSSC-CCBSEEE
T ss_pred             EEEEeCcHHHHHHHHHHHhcc-----ccchhhhhccchhhhh----hhhhcceeehhH-----HHH--hccc-cccceEE
Confidence            799999999999999888765     6788888888775433    356789999995     443  4577 6687765

>d2p6ra4 c.37.1.19 (A:203-403) Hel308 helicase {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Hel308 helicase
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=92.82  E-value=0.99  Score=31.44  Aligned_cols=120  Identities=8%  Similarity=0.030  Sum_probs=66.4

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCC-------------------------ceEEEEEcCcchHHHHH---HHHhcCC
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPD-------------------------VKSVLLVGGVEVKADVK---KIEEEGA   52 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~-------------------------~~~~~~~g~~~~~~~~~---~l~~~~~   52 (183)
                      ++||.||||.-|..+...+.........                         -.++...||.+..+...   ...++..
T Consensus        42 ~~LVF~~sRk~~~~~A~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~GIa~hh~~l~~~~r~~ie~~f~~g~i  121 (201)
T d2p6ra4          42 GVLVFESTRRGAEKTAVKLSAITAKYVENEGLEKAILEENEGEMSRKLAECVRKGAAFHHAGLLNGQRRVVEDAFRRGNI  121 (201)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHHTTCCCSSHHHHHHTTCCSHHHHHHHHHHHTTCCEECTTSCHHHHHHHHHHHHTTSC
T ss_pred             cEEEEeCCHHHHHHHHHHHHHHHHhhhchhHHHHHHHHhhhhhhhHHHHHHHhccHHHHHHHhhhhhHHHHHHHHhCCCc
Confidence            5899999998888777777665432111                         11566677765433322   3345679


Q ss_pred             cEEEeCcHHHHHHHHhcCCcCCCCceEEEEc-----ccchhhccchHHHHHHHHHhCCC---CCeEEEEeecCChHHHHH
Q 030094           53 NLLIGTPGRLYDIMERMDVLDFRNLEILVLD-----EADRLLDMGFQKQISYIISRLPK---LRRTGLFSATQTEAVEEL  124 (183)
Q Consensus        53 ~IiV~TP~~l~~~l~~~~~~~l~~l~~lVvD-----Ead~ll~~~~~~~l~~i~~~l~~---~~Q~v~~SAT~~~~v~~~  124 (183)
                      +|+|||.     .+.  .++|+.....+|.|     ..+.-   .....+..+..+.++   +.+-..+--+-+.+-...
T Consensus       122 ~vlvaT~-----~l~--~Gin~p~~~vvi~~~~~~d~~~~~---~~~~~~~q~~GRAGR~g~~~~G~~~l~~~~~~~~~~  191 (201)
T d2p6ra4         122 KVVVATP-----TLA--AGVNLPARRVIVRSLYRFDGYSKR---IKVSEYKQMAGRAGRPGMDERGEAIIIVGKRDREIA  191 (201)
T ss_dssp             CEEEECS-----TTT--SSSCCCBSEEEECCSEEESSSEEE---CCHHHHHHHHTTBSCTTTCSCEEEEEECCGGGHHHH
T ss_pred             eEEEech-----HHH--hhcCCCCceEEEecceeccCCcCC---CCHHHHHHHhcccCCCCCCCeeEEEEEeCCCChHHH
Confidence            9999997     222  46888777777653     22211   123445555555543   223222222333444445


Q ss_pred             HHhhCC
Q 030094          125 SKAGLR  130 (183)
Q Consensus       125 ~~~~~~  130 (183)
                      .++++.
T Consensus       192 ~k~~~~  197 (201)
T d2p6ra4         192 VKRYIF  197 (201)
T ss_dssp             HHTTTS
T ss_pred             HHHHhc
Confidence            666654

>d1yksa2 c.37.1.14 (A:325-623) YFV helicase domain {Yellow fever virus [TaxId: 11089]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: YFV helicase domain
species: Yellow fever virus [TaxId: 11089]

Probab=91.90  E-value=0.16  Score=38.23  Aligned_cols=66  Identities=12%  Similarity=0.110  Sum_probs=42.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCCCceEEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLEILV   81 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~~l~~lV   81 (183)
                      .+|+||+..-+.++.+.+++.     +.++..++|.....++ ....++..+|||+|.     ..+  .++++ ++.++|
T Consensus        39 ~~~F~~s~~~~~~~a~~L~~~-----g~~V~~l~~~~~~~e~-~~~~~~~~~~~~~t~-----~~~--~~~~~-~~~~vi  104 (299)
T d1yksa2          39 TAWFLPSIRAANVMAASLRKA-----GKSVVVLNRKTFEREY-PTIKQKKPDFILATD-----IAE--MGANL-CVERVL  104 (299)
T ss_dssp             EEEECSCHHHHHHHHHHHHHT-----TCCEEECCSSSCC---------CCCSEEEESS-----STT--CCTTC-CCSEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHhc-----CCeEEEEcCcCcHhHH-hhhhcCCcCEEEEec-----hhh--hceec-CceEEE
Confidence            689999999999888887764     4567778876654444 445567899999996     333  45666 355443

>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=90.83  E-value=0.38  Score=34.05  Aligned_cols=112  Identities=14%  Similarity=0.202  Sum_probs=60.7

Q ss_pred             EeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchH------HHHHHHHhcCCcEEEeCcHHHHHHHHh---cCCc---
Q 030094            5 ISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVK------ADVKKIEEEGANLLIGTPGRLYDIMER---MDVL---   72 (183)
Q Consensus         5 l~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~------~~~~~l~~~~~~IiV~TP~~l~~~l~~---~~~~---   72 (183)
                      +.|+.++|.+..+.+.+-.+  +......++|.....      .-.......+..++..+...+...+..   .+..   
T Consensus        14 vg~~N~~a~~~~~~~~~~~~--~~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   91 (213)
T d1l8qa2          14 VGEGNRLAYEVVKEALENLG--SLYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINEF   91 (213)
T ss_dssp             CCTTTHHHHHHHHHHHHTTT--TSCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHHHHHHHHHHHHTCHHHH
T ss_pred             CCCcHHHHHHHHHHHHhCcC--CCCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEechHHHHHHHHHHHHccchhhH
Confidence            45667777765554433211  123446778765421      111233345667777666665544321   0111   


Q ss_pred             --CCCCceEEEEcccchhhccc-hHHHHHHHHHhCC-CCCeEEEEeecCC
Q 030094           73 --DFRNLEILVLDEADRLLDMG-FQKQISYIISRLP-KLRRTGLFSATQT  118 (183)
Q Consensus        73 --~l~~l~~lVvDEad~ll~~~-~~~~l~~i~~~l~-~~~Q~v~~SAT~~  118 (183)
                        .+.+.+++++|++|.+.+.. ....+-+++..+. .+.++++.|...+
T Consensus        92 ~~~~~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p  141 (213)
T d1l8qa2          92 RNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHP  141 (213)
T ss_dssp             HHHHHTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCG
T ss_pred             HHHHhhccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcc
Confidence              14567899999999997543 3455666666654 4556666554433

>d1gm5a4 c.37.1.19 (A:550-755) RecG helicase domain {Thermotoga maritima [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: RecG helicase domain
species: Thermotoga maritima [TaxId: 2336]

Probab=90.59  E-value=0.032  Score=40.07  Aligned_cols=95  Identities=18%  Similarity=0.303  Sum_probs=58.4

Q ss_pred             CEEEEeCcHHHHH-----HHHHHHHHhhh-hCCCceEEEEEcCcch---HHHHHHHHhcCCcEEEeCcHHHHHHHHhcCC
Q 030094            1 MGMIISPTRELSS-----QIYHVAQPFIS-TLPDVKSVLLVGGVEV---KADVKKIEEEGANLLIGTPGRLYDIMERMDV   71 (183)
Q Consensus         1 ~alIl~PtreLa~-----Qi~~~~~~l~~-~~~~~~~~~~~g~~~~---~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~   71 (183)
                      |+-++||.-|-..     ...+....+.+ .+|+.++..+.|+.+.   +.-+....++..+|+|||-     .++  .+
T Consensus        31 QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTt-----ViE--~G  103 (206)
T d1gm5a4          31 QAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTT-----VIE--VG  103 (206)
T ss_dssp             CBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSS-----CCC--SC
T ss_pred             CEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEeh-----hhh--cc
Confidence            3446777543221     22334445443 4578888889998663   4445555567899999995     454  47


Q ss_pred             cCCCCceEEEEcccchhhccchHHHHHHHHHhCCC
Q 030094           72 LDFRNLEILVLDEADRLLDMGFQKQISYIISRLPK  106 (183)
Q Consensus        72 ~~l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~  106 (183)
                      +|..++.++|+..|+..-    ..++..+..+.++
T Consensus       104 IDip~a~~iii~~a~~fg----lsqlhQlrGRvGR  134 (206)
T d1gm5a4         104 IDVPRANVMVIENPERFG----LAQLHQLRGRVGR  134 (206)
T ss_dssp             SCCTTCCEEEBCSCSSSC----TTHHHHHHHTSCC
T ss_pred             ccccCCcEEEEEccCCcc----HHHHHhhhhheee
Confidence            999999999999999851    3355555566654

>d1wp9a2 c.37.1.19 (A:201-486) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

Probab=90.53  E-value=0.67  Score=33.90  Aligned_cols=73  Identities=21%  Similarity=0.271  Sum_probs=50.6

Q ss_pred             CEEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcch-----------HHHHHHHHhcCCcEEEeCcHHHHHHHHhc
Q 030094            1 MGMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEV-----------KADVKKIEEEGANLLIGTPGRLYDIMERM   69 (183)
Q Consensus         1 ~alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~-----------~~~~~~l~~~~~~IiV~TP~~l~~~l~~~   69 (183)
                      .+||.|++++-|..+++.+.+-     ++++..+.|....           ........++.++|+|+|-     ...  
T Consensus       163 k~iiF~~~~~~~~~~~~~L~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~-----~~~--  230 (286)
T d1wp9a2         163 KIIVFTNYRETAKKIVNELVKD-----GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATS-----VGE--  230 (286)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHT-----TCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECG-----GGG--
T ss_pred             cEEEEeCcHHhHHHHHHHHHHc-----CCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEcc-----cee--
Confidence            4799999999999888876653     5666666664321           1223344456789999994     333  


Q ss_pred             CCcCCCCceEEEEccc
Q 030094           70 DVLDFRNLEILVLDEA   85 (183)
Q Consensus        70 ~~~~l~~l~~lVvDEa   85 (183)
                      .++|+..+.++|.=+.
T Consensus       231 ~Gld~~~~~~Vi~~d~  246 (286)
T d1wp9a2         231 EGLDVPEVDLVVFYEP  246 (286)
T ss_dssp             GGGGSTTCCEEEESSC
T ss_pred             ccccCCCCCEEEEeCC
Confidence            5799999999986443

>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=89.26  E-value=2.4  Score=29.31  Aligned_cols=99  Identities=12%  Similarity=0.148  Sum_probs=57.7

Q ss_pred             HHHHHhhhhCCCceEEEEEcCcchH-HHHH-----HHH---hcCCcEEEeCcHH-------HHHHHHhc-CCcCCCCceE
Q 030094           17 HVAQPFISTLPDVKSVLLVGGVEVK-ADVK-----KIE---EEGANLLIGTPGR-------LYDIMERM-DVLDFRNLEI   79 (183)
Q Consensus        17 ~~~~~l~~~~~~~~~~~~~g~~~~~-~~~~-----~l~---~~~~~IiV~TP~~-------l~~~l~~~-~~~~l~~l~~   79 (183)
                      +.++++...- .....+++|..... ....     .+.   ..-||++.-.|+.       +.++.+.. ..-....-++
T Consensus         4 ~~l~~~i~~~-~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~~~~~~Kv   82 (198)
T d2gnoa2           4 ETLKRIIEKS-EGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKY   82 (198)
T ss_dssp             HHHHHHHHTC-SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEE
T ss_pred             HHHHHHHhcC-CCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCCCHHHHHHHHHHHhhCcccCCCEE
Confidence            3445554443 56677778765432 1111     111   1237898877742       34433321 1112366789


Q ss_pred             EEEcccchhhccchHHHHHHHHHhCCCCCeEEEEeecC
Q 030094           80 LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ  117 (183)
Q Consensus        80 lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~SAT~  117 (183)
                      +|+||||.|-.. ....+...++.-|+++.+++.+...
T Consensus        83 iIId~ad~l~~~-aqNaLLK~LEEPp~~t~fiLit~~~  119 (198)
T d2gnoa2          83 VIVHDCERMTQQ-AANAFLKALEEPPEYAVIVLNTRRW  119 (198)
T ss_dssp             EEETTGGGBCHH-HHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             EEEeCccccchh-hhhHHHHHHhCCCCCceeeeccCCh
Confidence            999999999543 4666777777777777777765544

>d1gkub2 c.37.1.16 (B:251-498) Helicase-like "domain" of reverse gyrase {Archaeon Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Helicase-like "domain" of reverse gyrase
domain: Helicase-like "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]

Probab=87.22  E-value=0.35  Score=34.90  Aligned_cols=75  Identities=24%  Similarity=0.291  Sum_probs=45.7

Q ss_pred             EEEEeCcHHHHHHHHHHHHHhhhhCCCceEEEEEcCcchHHHHHHHHhcCCcEEEeCcHHHHHHHHhcCCcCCC-CceEE
Q 030094            2 GMIISPTRELSSQIYHVAQPFISTLPDVKSVLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFR-NLEIL   80 (183)
Q Consensus         2 alIl~PtreLa~Qi~~~~~~l~~~~~~~~~~~~~g~~~~~~~~~~l~~~~~~IiV~TP~~l~~~l~~~~~~~l~-~l~~l   80 (183)
                      +||.|+|++-|..+++.++..      ++...  ......+-...+..+.++|+|||... ...+.  .++|+. .++++
T Consensus        28 ~iif~~~~~~~~~l~~~l~~~------~hg~~--~~~~R~~~~~~f~~g~~~vLVaT~a~-~~v~~--rGlDip~~v~~V   96 (248)
T d1gkub2          28 GIIYARTGEEAEEIYESLKNK------FRIGI--VTATKKGDYEKFVEGEIDHLIGTAHY-YGTLV--RGLDLPERIRFA   96 (248)
T ss_dssp             EEEEESSHHHHHHHHHTTTTS------SCEEE--CTTSSSHHHHHHHHTSCSEEEEECC---------CCSCCTTTCCEE
T ss_pred             EEEEECCHHHHHHHHHHHHHh------ccCCC--CHHHHHHHHHHHHhCCCeEEEEeccc-cchhh--hccCccccccEE
Confidence            799999999999887755431      22111  11223344555667789999999631 11222  578885 59999


Q ss_pred             EEcccch
Q 030094           81 VLDEADR   87 (183)
Q Consensus        81 VvDEad~   87 (183)
                      |.=++..
T Consensus        97 I~~d~P~  103 (248)
T d1gkub2          97 VFVGCPS  103 (248)
T ss_dssp             EEESCCE
T ss_pred             EEeCCCc
Confidence            8655553

>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=85.87  E-value=0.43  Score=32.37  Aligned_cols=53  Identities=13%  Similarity=0.204  Sum_probs=44.7

Q ss_pred             CCCceEEEEcccchhhccch--HHHHHHHHHhCCCCCeEEEEeecCChHHHHHHH
Q 030094           74 FRNLEILVLDEADRLLDMGF--QKQISYIISRLPKLRRTGLFSATQTEAVEELSK  126 (183)
Q Consensus        74 l~~l~~lVvDEad~ll~~~~--~~~l~~i~~~l~~~~Q~v~~SAT~~~~v~~~~~  126 (183)
                      -....++|+||+-..++.++  .+.+..+++..|...-+|+.+-..|+++.+.++
T Consensus        92 ~~~~dllILDEi~~Ai~~gli~~~~v~~ll~~rp~~~evVlTGr~~p~~L~e~AD  146 (157)
T d1g5ta_          92 DPLLDMVVLDELTYMVAYDYLPLEEVISALNARPGHQTVIITGRGCHRDILDLAD  146 (157)
T ss_dssp             CTTCSEEEEETHHHHHHTTSSCHHHHHHHHHTSCTTCEEEEECSSCCHHHHHHCS
T ss_pred             cCccCEEeHHHHHHHHHcCCCCHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhcc
Confidence            45578999999999988775  678888999888889999988889988877765

>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=85.14  E-value=1  Score=34.45  Aligned_cols=39  Identities=31%  Similarity=0.425  Sum_probs=31.1

Q ss_pred             cCCCCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEe
Q 030094           72 LDFRNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFS  114 (183)
Q Consensus        72 ~~l~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~S  114 (183)
                      .+....+++|+|||-++ +   ...+..++..+++.+++|+++
T Consensus       257 ~~~l~~d~lIIDEaSmv-~---~~l~~~ll~~~~~~~~lILvG  295 (359)
T d1w36d1         257 GNPLHLDVLVVDEASMI-D---LPMMSRLIDALPDHARVIFLG  295 (359)
T ss_dssp             TSCCSCSEEEECSGGGC-B---HHHHHHHHHTCCTTCEEEEEE
T ss_pred             hcccccceeeehhhhcc-C---HHHHHHHHHHhcCCCEEEEEC
Confidence            44567789999999775 2   456778889999889999876

>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=80.36  E-value=1  Score=32.00  Aligned_cols=39  Identities=13%  Similarity=0.139  Sum_probs=26.1

Q ss_pred             CCceEEEEcccchhhccchHHHHHHHHHhCCCCCeEEEEe
Q 030094           75 RNLEILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFS  114 (183)
Q Consensus        75 ~~l~~lVvDEad~ll~~~~~~~l~~i~~~l~~~~Q~v~~S  114 (183)
                      ..-+++|+||+|.|-. .....+..+++..++.+.+++.+
T Consensus       114 ~~~kviiIde~d~l~~-~~q~~Llk~lE~~~~~~~~il~t  152 (239)
T d1njfa_         114 GRFKVYLIDEVHMLSR-HSFNALLKTLEEPPEHVKFLLAT  152 (239)
T ss_dssp             SSSEEEEEETGGGSCH-HHHHHHHHHHHSCCTTEEEEEEE
T ss_pred             CCCEEEEEECcccCCH-HHHHHHHHHHhcCCCCeEEEEEc
Confidence            4567999999999843 34555666777655556555544