Citrus Sinensis ID: 028826

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200---
Protein Sequence
MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSEDG
Secondary Structure (PSIPRED)
cEEEEcccHHHHHHHHHHHHHHHHcccccEEEEEEccccHHHHHHHHHHccccEEEEcccHHHHHHccccccccccccEEEEEcccccccccHHHHHHHHHHHcccccccccEEcccccHHHHHHHHcccccEEEEEEcccccccccccccccccccccccEEEEEEEccccccHHHHHHHHHHccccEEEEEEccccccccc
Secondary Structure Prediction (SSPRO)
ccEEEccHHHHHHHHHHHHHHHHHHccccEEEEEEccccccHHHHHHHHcccEEEEEcccHHHHHHHccccEcHHcEEEEEEccHHHHHccccHHHHHHHHHccccccEEEEEEccccHHHHHHHHHHccccEEEEcccccccccccccccccccccccccEEEEEEEcccHHHHHHHHHHHHHcccccEEEEEEEccccccc
Coil and Loop (DISEMBL)
MGMIISPTRELSAQIYHVAqpfistlpdvKSMLLVGGVEVKADVKKIEEEGAnlligtpgrlyDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLpklrrtglfsaTQTEAVEELSKaglrnpvriEVRAeskshhasassqqlassktplglhleylecesdkkpsQLVDLLIKNKSKKIIMYVQhgnfsedg
Flexible Loop (DISEMBL)
MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIeeeganlligtpgrLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVeelskaglrnpvRIEVRAESkshhasassqqlassKTPLGLHLEYLEcesdkkpsQLVDLLIKNKSKKIIMYVQHGNFSEDG
Low Complexity Region (SEG)
MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAEskshhasassqqlasskTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSEDG
Disordered region (IsUnstruct)
**********LSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSA**********************************************LHLEYLEC*******QLVDLLIKNKSKKIIMYVQH*******
Disordered Region (DISOPRED)
MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKS*********LASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQ*GN*****
Disordered Region (DISEMBL)
MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVR******************KTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSEDG
Disordered Region (DISPRO)
MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAE****************KTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGN*****
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSEDG
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	203	2.2.26 [Sep-21-2011]
Q9FLB0	593	DEAD-box ATP-dependent RN	yes	no	0.931	0.318	0.777	4e-83
Q761Z9	647	DEAD-box ATP-dependent RN	yes	no	0.950	0.298	0.678	2e-75
Q8GXD6	558	DEAD-box ATP-dependent RN	no	no	0.886	0.322	0.673	4e-69
Q9FVV4	465	DEAD-box ATP-dependent RN	no	no	0.748	0.326	0.559	1e-51
Q6AZV7	594	ATP-dependent RNA helicas	N/A	no	0.906	0.309	0.461	3e-40
Q5ZLN8	591	ATP-dependent RNA helicas	yes	no	0.906	0.311	0.467	7e-40
Q2NL08	601	ATP-dependent RNA helicas	yes	no	0.906	0.306	0.472	1e-39
Q8NHQ9	600	ATP-dependent RNA helicas	yes	no	0.906	0.306	0.461	2e-39
Q8JHJ2	593	ATP-dependent RNA helicas	yes	no	0.906	0.310	0.467	8e-39
Q6ZPL9	600	ATP-dependent RNA helicas	yes	no	0.906	0.306	0.451	5e-38

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

 Score =  306 bits (785), Expect = 4e-83,   Method: Compositional matrix adjust.
 Identities = 150/193 (77%), Positives = 173/193 (89%), Gaps = 4/193 (2%)

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

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL DIMERM++LDFRNL IL+LDEADRLL+MGFQ+Q++YIISRLPK RRTGLFSATQTE 
Sbjct: 152 RLSDIMERMEILDFRNLEILILDEADRLLEMGFQRQVNYIISRLPKQRRTGLFSATQTEG 211

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           VEEL+KAGLRNPVR+EVRA+SKS     SSQQL +SKTP GLHLEY+ECE+DKK SQLVD
Sbjct: 212 VEELAKAGLRNPVRVEVRAKSKSE----SSQQLTNSKTPSGLHLEYMECEADKKSSQLVD 267

Query: 181 LLIKNKSKKIIMY 193
           LLIKN  KK+I++
Sbjct: 268 LLIKNSDKKLIVF 280

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 =  281 bits (720), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 131/193 (67%), Positives = 166/193 (86%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +G+IISPTRELS+QIY+VAQPF +TL  V SMLLVGG ++KA++KK+EEEGAN+L+GTPG
Sbjct: 98  LGIIISPTRELSSQIYNVAQPFFATLKGVSSMLLVGGFDIKAELKKLEEEGANILVGTPG 157

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           +L+D+MER+D L+++NL IL+LDEADRLLD+GFQKQI+ IIS+LPKLRRTGLFSATQTEA
Sbjct: 158 KLFDVMERLDTLNYKNLEILILDEADRLLDLGFQKQITSIISKLPKLRRTGLFSATQTEA 217

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           V+EL+KAGLRNPVR+EV+ E K      + Q+L  SKTPLGL LEY+ CE+  K SQLVD
Sbjct: 218 VKELAKAGLRNPVRVEVKTEVKPTGKDGAQQELGPSKTPLGLRLEYMICEASNKSSQLVD 277

Query: 181 LLIKNKSKKIIMY 193
            L++N  KKI++Y
Sbjct: 278 FLVQNNGKKIMVY 290

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 =  260 bits (665), Expect = 4e-69,   Method: Compositional matrix adjust.
 Identities = 130/193 (67%), Positives = 160/193 (82%), Gaps = 13/193 (6%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+IISPTRELSAQI+ VA+PF+STLP+V S+LLVGG EV+AD+  +EEEGANLLIGTPG
Sbjct: 92  MGVIISPTRELSAQIHKVAEPFVSTLPNVNSVLLVGGREVEADMNTLEEEGANLLIGTPG 151

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL D+M+RM+ LDFRNL IL+LDEADRLLDMGFQKQ++YIISRLPK RRTGLFSATQT+A
Sbjct: 152 RLSDMMKRMEFLDFRNLEILILDEADRLLDMGFQKQVNYIISRLPKQRRTGLFSATQTQA 211

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           V +L+KAGLRN + +   AESK             SKT  GL+ EYL+CE+D+K SQLV 
Sbjct: 212 VADLAKAGLRNAMEVISGAESK-------------SKTSSGLYCEYLKCEADQKSSQLVH 258

Query: 181 LLIKNKSKKIIMY 193
           LLI+NK+KK++++
Sbjct: 259 LLIENKNKKLVVF 271

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 =  202 bits (514), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 108/193 (55%), Positives = 133/193 (68%), Gaps = 41/193 (21%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+IISPTRELSAQI+ VA+         +        EV+AD+  +EEEGANLLIGTPG
Sbjct: 93  MGVIISPTRELSAQIHKVARAVRLDFAKCR--------EVEADMNTLEEEGANLLIGTPG 144

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL D+M+RM+ LDFRNL IL+LDEADRLLDMGFQKQ++YIISRLPK RRTGLFSATQT+A
Sbjct: 145 RLSDMMKRMEFLDFRNLEILILDEADRLLDMGFQKQVNYIISRLPKQRRTGLFSATQTQA 204

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           V +L+KAGLRNP                                 YL+CE+D+K SQLV 
Sbjct: 205 VADLAKAGLRNP---------------------------------YLKCEADQKSSQLVH 231

Query: 181 LLIKNKSKKIIMY 193
           LLI+NK+KK++++
Sbjct: 232 LLIENKNKKLVVF 244

Arabidopsis thaliana (taxid: 3702)

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 =  164 bits (416), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 91/197 (46%), Positives = 125/197 (63%), Gaps = 13/197 (6%)

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

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

Query: 117 QTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPS 176
           QT+ +E L +AGLRNPVRI V    K    +A+S Q    KTP+ L   Y+ C++D+K +
Sbjct: 205 QTQELENLVRAGLRNPVRIAV----KEKGVAATSTQ----KTPIRLQNYYMICKADEKFN 256

Query: 177 QLVDLLIKNKSKKIIMY 193
           +L+  L K K +K +++
Sbjct: 257 KLIAFLQKRKQEKHLVF 273

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 =  163 bits (413), Expect = 7e-40,   Method: Compositional matrix adjust.
 Identities = 92/197 (46%), Positives = 127/197 (64%), Gaps = 13/197 (6%)

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

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

Query: 117 QTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPS 176
           QT+ VE L +AGLRNPVRI V    K    +A++ Q    KTP  L   Y+ C++D+K +
Sbjct: 205 QTQEVENLVRAGLRNPVRISV----KEKGVAATNTQ----KTPTRLENYYMICKADEKFN 256

Query: 177 QLVDLLIKNKSKKIIMY 193
           QLV  L ++K +K +++
Sbjct: 257 QLVHFLRQHKQEKHLVF 273

Probable ATP-binding RNA helicase.

Gallus gallus (taxid: 9031)

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 =  162 bits (410), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 93/197 (47%), Positives = 123/197 (62%), Gaps = 13/197 (6%)

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

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

Query: 117 QTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPS 176
           QT+ VE L +AGLRNPVRI V    K    +ASS Q    KTP  L   Y+ C++D+K +
Sbjct: 205 QTQEVENLVRAGLRNPVRISV----KEKGVAASSTQ----KTPSRLENHYMVCKADEKFN 256

Query: 177 QLVDLLIKNKSKKIIMY 193
           QLV  L  +K +K +++
Sbjct: 257 QLVHFLRNHKQEKHLVF 273

Probable ATP-binding RNA helicase.

Bos taurus (taxid: 9913)

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 =  161 bits (408), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 91/197 (46%), Positives = 126/197 (63%), Gaps = 13/197 (6%)

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

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

Query: 117 QTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPS 176
           QT+ VE L +AGLRNPVR+ V    K    +ASS Q    KTP  L   Y+ C++D+K +
Sbjct: 205 QTQEVENLVRAGLRNPVRVSV----KEKGVAASSAQ----KTPSRLENYYMVCKADEKFN 256

Query: 177 QLVDLLIKNKSKKIIMY 193
           QLV  L  +K +K +++
Sbjct: 257 QLVHFLRNHKQEKHLVF 273

Probable ATP-binding RNA helicase.

Homo sapiens (taxid: 9606)

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 =  160 bits (404), Expect = 8e-39,   Method: Compositional matrix adjust.
 Identities = 92/197 (46%), Positives = 127/197 (64%), Gaps = 13/197 (6%)

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

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

Query: 117 QTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPS 176
           QT+ +E+L +AGLRNPVRI V    K    +ASS Q    KTP  L   Y  C +++K +
Sbjct: 205 QTQELEKLVRAGLRNPVRITV----KEKGVAASSVQ----KTPAKLSNYYTMCRAEEKFN 256

Query: 177 QLVDLLIKNKSKKIIMY 193
            LV  L ++K +K +++
Sbjct: 257 TLVAFLRQHKHEKQLVF 273

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

 Score =  157 bits (397), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 89/197 (45%), Positives = 123/197 (62%), Gaps = 13/197 (6%)

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

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

Query: 117 QTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPS 176
           QT+ VE L +AGLRNPVRI V    K    +ASS Q    KTP  L   Y+ C++D+K +
Sbjct: 205 QTQEVENLVRAGLRNPVRISV----KEKGVAASSTQ----KTPSRLENHYMICKADEKFN 256

Query: 177 QLVDLLIKNKSKKIIMY 193
           QLV  L   + +K +++
Sbjct: 257 QLVHFLRSRQQEKHLVF 273

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	203
224101199	592	predicted protein [Populus trichocarpa]	0.950	0.326	0.829	6e-88
225448554	595	PREDICTED: DEAD-box ATP-dependent RNA he	0.896	0.305	0.868	1e-86
297736552	576	unnamed protein product [Vitis vinifera]	0.896	0.315	0.868	1e-86
356568033	589	PREDICTED: DEAD-box ATP-dependent RNA he	0.950	0.327	0.818	1e-86
356540003	589	PREDICTED: DEAD-box ATP-dependent RNA he	0.950	0.327	0.813	4e-86
357461389	659	DEAD-box ATP-dependent RNA helicase [Med	0.950	0.292	0.757	4e-84
297806553	593	hypothetical protein ARALYDRAFT_908458 [	0.931	0.318	0.777	2e-81
15239115	593	DEAD-box ATP-dependent RNA helicase 18 [	0.931	0.318	0.777	2e-81
255559531	592	dead box ATP-dependent RNA helicase, put	0.945	0.324	0.808	6e-81
449460880	587	PREDICTED: DEAD-box ATP-dependent RNA he	0.940	0.325	0.772	2e-80

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

 Score =  328 bits (842), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 160/193 (82%), Positives = 181/193 (93%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+IISPTRELS+QIY+VAQPFI+TL + KSMLLVGG++VKADVK IEEEGANLLIGTPG
Sbjct: 92  MGIIISPTRELSSQIYNVAQPFIATLSNFKSMLLVGGMDVKADVKMIEEEGANLLIGTPG 151

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL+DIM+R+DVLDFRNL +L+LDEADRLLDMGFQKQ++ IISRLPKLRRTGLFSATQTEA
Sbjct: 152 RLFDIMDRVDVLDFRNLEVLILDEADRLLDMGFQKQLNSIISRLPKLRRTGLFSATQTEA 211

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           VEELSKAGLRNPV++EVRAE+KS + S S QQLA SKTP GL LEYLECE+DKKPSQLVD
Sbjct: 212 VEELSKAGLRNPVKVEVRAETKSLNNSVSGQQLAPSKTPSGLLLEYLECEADKKPSQLVD 271

Query: 181 LLIKNKSKKIIMY 193
           LL+KNKSKKII+Y
Sbjct: 272 LLVKNKSKKIIIY 284

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  325 bits (832), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 158/182 (86%), Positives = 176/182 (96%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +G+I+SPTRELS+QIY+VAQPFISTLP+VKS+LLVGGVEVK+D+KKIEEEGANLLIGTPG
Sbjct: 95  LGVILSPTRELSSQIYNVAQPFISTLPNVKSVLLVGGVEVKSDLKKIEEEGANLLIGTPG 154

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RLYDIMERMDVLDFRNL IL+LDEADRLLDMGFQKQI+ II+RLPKLRRTGLFSATQTEA
Sbjct: 155 RLYDIMERMDVLDFRNLEILILDEADRLLDMGFQKQITSIIARLPKLRRTGLFSATQTEA 214

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           VEELSKAGLRNPVR+EVRAE+KS + S SSQQLASSKTP GL++EYLECE+DKKPSQLVD
Sbjct: 215 VEELSKAGLRNPVRVEVRAEAKSLNDSVSSQQLASSKTPSGLNIEYLECEADKKPSQLVD 274

Query: 181 LL 182
           LL
Sbjct: 275 LL 276

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 =  324 bits (831), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 158/182 (86%), Positives = 176/182 (96%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +G+I+SPTRELS+QIY+VAQPFISTLP+VKS+LLVGGVEVK+D+KKIEEEGANLLIGTPG
Sbjct: 95  LGVILSPTRELSSQIYNVAQPFISTLPNVKSVLLVGGVEVKSDLKKIEEEGANLLIGTPG 154

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RLYDIMERMDVLDFRNL IL+LDEADRLLDMGFQKQI+ II+RLPKLRRTGLFSATQTEA
Sbjct: 155 RLYDIMERMDVLDFRNLEILILDEADRLLDMGFQKQITSIIARLPKLRRTGLFSATQTEA 214

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           VEELSKAGLRNPVR+EVRAE+KS + S SSQQLASSKTP GL++EYLECE+DKKPSQLVD
Sbjct: 215 VEELSKAGLRNPVRVEVRAEAKSLNDSVSSQQLASSKTPSGLNIEYLECEADKKPSQLVD 274

Query: 181 LL 182
           LL
Sbjct: 275 LL 276

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 =  324 bits (831), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 158/193 (81%), Positives = 177/193 (91%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +G+IISPTRELS QIYHVAQPFISTL +VKSMLLVGG EVKAD+KKIEEEGAN+LIGTPG
Sbjct: 90  LGIIISPTRELSTQIYHVAQPFISTLANVKSMLLVGGAEVKADLKKIEEEGANILIGTPG 149

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RLYDIM RMDVLD +NL IL+LDEADRLLDMGFQKQI+ II+ LPKLRRTGLFSATQTEA
Sbjct: 150 RLYDIMNRMDVLDLKNLEILILDEADRLLDMGFQKQITSIITLLPKLRRTGLFSATQTEA 209

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           +EEL+KAGLRNPVR+EVRAE+KS +  ASS+Q  SSKTP GLH+EYLECE+DKKPSQLV 
Sbjct: 210 IEELAKAGLRNPVRVEVRAETKSENGPASSKQPESSKTPSGLHIEYLECEADKKPSQLVH 269

Query: 181 LLIKNKSKKIIMY 193
           +LIKN SKKII+Y
Sbjct: 270 ILIKNLSKKIIIY 282

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

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

 Score =  323 bits (827), Expect = 4e-86,   Method: Compositional matrix adjust.
 Identities = 157/193 (81%), Positives = 175/193 (90%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +G+IISPTRELS QIYHVAQ FISTL +VKSMLLVGG EVK D+KKIEEEGAN+LIGTPG
Sbjct: 90  LGIIISPTRELSTQIYHVAQSFISTLMNVKSMLLVGGAEVKTDIKKIEEEGANILIGTPG 149

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RLYDIM RMDVLD +NL IL+LDEADRLLDMGFQKQI+ IIS LPKLRRTGLFSATQTEA
Sbjct: 150 RLYDIMNRMDVLDLKNLEILILDEADRLLDMGFQKQITSIISLLPKLRRTGLFSATQTEA 209

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           +EEL+KAGLRNPVR+EVRAE+KS    ASS+Q  SSKTP GLH+EYLECE DKKPSQL+D
Sbjct: 210 IEELAKAGLRNPVRVEVRAETKSEKGPASSKQPESSKTPSGLHIEYLECEEDKKPSQLLD 269

Query: 181 LLIKNKSKKIIMY 193
           +LIKN+SKKII+Y
Sbjct: 270 ILIKNRSKKIIIY 282

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

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 =  316 bits (809), Expect = 4e-84,   Method: Compositional matrix adjust.
 Identities = 153/202 (75%), Positives = 181/202 (89%), Gaps = 9/202 (4%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +G+IISPTREL++QIYHVAQPFISTL +VKSMLLVGGVEVKAD+KKIEEEGAN+LIGTPG
Sbjct: 104 LGVIISPTRELASQIYHVAQPFISTLANVKSMLLVGGVEVKADIKKIEEEGANVLIGTPG 163

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

Query: 112 LFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECES 171
           LFSATQT+AVEEL+KAGLRNPVR+EVRAE+K+ + SASS+++ SSKTP GL +EYLECE+
Sbjct: 224 LFSATQTQAVEELAKAGLRNPVRVEVRAETKTANDSASSKKIESSKTPSGLQIEYLECEA 283

Query: 172 DKKPSQLVDLLIKNKSKKIIMY 193
           DKKPSQLVD L+KN+SKKII+Y
Sbjct: 284 DKKPSQLVDFLVKNRSKKIIIY 305

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

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 =  307 bits (786), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 150/193 (77%), Positives = 173/193 (89%), Gaps = 4/193 (2%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+IISPTRELS+QIY+VAQPF+STL +V S+LLVGG EVKAD+K IEEEG NLLIGTPG
Sbjct: 92  MGVIISPTRELSSQIYNVAQPFVSTLANVNSVLLVGGREVKADMKIIEEEGCNLLIGTPG 151

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL DIMERM++LDFRNL IL+LDEADRLL+MGFQ+Q++YIISRLPK RRTGLFSATQTE 
Sbjct: 152 RLSDIMERMEILDFRNLEILILDEADRLLEMGFQRQVNYIISRLPKQRRTGLFSATQTEG 211

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           VEEL+KAGLRNPVR+EVRA+SKS     SSQQ  +SKTP GLHLEY+ECE+DKK SQLVD
Sbjct: 212 VEELAKAGLRNPVRVEVRAKSKSE----SSQQFTNSKTPSGLHLEYIECEADKKSSQLVD 267

Query: 181 LLIKNKSKKIIMY 193
           LLIKN  KK+I++
Sbjct: 268 LLIKNSDKKLIVF 280

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 =  306 bits (785), Expect = 2e-81,   Method: Compositional matrix adjust.
 Identities = 150/193 (77%), Positives = 173/193 (89%), Gaps = 4/193 (2%)

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

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL DIMERM++LDFRNL IL+LDEADRLL+MGFQ+Q++YIISRLPK RRTGLFSATQTE 
Sbjct: 152 RLSDIMERMEILDFRNLEILILDEADRLLEMGFQRQVNYIISRLPKQRRTGLFSATQTEG 211

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           VEEL+KAGLRNPVR+EVRA+SKS     SSQQL +SKTP GLHLEY+ECE+DKK SQLVD
Sbjct: 212 VEELAKAGLRNPVRVEVRAKSKSE----SSQQLTNSKTPSGLHLEYMECEADKKSSQLVD 267

Query: 181 LLIKNKSKKIIMY 193
           LLIKN  KK+I++
Sbjct: 268 LLIKNSDKKLIVF 280

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 =  305 bits (782), Expect = 6e-81,   Method: Compositional matrix adjust.
 Identities = 156/193 (80%), Positives = 179/193 (92%), Gaps = 1/193 (0%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+I+SPTRELS+QIY+VAQPFI TL +VKSMLLVGGV+VKADVKKIEEEGAN+LIGTPG
Sbjct: 93  MGIILSPTRELSSQIYNVAQPFIETLSNVKSMLLVGGVDVKADVKKIEEEGANILIGTPG 152

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL+DIMER+D+LDFRNL +L+LDEADRLLDMGFQKQI+ IISRLPKLRRTGLFSATQTEA
Sbjct: 153 RLFDIMERVDILDFRNLEVLILDEADRLLDMGFQKQITSIISRLPKLRRTGLFSATQTEA 212

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           VEEL+KAGLRNPVR+EVRA++KS +  ++S QL+SSKTP GL LEYLECE+D KPS LV 
Sbjct: 213 VEELAKAGLRNPVRVEVRAQTKSLN-ESASSQLSSSKTPSGLQLEYLECEADMKPSHLVS 271

Query: 181 LLIKNKSKKIIMY 193
           LL KNKSKKII+Y
Sbjct: 272 LLNKNKSKKIIVY 284

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449460880|ref|XP_004148172.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 18-like [Cucumis sativus] gi|449515784|ref|XP_004164928.1| PREDICTED: DEAD-box ATP-dependent RNA helicase 18-like [Cucumis sativus]

 Score =  304 bits (778), Expect = 2e-80,   Method: Compositional matrix adjust.
 Identities = 149/193 (77%), Positives = 173/193 (89%), Gaps = 2/193 (1%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           MG+IISPTRELS+QIY VA+PF+STL + K++LLVGG +VK D+K IEEEGANLLIGTPG
Sbjct: 90  MGIIISPTRELSSQIYEVARPFVSTLSNFKAVLLVGGADVKVDMKVIEEEGANLLIGTPG 149

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL+DIM+R++ LDFRN  +L+LDEADRLLDMGFQKQI+ IISRLPKLRRTGLFSATQTEA
Sbjct: 150 RLFDIMDRIENLDFRNFEVLILDEADRLLDMGFQKQITSIISRLPKLRRTGLFSATQTEA 209

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           VEELSKAGLRNP+R+EV+AESK      SS QLASSKTP  LH+EYLECE+DKK +QLVD
Sbjct: 210 VEELSKAGLRNPIRVEVKAESKP--GPLSSTQLASSKTPSSLHIEYLECEADKKSTQLVD 267

Query: 181 LLIKNKSKKIIMY 193
           +LIKNKSKKII+Y
Sbjct: 268 ILIKNKSKKIIVY 280

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

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	203
TAIR|locus:2153564	593	AT5G05450 [Arabidopsis thalian	0.931	0.318	0.725	8e-69
TAIR|locus:2825324	558	AT1G71370 [Arabidopsis thalian	0.886	0.322	0.652	2.2e-59
TAIR|locus:2032338	465	AT1G71280 [Arabidopsis thalian	0.610	0.266	0.704	7.7e-50
UNIPROTKB|F1NJA0	591	DDX55 "ATP-dependent RNA helic	0.901	0.309	0.448	2.4e-35
UNIPROTKB|Q5ZLN8	591	DDX55 "ATP-dependent RNA helic	0.901	0.309	0.448	2.4e-35
UNIPROTKB|E2R316	483	DDX55 "Uncharacterized protein	0.901	0.378	0.433	8.3e-35
UNIPROTKB|F1P8J6	599	DDX55 "Uncharacterized protein	0.901	0.305	0.433	2.2e-34
UNIPROTKB|F5H5U2	569	DDX55 "ATP-dependent RNA helic	0.901	0.321	0.433	2.4e-34
UNIPROTKB|F1MW45	601	DDX55 "ATP-dependent RNA helic	0.901	0.304	0.443	2.9e-34
UNIPROTKB|Q2NL08	601	DDX55 "ATP-dependent RNA helic	0.901	0.304	0.443	2.9e-34

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

 Score = 698 (250.8 bits), Expect = 8.0e-69, P = 8.0e-69
 Identities = 140/193 (72%), Positives = 162/193 (83%)

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

Query:    61 RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
             RL DIMERM++LDFRNL IL+LDEADRLL+MGFQ+Q++YIISRLPK RRTGLFSATQTE 
Sbjct:   152 RLSDIMERMEILDFRNLEILILDEADRLLEMGFQRQVNYIISRLPKQRRTGLFSATQTEG 211

Query:   121 VEELSKAGLRNPVRIEVRAEXXXXXXXXXXXXXXXXXTPLGLHLEYLECESDKKPSQLVD 180
             VEEL+KAGLRNPVR+EVRA+                 TP GLHLEY+ECE+DKK SQLVD
Sbjct:   212 VEELAKAGLRNPVRVEVRAKSKSESSQQLTNSK----TPSGLHLEYMECEADKKSSQLVD 267

Query:   181 LLIKNKSKKIIMY 193
             LLIKN  KK+I++
Sbjct:   268 LLIKNSDKKLIVF 280

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 = 609 (219.4 bits), Expect = 2.2e-59, P = 2.2e-59
 Identities = 126/193 (65%), Positives = 156/193 (80%)

Query:     1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             MG+IISPTRELSAQI+ VA+PF+STLP+V S+LLVGG EV+AD+  +EEEGANLLIGTPG
Sbjct:    92 MGVIISPTRELSAQIHKVAEPFVSTLPNVNSVLLVGGREVEADMNTLEEEGANLLIGTPG 151

Query:    61 RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
             RL D+M+RM+ LDFRNL IL+LDEADRLLDMGFQKQ++YIISRLPK RRTGLFSATQT+A
Sbjct:   152 RLSDMMKRMEFLDFRNLEILILDEADRLLDMGFQKQVNYIISRLPKQRRTGLFSATQTQA 211

Query:   121 VEELSKAGLRNPVRIEVRAEXXXXXXXXXXXXXXXXXTPLGLHLEYLECESDKKPSQLVD 180
             V +L+KAGLRN + +   AE                 T  GL+ EYL+CE+D+K SQLV 
Sbjct:   212 VADLAKAGLRNAMEVISGAESKSK-------------TSSGLYCEYLKCEADQKSSQLVH 258

Query:   181 LLIKNKSKKIIMY 193
             LLI+NK+KK++++
Sbjct:   259 LLIENKNKKLVVF 271

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 = 432 (157.1 bits), Expect = 7.7e-50, Sum P(2) = 7.7e-50
 Identities = 93/132 (70%), Positives = 108/132 (81%)

Query:     1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             MG+IISPTRELSAQI+ VA+     L   K        EV+AD+  +EEEGANLLIGTPG
Sbjct:    93 MGVIISPTRELSAQIHKVARAV--RLDFAKCR------EVEADMNTLEEEGANLLIGTPG 144

Query:    61 RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
             RL D+M+RM+ LDFRNL IL+LDEADRLLDMGFQKQ++YIISRLPK RRTGLFSATQT+A
Sbjct:   145 RLSDMMKRMEFLDFRNLEILILDEADRLLDMGFQKQVNYIISRLPKQRRTGLFSATQTQA 204

Query:   121 VEELSKAGLRNP 132
             V +L+KAGLRNP
Sbjct:   205 VADLAKAGLRNP 216

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

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

 Score = 385 (140.6 bits), Expect = 2.4e-35, P = 2.4e-35
 Identities = 88/196 (44%), Positives = 122/196 (62%)

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

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

Query:   118 TEAVEELSKAGLRNPVRIEVRAEXXXXXXXXXXXXXXXXXTPLGLHLEYLECESDKKPSQ 177
             T+ VE L +AGLRNPVRI V+ +                 TP  L   Y+ C++D+K +Q
Sbjct:   206 TQEVENLVRAGLRNPVRISVKEKGVAATNTQK--------TPTRLENYYMICKADEKFNQ 257

Query:   178 LVDLLIKNKSKKIIMY 193
             LV  L ++K +K +++
Sbjct:   258 LVHFLRQHKQEKHLVF 273

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 = 385 (140.6 bits), Expect = 2.4e-35, P = 2.4e-35
 Identities = 88/196 (44%), Positives = 122/196 (62%)

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

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

Query:   118 TEAVEELSKAGLRNPVRIEVRAEXXXXXXXXXXXXXXXXXTPLGLHLEYLECESDKKPSQ 177
             T+ VE L +AGLRNPVRI V+ +                 TP  L   Y+ C++D+K +Q
Sbjct:   206 TQEVENLVRAGLRNPVRISVKEKGVAATNTQK--------TPTRLENYYMICKADEKFNQ 257

Query:   178 LVDLLIKNKSKKIIMY 193
             LV  L ++K +K +++
Sbjct:   258 LVHFLRQHKQEKHLVF 273

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

GO:0003723 "RNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

 Score = 377 (137.8 bits), Expect = 8.3e-35, P = 8.3e-35
 Identities = 85/196 (43%), Positives = 121/196 (61%)

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

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

Query:   118 TEAVEELSKAGLRNPVRIEVRAEXXXXXXXXXXXXXXXXXTPLGLHLEYLECESDKKPSQ 177
             T+ VE L +AGLRNPVRI V+ +                 TP  L   Y+ C++D+K +Q
Sbjct:   206 TQEVESLVRAGLRNPVRISVKEKGVAASSTQK--------TPSRLENYYMVCKADEKFNQ 257

Query:   178 LVDLLIKNKSKKIIMY 193
             LV  L  +K +K +++
Sbjct:   258 LVHFLRNHKQEKHLIF 273

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

GO:0005524 "ATP binding" evidence=IEA

GO:0003676 "nucleic acid binding" evidence=IEA

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

 Score = 377 (137.8 bits), Expect = 2.2e-34, P = 2.2e-34
 Identities = 85/196 (43%), Positives = 121/196 (61%)

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

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

Query:   118 TEAVEELSKAGLRNPVRIEVRAEXXXXXXXXXXXXXXXXXTPLGLHLEYLECESDKKPSQ 177
             T+ VE L +AGLRNPVRI V+ +                 TP  L   Y+ C++D+K +Q
Sbjct:   206 TQEVESLVRAGLRNPVRISVKEKGVAASSTQK--------TPSRLENYYMVCKADEKFNQ 257

Query:   178 LVDLLIKNKSKKIIMY 193
             LV  L  +K +K +++
Sbjct:   258 LVHFLRNHKQEKHLIF 273

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 = 375 (137.1 bits), Expect = 2.4e-34, P = 2.4e-34
 Identities = 85/196 (43%), Positives = 121/196 (61%)

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

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

Query:   118 TEAVEELSKAGLRNPVRIEVRAEXXXXXXXXXXXXXXXXXTPLGLHLEYLECESDKKPSQ 177
             T+ VE L +AGLRNPVR+ V+ +                 TP  L   Y+ C++D+K +Q
Sbjct:   206 TQEVENLVRAGLRNPVRVSVKEKGVAASSAQK--------TPSRLENYYMVCKADEKFNQ 257

Query:   178 LVDLLIKNKSKKIIMY 193
             LV  L  +K +K +++
Sbjct:   258 LVHFLRNHKQEKHLVF 273

GO:0003676 "nucleic acid binding" evidence=IEA

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

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1MW45 DDX55 "ATP-dependent RNA helicase DDX55" [Bos taurus (taxid:9913)]

 Score = 376 (137.4 bits), Expect = 2.9e-34, P = 2.9e-34
 Identities = 87/196 (44%), Positives = 118/196 (60%)

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

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

Query:   118 TEAVEELSKAGLRNPVRIEVRAEXXXXXXXXXXXXXXXXXTPLGLHLEYLECESDKKPSQ 177
             T+ VE L +AGLRNPVRI V+ +                 TP  L   Y+ C++D+K +Q
Sbjct:   206 TQEVENLVRAGLRNPVRISVKEKGVAASSTQK--------TPSRLENHYMVCKADEKFNQ 257

Query:   178 LVDLLIKNKSKKIIMY 193
             LV  L  +K +K +++
Sbjct:   258 LVHFLRNHKQEKHLVF 273

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

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

UNIPROTKB|Q2NL08 DDX55 "ATP-dependent RNA helicase DDX55" [Bos taurus (taxid:9913)]

 Score = 376 (137.4 bits), Expect = 2.9e-34, P = 2.9e-34
 Identities = 87/196 (44%), Positives = 118/196 (60%)

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

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

Query:   118 TEAVEELSKAGLRNPVRIEVRAEXXXXXXXXXXXXXXXXXTPLGLHLEYLECESDKKPSQ 177
             T+ VE L +AGLRNPVRI V+ +                 TP  L   Y+ C++D+K +Q
Sbjct:   206 TQEVENLVRAGLRNPVRISVKEKGVAASSTQK--------TPSRLENHYMVCKADEKFNQ 257

Query:   178 LVDLLIKNKSKKIIMY 193
             LV  L  +K +K +++
Sbjct:   258 LVHFLRNHKQEKHLVF 273

GO:0005524 "ATP binding" evidence=IEA

GO:0003723 "RNA binding" evidence=IEA

GO:0008026 "ATP-dependent helicase activity" 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	0.7772	0.9310	0.3187	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

Your Input:
	fgenesh4_pm.C_LG_VIII000290	hypothetical protein (592 aa)
		(Populus trichocarpa)
Predicted Functional Partners:
	gw1.8412.1.1	annotation not avaliable (96 aa)			•						0.504

---

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	203
cd00268	203	cd00268, DEADc, DEAD-box helicases	3e-52
COG0513	513	COG0513, SrmB, Superfamily II DNA and RNA helicase	4e-45
PRK11776	460	PRK11776, PRK11776, ATP-dependent RNA helicase Dbp	2e-34
pfam00270	169	pfam00270, DEAD, DEAD/DEAH box helicase	4e-34
smart00487	201	smart00487, DEXDc, DEAD-like helicases superfamily	2e-28
PRK10590	456	PRK10590, PRK10590, ATP-dependent RNA helicase Rhl	7e-27
PRK04837	423	PRK04837, PRK04837, ATP-dependent RNA helicase Rhl	4e-26
PRK01297	475	PRK01297, PRK01297, ATP-dependent RNA helicase Rhl	8e-26
PTZ00424	401	PTZ00424, PTZ00424, helicase 45; Provisional	7e-24
PRK04537	572	PRK04537, PRK04537, ATP-dependent RNA helicase Rhl	2e-23
cd00046	144	cd00046, DEXDc, DEAD-like helicases superfamily	4e-22
PTZ00110	545	PTZ00110, PTZ00110, helicase; Provisional	6e-22
PLN00206	518	PLN00206, PLN00206, DEAD-box ATP-dependent RNA hel	4e-21
PRK11634	629	PRK11634, PRK11634, ATP-dependent RNA helicase Dea	6e-21
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-16

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

 Score =  166 bits (422), Expect = 3e-52
 Identities = 60/136 (44%), Positives = 90/136 (66%), Gaps = 3/136 (2%)

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

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

Query: 121 VEELSKAGLRNPVRIE 136
           V +L++  LRNPVRI 
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 =  155 bits (394), Expect = 4e-45
 Identities = 67/193 (34%), Positives = 107/193 (55%), Gaps = 16/193 (8%)

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

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

Query: 123 ELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECES-DKKPSQLVDL 181
           EL++  L +PV IEV  E                +T   +   YLE ES ++K   L+ L
Sbjct: 221 ELARRYLNDPVEIEVSVE-------------KLERTLKKIKQFYLEVESEEEKLELLLKL 267

Query: 182 LIKNKSKKIIMYV 194
           L      ++I++V
Sbjct: 268 LKDEDEGRVIVFV 280

Length = 513

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

 Score =  126 bits (318), Expect = 2e-34
 Identities = 67/184 (36%), Positives = 99/184 (53%), Gaps = 26/184 (14%)

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

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

Query: 119 EAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQL 178
           E +  +S+   R+PV ++V +    H   A  Q+             + E   D++   L
Sbjct: 190 EGIAAISQRFQRDPVEVKVEST---HDLPAIEQR-------------FYEVSPDERLPAL 233

Query: 179 VDLL 182
             LL
Sbjct: 234 QRLL 237

Length = 460

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

 Score =  118 bits (299), Expect = 4e-34
 Identities = 52/124 (41%), Positives = 78/124 (62%), Gaps = 1/124 (0%)

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

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 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|214692 smart00487, DEXDc, DEAD-like helicases superfamily

 Score =  105 bits (263), Expect = 2e-28
 Identities = 50/135 (37%), Positives = 78/135 (57%), Gaps = 2/135 (1%)

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

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

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

Length = 201

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

 Score =  105 bits (264), Expect = 7e-27
 Identities = 54/135 (40%), Positives = 89/135 (65%), Gaps = 3/135 (2%)

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

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

Query: 123 ELSKAGLRNPVRIEV 137
            L++  L NP+ IEV
Sbjct: 196 ALAEKLLHNPLEIEV 210

Length = 456

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

 Score =  103 bits (258), Expect = 4e-26
 Identities = 55/145 (37%), Positives = 83/145 (57%), Gaps = 5/145 (3%)

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

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

Query: 121 VEELSKAGLRNPVRIEVRAESKSHH 145
           V EL+   + NP  +EV  E K+ H
Sbjct: 204 VRELAFEHMNNPEYVEVEPEQKTGH 228

Length = 423

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

 Score =  103 bits (257), Expect = 8e-26
 Identities = 57/144 (39%), Positives = 87/144 (60%), Gaps = 6/144 (4%)

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

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

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

Length = 475

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

 Score = 96.8 bits (241), Expect = 7e-24
 Identities = 51/138 (36%), Positives = 83/138 (60%), Gaps = 3/138 (2%)

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

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

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

Length = 401

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

 Score = 96.9 bits (241), Expect = 2e-23
 Identities = 52/141 (36%), Positives = 88/141 (62%), Gaps = 4/141 (2%)

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

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

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

Length = 572

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

 Score = 87.0 bits (216), Expect = 4e-22
 Identities = 42/113 (37%), Positives = 64/113 (56%), Gaps = 4/113 (3%)

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

Query: 64  DIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT 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|240273 PTZ00110, PTZ00110, helicase; Provisional

 Score = 92.1 bits (229), Expect = 6e-22
 Identities = 49/136 (36%), Positives = 80/136 (58%), Gaps = 4/136 (2%)

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

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

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

Length = 545

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

 Score = 89.8 bits (223), Expect = 4e-21
 Identities = 55/182 (30%), Positives = 100/182 (54%), Gaps = 19/182 (10%)

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

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

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVD 180
           VE+ + +  ++ + I +      +  + + +QLA            +  E+ +K  +L D
Sbjct: 314 VEKFASSLAKDIILISI---GNPNRPNKAVKQLA------------IWVETKQKKQKLFD 358

Query: 181 LL 182
           +L
Sbjct: 359 IL 360

Length = 518

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

 Score = 89.5 bits (222), Expect = 6e-21
 Identities = 49/139 (35%), Positives = 82/139 (58%), Gaps = 4/139 (2%)

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

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

Query: 123 ELSKAGLRNPVRIEVRAES 141
            +++  ++ P   EVR +S
Sbjct: 196 RITRRFMKEPQ--EVRIQS 212

Length = 629

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

 Score = 76.9 bits (190), Expect = 1e-16
 Identities = 49/155 (31%), Positives = 85/155 (54%), Gaps = 16/155 (10%)

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

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

Query: 120 AVEELSKAGLRNPVRIEV---RAESKS-----HHA 146
           AV++ ++  L +PV +E    R E K      + A
Sbjct: 192 AVQDFAERLLNDPVEVEAEPSRRERKKIHQWYYRA 226

Length = 434

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	203
KOG0330	476	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	100.0
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	100.0
KOG0343	758	consensus RNA Helicase [RNA processing and modific	100.0
KOG0338	691	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0345	567	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0326	459	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0339	731	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	100.0
KOG0342	543	consensus ATP-dependent RNA helicase pitchoune [RN	100.0
KOG4284	980	consensus DEAD box protein [Transcription]	100.0
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	100.0
KOG0346	569	consensus RNA helicase [RNA processing and modific	100.0
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	100.0
PTZ00110	545	helicase; Provisional	100.0
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	100.0
KOG0348	708	consensus ATP-dependent RNA helicase [RNA processi	100.0
KOG0335	482	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	100.0
KOG0329	387	consensus ATP-dependent RNA helicase [RNA processi	100.0
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	100.0
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	100.0
KOG0327	397	consensus Translation initiation factor 4F, helica	100.0
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	99.98
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	99.97
KOG0336	629	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0337	529	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0341	610	consensus DEAD-box protein abstrakt [RNA processin	99.97
KOG0340	442	consensus ATP-dependent RNA helicase [RNA processi	99.97
KOG0347	731	consensus RNA helicase [RNA processing and modific	99.97
KOG0334	997	consensus RNA helicase [RNA processing and modific	99.96
KOG0350	620	consensus DEAD-box ATP-dependent RNA helicase [RNA	99.96
PTZ00424	401	helicase 45; Provisional	99.96
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	99.94
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	99.93
PRK09401	1176	reverse gyrase; Reviewed	99.93
PRK14701	1638	reverse gyrase; Provisional	99.9
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	99.9
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	99.9
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	99.88
cd00268	203	DEADc DEAD-box helicases. A diverse family of prot	99.87
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	99.87
PRK00254	720	ski2-like helicase; Provisional	99.87
KOG0349	725	consensus Putative DEAD-box RNA helicase DDX1 [RNA	99.86
PRK13767	876	ATP-dependent helicase; Provisional	99.85
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	99.85
PRK02362	737	ski2-like helicase; Provisional	99.85
PRK10689	1147	transcription-repair coupling factor; Provisional	99.84
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	99.84
PF00270	169	DEAD: DEAD/DEAH box helicase; InterPro: IPR011545	99.83
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	99.83
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	99.82
COG1204	766	Superfamily II helicase [General function predicti	99.81
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	99.81
PRK01172	674	ski2-like helicase; Provisional	99.8
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	99.79
COG1201	814	Lhr Lhr-like helicases [General function predictio	99.78
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	99.77
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	99.77
PHA02653	675	RNA helicase NPH-II; Provisional	99.77
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	99.75
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	99.74
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	99.74
COG1205	851	Distinct helicase family with a unique C-terminal	99.71
COG1202	830	Superfamily II helicase, archaea-specific [General	99.67
PRK12898	656	secA preprotein translocase subunit SecA; Reviewed	99.64
COG0514	590	RecQ Superfamily II DNA helicase [DNA replication,	99.63
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	99.59
PHA02558	501	uvsW UvsW helicase; Provisional	99.58
TIGR00963	745	secA preprotein translocase, SecA subunit. The pro	99.57
smart00487	201	DEXDc DEAD-like helicases superfamily.	99.56
PRK09200	790	preprotein translocase subunit SecA; Reviewed	99.55
TIGR03714	762	secA2 accessory Sec system translocase SecA2. Memb	99.55
COG4581	1041	Superfamily II RNA helicase [DNA replication, reco	99.54
KOG0948	1041	consensus Nuclear exosomal RNA helicase MTR4, DEAD	99.54
KOG0947	1248	consensus Cytoplasmic exosomal RNA helicase SKI2,	99.54
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	99.52
PRK05580	679	primosome assembly protein PriA; Validated	99.52
PRK12904	830	preprotein translocase subunit SecA; Reviewed	99.5
TIGR00595	505	priA primosomal protein N'. All proteins in this f	99.49
PRK12899	970	secA preprotein translocase subunit SecA; Reviewed	99.49
KOG0351	941	consensus ATP-dependent DNA helicase [Replication,	99.43
PRK13766	773	Hef nuclease; Provisional	99.38
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	99.38
PRK13104	896	secA preprotein translocase subunit SecA; Reviewed	99.36
COG1111	542	MPH1 ERCC4-like helicases [DNA replication, recomb	99.35
cd00046	144	DEXDc DEAD-like helicases superfamily. A diverse f	99.34
PRK09694	878	helicase Cas3; Provisional	99.25
KOG0353	695	consensus ATP-dependent DNA helicase [General func	99.22
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	99.16
PF06862	442	DUF1253: Protein of unknown function (DUF1253); In	99.11
TIGR00603	732	rad25 DNA repair helicase rad25. All proteins in t	99.11
KOG0352	641	consensus ATP-dependent DNA helicase [Replication,	99.08
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	99.02
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	98.97
COG1061	442	SSL2 DNA or RNA helicases of superfamily II [Trans	98.96
PRK13107	908	preprotein translocase subunit SecA; Reviewed	98.95
KOG0354	746	consensus DEAD-box like helicase [General function	98.85
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	98.76
PF04851	184	ResIII: Type III restriction enzyme, res subunit;	98.62
KOG0950	1008	consensus DNA polymerase theta/eta, DEAD-box super	98.48
COG1198	730	PriA Primosomal protein N' (replication factor Y)	98.47
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	98.45
KOG0949	1330	consensus Predicted helicase, DEAD-box superfamily	98.42
PRK12906	796	secA preprotein translocase subunit SecA; Reviewed	98.41
PF14617	252	CMS1: U3-containing 90S pre-ribosomal complex subu	98.4
PRK14873	665	primosome assembly protein PriA; Provisional	98.29
PRK04914	956	ATP-dependent helicase HepA; Validated	98.28
TIGR00348	667	hsdR type I site-specific deoxyribonuclease, HsdR	98.21
PF00176	299	SNF2_N: SNF2 family N-terminal domain; InterPro: I	98.2
PRK11448	1123	hsdR type I restriction enzyme EcoKI subunit R; Pr	98.16
PF07652	148	Flavi_DEAD: Flavivirus DEAD domain ; InterPro: IPR	98.13
COG1203	733	CRISPR-associated helicase Cas3 [Defense mechanism	98.09
KOG0951	1674	consensus RNA helicase BRR2, DEAD-box superfamily	98.07
KOG2340	698	consensus Uncharacterized conserved protein [Funct	98.05
KOG0385	971	consensus Chromatin remodeling complex WSTF-ISWI,	98.04
PRK13103	913	secA preprotein translocase subunit SecA; Reviewed	97.96
PLN03142	1033	Probable chromatin-remodeling complex ATPase chain	97.94
COG4096	875	HsdR Type I site-specific restriction-modification	97.9
KOG0389	941	consensus SNF2 family DNA-dependent ATPase [Chroma	97.76
COG1643	845	HrpA HrpA-like helicases [DNA replication, recombi	97.68
KOG4150	1034	consensus Predicted ATP-dependent RNA helicase [RN	97.66
PF07517	266	SecA_DEAD: SecA DEAD-like domain; InterPro: IPR011	97.63
PRK12326	764	preprotein translocase subunit SecA; Reviewed	97.57
TIGR03117	636	cas_csf4 CRISPR-associated DEAD/DEAH-box helicase	97.57
PRK07246	820	bifunctional ATP-dependent DNA helicase/DNA polyme	97.4
CHL00122	870	secA preprotein translocase subunit SecA; Validate	97.39
KOG0387	923	consensus Transcription-coupled repair protein CSB	97.34
KOG1123	776	consensus RNA polymerase II transcription initiati	97.28
PRK12902	939	secA preprotein translocase subunit SecA; Reviewed	97.28
KOG0952	1230	consensus DNA/RNA helicase MER3/SLH1, DEAD-box sup	97.09
KOG0922	674	consensus DEAH-box RNA helicase [RNA processing an	97.0
PF02399	824	Herpes_ori_bp: Origin of replication binding prote	96.9
KOG0390	776	consensus DNA repair protein, SNF2 family [Replica	96.77
TIGR01407	850	dinG_rel DnaQ family exonuclease/DinG family helic	96.64
KOG0392	1549	consensus SNF2 family DNA-dependent ATPase domain-	96.54
PRK10689	1147	transcription-repair coupling factor; Provisional	96.45
TIGR00580	926	mfd transcription-repair coupling factor (mfd). Al	96.31
TIGR02562	1110	cas3_yersinia CRISPR-associated helicase Cas3. The	96.31
KOG0391	1958	consensus SNF2 family DNA-dependent ATPase [Genera	96.3
KOG4439	901	consensus RNA polymerase II transcription terminat	96.23
COG0610	962	Type I site-specific restriction-modification syst	95.94
KOG1002	791	consensus Nucleotide excision repair protein RAD16	95.93
PRK04537	572	ATP-dependent RNA helicase RhlB; Provisional	95.9
PRK04837	423	ATP-dependent RNA helicase RhlB; Provisional	95.89
KOG0384	1373	consensus Chromodomain-helicase DNA-binding protei	95.89
TIGR00631	655	uvrb excinuclease ABC, B subunit. This family is b	95.85
COG1197	1139	Mfd Transcription-repair coupling factor (superfam	95.71
TIGR00596	814	rad1 DNA repair protein (rad1). This family is bas	95.64
TIGR00643	630	recG ATP-dependent DNA helicase RecG.	95.49
PRK10917	681	ATP-dependent DNA helicase RecG; Provisional	95.35
PRK10590	456	ATP-dependent RNA helicase RhlE; Provisional	95.34
PRK11192	434	ATP-dependent RNA helicase SrmB; Provisional	95.34
KOG3089	271	consensus Predicted DEAD-box-containing helicase [	95.33
KOG0925	699	consensus mRNA splicing factor ATP-dependent RNA h	95.31
KOG0920	924	consensus ATP-dependent RNA helicase A [RNA proces	95.19
COG0513	513	SrmB Superfamily II DNA and RNA helicases [DNA rep	95.13
PRK11776	460	ATP-dependent RNA helicase DbpA; Provisional	95.12
TIGR00614	470	recQ_fam ATP-dependent DNA helicase, RecQ family.	95.05
PRK12903	925	secA preprotein translocase subunit SecA; Reviewed	95.04
PRK11634	629	ATP-dependent RNA helicase DeaD; Provisional	94.85
PTZ00110	545	helicase; Provisional	94.84
KOG0923	902	consensus mRNA splicing factor ATP-dependent RNA h	94.84
KOG0333	673	consensus U5 snRNP-like RNA helicase subunit [RNA	94.79
PF13872	303	AAA_34: P-loop containing NTP hydrolase pore-1	94.78
PRK01297	475	ATP-dependent RNA helicase RhlB; Provisional	94.42
PRK11057	607	ATP-dependent DNA helicase RecQ; Provisional	94.39
COG0556	663	UvrB Helicase subunit of the DNA excision repair c	94.37
TIGR01054	1171	rgy reverse gyrase. Generally, these gyrases are e	94.35
KOG1001	674	consensus Helicase-like transcription factor HLTF/	94.26
PLN00206	518	DEAD-box ATP-dependent RNA helicase; Provisional	94.26
KOG1000	689	consensus Chromatin remodeling protein HARP/SMARCA	94.25
PTZ00424	401	helicase 45; Provisional	94.05
TIGR01389	591	recQ ATP-dependent DNA helicase RecQ. The ATP-depe	93.94
PRK09401	1176	reverse gyrase; Reviewed	93.94
KOG0388	1185	consensus SNF2 family DNA-dependent ATPase [Replic	93.77
PRK11664	812	ATP-dependent RNA helicase HrpB; Provisional	93.74
PRK05580	679	primosome assembly protein PriA; Validated	93.71
PRK05298	652	excinuclease ABC subunit B; Provisional	93.67
PRK13767	876	ATP-dependent helicase; Provisional	93.58
COG4889	1518	Predicted helicase [General function prediction on	93.48
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	93.31
TIGR01970	819	DEAH_box_HrpB ATP-dependent helicase HrpB. This mo	93.28
PRK05642	234	DNA replication initiation factor; Validated	93.17
KOG0331	519	consensus ATP-dependent RNA helicase [RNA processi	93.12
cd00079	131	HELICc Helicase superfamily c-terminal domain; ass	92.84
PF09848	352	DUF2075: Uncharacterized conserved protein (DUF207	92.74
COG0553	866	HepA Superfamily II DNA/RNA helicases, SNF2 family	92.72
PHA02653	675	RNA helicase NPH-II; Provisional	92.71
KOG0328	400	consensus Predicted ATP-dependent RNA helicase FAL	92.3
PRK12422	445	chromosomal replication initiation protein; Provis	92.19
TIGR00595	505	priA primosomal protein N'. All proteins in this f	91.92
PF02463	220	SMC_N: RecF/RecN/SMC N terminal domain; InterPro:	91.9
KOG0386	1157	consensus Chromatin remodeling complex SWI/SNF, co	91.78
PF00308	219	Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013	91.68
PLN03137	1195	ATP-dependent DNA helicase; Q4-like; Provisional	91.67
TIGR03817	742	DECH_helic helicase/secretion neighborhood putativ	91.59
PRK15483	986	type III restriction-modification system StyLTI en	91.42
PRK09694	878	helicase Cas3; Provisional	91.25
TIGR03158	357	cas3_cyano CRISPR-associated helicase, Cyano-type.	91.2
KOG0344	593	consensus ATP-dependent RNA helicase [RNA processi	91.0
PHA02544	316	44 clamp loader, small subunit; Provisional	90.84
PF13401	131	AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S	90.84
KOG0332	477	consensus ATP-dependent RNA helicase [RNA processi	90.83
TIGR03420	226	DnaA_homol_Hda DnaA regulatory inactivator Hda. Me	90.66
COG1200	677	RecG RecG-like helicase [DNA replication, recombin	90.46
KOG0924	1042	consensus mRNA splicing factor ATP-dependent RNA h	90.41
COG1198	730	PriA Primosomal protein N' (replication factor Y)	90.34
PRK14701	1638	reverse gyrase; Provisional	90.32
TIGR01587	358	cas3_core CRISPR-associated helicase Cas3. This mo	90.13
PRK12901	1112	secA preprotein translocase subunit SecA; Reviewed	90.12
PRK14087	450	dnaA chromosomal replication initiation protein; P	90.0
PRK08903	227	DnaA regulatory inactivator Hda; Validated	89.67
PRK14088	440	dnaA chromosomal replication initiation protein; P	89.27
PF06733	174	DEAD_2: DEAD_2; InterPro: IPR010614 This represent	88.91
PF05621	302	TniB: Bacterial TniB protein; InterPro: IPR008868	88.85
KOG0989	346	consensus Replication factor C, subunit RFC4 [Repl	88.78
KOG0926	1172	consensus DEAH-box RNA helicase [RNA processing an	88.75
PRK04914	956	ATP-dependent helicase HepA; Validated	88.26
PHA02558	501	uvsW UvsW helicase; Provisional	88.14
TIGR00362	405	DnaA chromosomal replication initiator protein Dna	88.08
COG4098	441	comFA Superfamily II DNA/RNA helicase required for	87.94
PRK05986	191	cob(I)alamin adenolsyltransferase/cobinamide ATP-d	87.81
PRK06893	229	DNA replication initiation factor; Validated	87.78
KOG2170	344	consensus ATPase of the AAA+ superfamily [General	87.7
PRK00149	450	dnaA chromosomal replication initiation protein; R	87.7
TIGR00708	173	cobA cob(I)alamin adenosyltransferase. Alternate n	87.51
cd00561	159	CobA_CobO_BtuR ATP:corrinoid adenosyltransferase B	87.41
COG0593	408	DnaA ATPase involved in DNA replication initiation	87.05
PRK08084	235	DNA replication initiation factor; Provisional	86.97
PRK11131	1294	ATP-dependent RNA helicase HrpA; Provisional	86.81
PRK14086	617	dnaA chromosomal replication initiation protein; P	86.67
PRK09751	1490	putative ATP-dependent helicase Lhr; Provisional	86.38
smart00488	289	DEXDc2 DEAD-like helicases superfamily.	86.21
smart00489	289	DEXDc3 DEAD-like helicases superfamily.	86.21
PRK07413	382	hypothetical protein; Validated	86.14
TIGR01967	1283	DEAH_box_HrpA ATP-dependent helicase HrpA. This mo	86.04
PF05127	177	Helicase_RecD: Helicase; InterPro: IPR007807 This	85.99
PF00271	78	Helicase_C: Helicase conserved C-terminal domain;	85.93
PF03354	477	Terminase_1: Phage Terminase ; InterPro: IPR005021	85.89
COG0497	557	RecN ATPase involved in DNA repair [DNA replicatio	85.83
PF13086	236	AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV	84.88
PRK12900	1025	secA preprotein translocase subunit SecA; Reviewed	84.63
PRK01172	674	ski2-like helicase; Provisional	84.47
PRK07414	178	cob(I)yrinic acid a,c-diamide adenosyltransferase;	84.47
COG1435	201	Tdk Thymidine kinase [Nucleotide transport and met	84.38
PRK06835	329	DNA replication protein DnaC; Validated	84.33
PRK08727	233	hypothetical protein; Validated	84.32
PF02572	172	CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase	83.77
PRK08074	928	bifunctional ATP-dependent DNA helicase/DNA polyme	83.49
COG0653	822	SecA Preprotein translocase subunit SecA (ATPase,	83.2
PF12340	229	DUF3638: Protein of unknown function (DUF3638); In	82.96
KOG0964	1200	consensus Structural maintenance of chromosome pro	82.53
PRK04195	482	replication factor C large subunit; Provisional	82.17
COG1110	1187	Reverse gyrase [DNA replication, recombination, an	81.86
PRK13766	773	Hef nuclease; Provisional	81.85
PF13173	128	AAA_14: AAA domain	81.79
KOG0354	746	consensus DEAD-box like helicase [General function	81.78
KOG0298	1394	consensus DEAD box-containing helicase-like transc	81.6
TIGR02621	844	cas3_GSU0051 CRISPR-associated helicase Cas3, Anae	81.52
PRK06620	214	hypothetical protein; Validated	81.49
COG2109	198	BtuR ATP:corrinoid adenosyltransferase [Coenzyme m	81.41
KOG1015	1567	consensus Transcription regulator XNP/ATRX, DEAD-b	81.17
COG3587	985	Restriction endonuclease [Defense mechanisms]	81.06
PRK11747	697	dinG ATP-dependent DNA helicase DinG; Provisional	80.99

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

Probab=100.00  E-value=2.2e-40  Score=263.68  Aligned_cols=184  Identities=35%  Similarity=0.580  Sum_probs=176.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +|+||+||||||.||..+++.|+... |++++.+.||.+...+..++ .++|||||+||+||++++.+.+.+++..++++
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-GLRVAVLVGGMDMMLQANQL-SKKPHILVATPGRLWDHLENTKGFSLEQLKFL  208 (476)
T ss_pred             eEEEecCcHHHHHHHHHHHHHhcccc-CeEEEEEecCchHHHHHHHh-hcCCCEEEeCcHHHHHHHHhccCccHHHhHHH
Confidence            69999999999999999999999998 99999999999999999998 57899999999999999997789999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||++++..|.+.+..|+..+|..+|+++||||||..+..+...-+.+|+.+.+...               +.+-+
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            999999999999999999999999999999999999999999999999999999999998               88999


Q ss_pred             ceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          161 GLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      .++|+|+.++..+|...|..+|++..+.+.|||||+...++
T Consensus       274 ~lkQ~ylfv~~k~K~~yLV~ll~e~~g~s~iVF~~t~~tt~  314 (476)
T KOG0330|consen  274 HLKQTYLFVPGKDKDTYLVYLLNELAGNSVIVFCNTCNTTR  314 (476)
T ss_pred             HhhhheEeccccccchhHHHHHHhhcCCcEEEEEeccchHH
Confidence            99999999999999999999999999999999999987654

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

Probab=100.00  E-value=1.3e-39  Score=272.01  Aligned_cols=186  Identities=33%  Similarity=0.542  Sum_probs=170.7

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+|||+||||||.|++.++++++... ++++.+++||.....|.+.+ +.+.||+||||+||.++++. +.+++++++++
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            37999999999999999999999988 79999999999999999999 57899999999999999999 99999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhC-CCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRL-PKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTP  159 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (203)
                      |+||||+|++.||+++++.|++.+ +..+|+++||||+|.+++.++..++.+|..+.+....+             ....
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 56669999999999999999999999999999876521             4567


Q ss_pred             CceeEEEEEcCCCCcHHHHHHHHhcC---CCCeEEEEeccCCcccC
Q 028826          160 LGLHLEYLECESDKKPSQLVDLLIKN---KSKKIIMYVQHGNFSED  202 (203)
Q Consensus       160 ~~i~~~~~~~~~~~k~~~l~~ll~~~---~~~~~lIF~ns~~~~e~  202 (203)
                      .++.|....|++..|...|..+|+..   ..+|+||||+|++.|++
T Consensus       311 ~~i~qive~~~~~~K~~~l~~lL~~~~~~~~~KvIIFc~tkr~~~~  356 (519)
T KOG0331|consen  311 HNIRQIVEVCDETAKLRKLGKLLEDISSDSEGKVIIFCETKRTCDE  356 (519)
T ss_pred             cchhhhhhhcCHHHHHHHHHHHHHHHhccCCCcEEEEecchhhHHH
Confidence            78999999999888999999988754   56799999999999875

>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=5.2e-39  Score=246.95  Aligned_cols=183  Identities=32%  Similarity=0.492  Sum_probs=174.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      |||||+||||||.|+.+.+..++.++ ++++..+.||.+..++.+.+ +.+.+++.|||+|+++|++. +.+.-..++++
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            68999999999999999999999988 99999999999999999988 58999999999999999999 99999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||.|++.||.+.+..+.+.+|+.+|++++|||+|.++.++.++|+.+|+.+.+..+               .....
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               56888


Q ss_pred             ceeEEEEEcCCCC-cHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          161 GLHLEYLECESDK-KPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      +++|+|..++.++ |++.|.+++....-.+++|||||++.++
T Consensus       239 gIKqf~v~ve~EewKfdtLcdLYd~LtItQavIFcnTk~kVd  280 (400)
T KOG0328|consen  239 GIKQFFVAVEKEEWKFDTLCDLYDTLTITQAVIFCNTKRKVD  280 (400)
T ss_pred             hhhhheeeechhhhhHhHHHHHhhhhehheEEEEecccchhh
Confidence            9999999998765 9999999999998889999999998763

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

Probab=100.00  E-value=1.1e-38  Score=273.35  Aligned_cols=186  Identities=37%  Similarity=0.619  Sum_probs=172.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      |||++||||||.||++++++++.+.+++++..++||.+...+...+. .++|||||||+|+++++.. +.+++++++++|
T Consensus       102 aLil~PTRELA~Qi~~~~~~~~~~~~~~~~~~i~GG~~~~~q~~~l~-~~~~ivVaTPGRllD~i~~-~~l~l~~v~~lV  179 (513)
T COG0513         102 ALILAPTRELAVQIAEELRKLGKNLGGLRVAVVYGGVSIRKQIEALK-RGVDIVVATPGRLLDLIKR-GKLDLSGVETLV  179 (513)
T ss_pred             eEEECCCHHHHHHHHHHHHHHHhhcCCccEEEEECCCCHHHHHHHHh-cCCCEEEECccHHHHHHHc-CCcchhhcCEEE
Confidence            89999999999999999999998875699999999999999998885 4799999999999999999 899999999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCc
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLG  161 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (203)
                      +||||+|++.||.+++..|+..+|.++|+++||||+|+.+..+++.++.+|..+.+.....             ......
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            9999999999999999999999999999999999999999999999999999888885511             237899


Q ss_pred             eeEEEEEcCCCC-cHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          162 LHLEYLECESDK-KPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       162 i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      +.|+|+.+++.+ |...|..+++.....++||||||+..|++
T Consensus       247 i~q~~~~v~~~~~k~~~L~~ll~~~~~~~~IVF~~tk~~~~~  288 (513)
T COG0513         247 IKQFYLEVESEEEKLELLLKLLKDEDEGRVIVFVRTKRLVEE  288 (513)
T ss_pred             ceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCcHHHHHH
Confidence            999999999876 99999999999988899999999988764

>KOG0343 consensus RNA Helicase [RNA processing and modification]

Probab=100.00  E-value=2.3e-37  Score=255.60  Aligned_cols=183  Identities=38%  Similarity=0.589  Sum_probs=171.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      |||++||||||.|+++++.+.+++. ++..+.+.||.+...+...+  ++.+|+|||||||++++..+..++.++++++|
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            8999999999999999999999988 89999999999988777776  57999999999999999987788999999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCc
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLG  161 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (203)
                      +||||++++.||...+..|++.+|..+|+++||||-+..+..+++..+.+|.+|.+.....             ...|.+
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            9999999999999999999999999999999999999999999999999999998874422             679999


Q ss_pred             eeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcc
Q 028826          162 LHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFS  200 (203)
Q Consensus       162 i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~  200 (203)
                      ++|+|+.++.++|++.|+.+++.+...++|||.+|.+.+
T Consensus       288 L~Q~y~~v~l~~Ki~~L~sFI~shlk~K~iVF~SscKqv  326 (758)
T KOG0343|consen  288 LQQSYVIVPLEDKIDMLWSFIKSHLKKKSIVFLSSCKQV  326 (758)
T ss_pred             hhheEEEEehhhHHHHHHHHHHhccccceEEEEehhhHH
Confidence            999999999999999999999999999999999997654

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

Probab=100.00  E-value=1.8e-37  Score=254.32  Aligned_cols=184  Identities=33%  Similarity=0.533  Sum_probs=172.6

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +|||+||||||.|++++.++++.+. ++.++.+.||.+...|...| ..+|||+|+||||+.+++++..+++++++..+|
T Consensus       255 VLVL~PTRELaiQv~sV~~qlaqFt-~I~~~L~vGGL~lk~QE~~L-Rs~PDIVIATPGRlIDHlrNs~sf~ldsiEVLv  332 (691)
T KOG0338|consen  255 VLVLVPTRELAIQVHSVTKQLAQFT-DITVGLAVGGLDLKAQEAVL-RSRPDIVIATPGRLIDHLRNSPSFNLDSIEVLV  332 (691)
T ss_pred             EEEEeccHHHHHHHHHHHHHHHhhc-cceeeeeecCccHHHHHHHH-hhCCCEEEecchhHHHHhccCCCccccceeEEE
Confidence            6999999999999999999999988 89999999999999999888 578999999999999999987889999999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCc
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLG  161 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (203)
                      +||||+|++.||.+.+..|++.+|+++|+++|||||+..+..++...|..|+.+.++..               ....+.
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               678899


Q ss_pred             eeEEEEEcCC---CCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          162 LHLEYLECES---DKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       162 i~~~~~~~~~---~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      +.|.|+.+..   ..+...|..++...-..++|||+.|++.|++
T Consensus       398 LtQEFiRIR~~re~dRea~l~~l~~rtf~~~~ivFv~tKk~AHR  441 (691)
T KOG0338|consen  398 LTQEFIRIRPKREGDREAMLASLITRTFQDRTIVFVRTKKQAHR  441 (691)
T ss_pred             hhHHHheeccccccccHHHHHHHHHHhcccceEEEEehHHHHHH
Confidence            9999987753   4688889999987778899999999998874

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

Probab=100.00  E-value=5.6e-37  Score=249.20  Aligned_cols=187  Identities=60%  Similarity=0.919  Sum_probs=175.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHh-CCCccCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMER-MDVLDFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~-~~~~~l~~v~~l   80 (203)
                      |||++||||||.||++++..|..+++++++.++.||.+.+++...+.+.+|+|+|||||||.+++.+ ...+++.+++++
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            8999999999999999999999998899999999999999999999999999999999999999987 345677899999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||+|++.||...++.|++.+|+.+.+-+||||..+.+.++.+..+++|+.|.+.....             ...|+
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            99999999999999999999999999999999999999999999999999999999988732             23889


Q ss_pred             ceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          161 GLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      .+..+|..|+..+|...|.++|.....+++|||..|-.+++
T Consensus       229 ~L~~~Y~v~~a~eK~~~lv~~L~~~~~kK~iVFF~TCasVe  269 (567)
T KOG0345|consen  229 SLALEYLVCEADEKLSQLVHLLNNNKDKKCIVFFPTCASVE  269 (567)
T ss_pred             hhcceeeEecHHHHHHHHHHHHhccccccEEEEecCcchHH
Confidence            99999999999999999999999999999999999877654

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

Probab=100.00  E-value=3.1e-37  Score=240.74  Aligned_cols=182  Identities=34%  Similarity=0.514  Sum_probs=173.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ||+|++||||||.|+...++.+++++ ++++..-+||.+...+.-.+ ..+.|++||||+|++++.++ +.-+++++.++
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            68999999999999999999999999 89999999999998888777 67899999999999999999 89999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||.|++..|.+.+.+++..+|+++|++++|||+|--|..|++.++.+|+.+..-.+                ..+.
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            999999999999999999999999999999999999999999999999999999988665                5788


Q ss_pred             ceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          161 GLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      ++.|+|.++.+..|..-|..++.+..-.+.||||||-+++|
T Consensus       296 GvtQyYafV~e~qKvhCLntLfskLqINQsIIFCNS~~rVE  336 (459)
T KOG0326|consen  296 GVTQYYAFVEERQKVHCLNTLFSKLQINQSIIFCNSTNRVE  336 (459)
T ss_pred             chhhheeeechhhhhhhHHHHHHHhcccceEEEeccchHhH
Confidence            99999999999999999999999998889999999988876

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

Probab=100.00  E-value=2.4e-35  Score=241.77  Aligned_cols=184  Identities=32%  Similarity=0.525  Sum_probs=167.7

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ++||+|||||||.||+.++++|++.+ ++++++++||.+..+|.+.|. .++.|||+||+||+++++. +..++.++.+|
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            58999999999999999999999998 999999999999999999995 8999999999999999999 99999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||+|++.||...++.|..++.+.+|+++||||++..++.+++.+|.+|+.+....-               .....
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            999999999999999999999999999999999999999999999999999998877655               44667


Q ss_pred             ceeEEEEEcCCC-CcHHHHHHHHh-cCCCCeEEEEeccCCcccC
Q 028826          161 GLHLEYLECESD-KKPSQLVDLLI-KNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       161 ~i~~~~~~~~~~-~k~~~l~~ll~-~~~~~~~lIF~ns~~~~e~  202 (203)
                      .|.|.+..|+.+ .|..+|..-|- ....+++|||+.-+.++|+
T Consensus       440 dITQ~V~V~~s~~~Kl~wl~~~L~~f~S~gkvlifVTKk~~~e~  483 (731)
T KOG0339|consen  440 DITQTVSVCPSEEKKLNWLLRHLVEFSSEGKVLIFVTKKADAEE  483 (731)
T ss_pred             chhheeeeccCcHHHHHHHHHHhhhhccCCcEEEEEeccCCHHH
Confidence            899999999764 67777766554 4567899999998887764

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

Probab=100.00  E-value=4e-35  Score=241.14  Aligned_cols=183  Identities=31%  Similarity=0.539  Sum_probs=172.7

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +|+|++||||||+||.++-.+|+..+ +++++.+.||.+.+++--++ ..+|+|+|+||++|.+.+.+ ..+-++++.++
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            58999999999999999999999999 89999999999999887777 57999999999999999998 88889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCC-------------------------CcEEEEeeecChhHHHHHHhcCCCCeEE
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKL-------------------------RRTGLFSATQTEAVEELSKAGLRNPVRI  135 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~-------------------------~q~i~~SAT~~~~v~~~~~~~l~~~~~i  135 (203)
                      |+||||.|+|.||.+++..++.++|..                         +|+++||||+|+.+..+++.|+.+|+.+
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            999999999999999999999999731                         5999999999999999999999999999


Q ss_pred             EeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          136 EVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       136 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      .++..               +...+.+.|.++.+++.+|...|..+|++...+|+|||+|+++.|+
T Consensus       481 tig~~---------------gk~~~rveQ~v~m~~ed~k~kkL~eil~~~~~ppiIIFvN~kk~~d  531 (673)
T KOG0333|consen  481 TIGSA---------------GKPTPRVEQKVEMVSEDEKRKKLIEILESNFDPPIIIFVNTKKGAD  531 (673)
T ss_pred             EeccC---------------CCCccchheEEEEecchHHHHHHHHHHHhCCCCCEEEEEechhhHH
Confidence            99998               6788999999999999999999999999998889999999999875

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

Probab=100.00  E-value=1.1e-34  Score=236.87  Aligned_cols=186  Identities=39%  Similarity=0.571  Sum_probs=169.8

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||||||.|++.+++++..+.+++.+..+.||.....+.+.+. ++++|+|+|||||++++.+.+.+-..+++++
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 GVLIICPTRELAMQIFAEAKELLKYHESITVGIVIGGNNFSVEADKLV-KGCNILIATPGRLLDHLQNTSGFLFRNLKCL  234 (543)
T ss_pred             eEEEecccHHHHHHHHHHHHHHHhhCCCcceEEEeCCccchHHHHHhh-ccccEEEeCCchHHhHhhcCCcchhhcccee
Confidence            379999999999999999999999888999999999999888888885 4999999999999999999777778899999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCC-CCeEEEeccCcccccccchhhhhccCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLR-NPVRIEVRAESKSHHASASSQQLASSKTP  159 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (203)
                      |+||||++++.||++++.+|+..+|+.+|..+||||.|+.|+++++..+. +|.++.+...++             ..+.
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            99999999999999999999999999999999999999999999997776 589998877643             5678


Q ss_pred             CceeEEEEEcCCCCcHHHHHHHHhcCCC-CeEEEEeccCCcc
Q 028826          160 LGLHLEYLECESDKKPSQLVDLLIKNKS-KKIIMYVQHGNFS  200 (203)
Q Consensus       160 ~~i~~~~~~~~~~~k~~~l~~ll~~~~~-~~~lIF~ns~~~~  200 (203)
                      ..+.|-|+.++...++..+..+|+++.. .++||||+|...+
T Consensus       302 e~l~Qgyvv~~~~~~f~ll~~~LKk~~~~~KiiVF~sT~~~v  343 (543)
T KOG0342|consen  302 ERLEQGYVVAPSDSRFSLLYTFLKKNIKRYKIIVFFSTCMSV  343 (543)
T ss_pred             hcccceEEeccccchHHHHHHHHHHhcCCceEEEEechhhHH
Confidence            8999999999999999999999998866 8999999987543

>KOG4284 consensus DEAD box protein [Transcription]

Probab=100.00  E-value=4.4e-34  Score=239.87  Aligned_cols=183  Identities=26%  Similarity=0.475  Sum_probs=170.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +++||+||||+|.||++.+.+++..+.|++|..+.||.....+...+  +.++|+||||||+.+++.. +.++.++++++
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            57999999999999999999999988899999999999998888888  4688999999999999999 99999999999


Q ss_pred             EEcchhHhhhh-chHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCC
Q 028826           81 VLDEADRLLDM-GFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTP  159 (203)
Q Consensus        81 ViDEad~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (203)
                      |+||||.|++. .|.+++..|+..+|.++|+++||||+|..+.+++.++|++|.+|..+..               ....
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            99999999985 4999999999999999999999999999999999999999999999888               6677


Q ss_pred             CceeEEEEEcCCC--------CcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          160 LGLHLEYLECESD--------KKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       160 ~~i~~~~~~~~~~--------~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      -+|+|+++..+.-        .|...|-+++++.++.++||||+...+|+
T Consensus       237 ~GikQyv~~~~s~nnsveemrlklq~L~~vf~~ipy~QAlVF~~~~sra~  286 (980)
T KOG4284|consen  237 FGIKQYVVAKCSPNNSVEEMRLKLQKLTHVFKSIPYVQALVFCDQISRAE  286 (980)
T ss_pred             echhheeeeccCCcchHHHHHHHHHHHHHHHhhCchHHHHhhhhhhhhhh
Confidence            8899999887653        48899999999999999999999988775

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=100.00  E-value=2.6e-33  Score=238.40  Aligned_cols=184  Identities=33%  Similarity=0.595  Sum_probs=168.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ++||++||||||.|+.+++++++...+++++..++||.+...+...+ ..+++|+||||+++.+++.. +.+++++++++
T Consensus        74 ~~lil~PtreLa~Q~~~~~~~~~~~~~~~~v~~~~Gg~~~~~~~~~l-~~~~~IvV~Tp~rl~~~l~~-~~~~l~~l~~l  151 (460)
T PRK11776         74 QALVLCPTRELADQVAKEIRRLARFIPNIKVLTLCGGVPMGPQIDSL-EHGAHIIVGTPGRILDHLRK-GTLDLDALNTL  151 (460)
T ss_pred             eEEEEeCCHHHHHHHHHHHHHHHhhCCCcEEEEEECCCChHHHHHHh-cCCCCEEEEChHHHHHHHHc-CCccHHHCCEE
Confidence            48999999999999999999998877689999999999998888887 47899999999999999998 88999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||+|++.+|..++..++..++..+|+++||||+|+.+..+...++.+|..+.+...               . ...
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            999999999999999999999999999999999999999999999999999998888665               2 345


Q ss_pred             ceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          161 GLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       161 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      .+.++|+.++..+|...|..++.....+++||||||++.|++
T Consensus       216 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~  257 (460)
T PRK11776        216 AIEQRFYEVSPDERLPALQRLLLHHQPESCVVFCNTKKECQE  257 (460)
T ss_pred             CeeEEEEEeCcHHHHHHHHHHHHhcCCCceEEEECCHHHHHH
Confidence            688999999988899999999998888899999999988763

>KOG0346 consensus RNA helicase [RNA processing and modification]

Probab=100.00  E-value=7e-34  Score=229.67  Aligned_cols=186  Identities=25%  Similarity=0.391  Sum_probs=166.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCC-CceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCC-ccCCCcc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLP-DVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDV-LDFRNLV   78 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~-~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~-~~l~~v~   78 (203)
                      .|+||+||||||+|+|.++.+|..+++ .++++-+.+..+......+| ...|||+|+||++++.++.. +. ..+..++
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            489999999999999999999988774 67887777666655555566 57899999999999999988 66 6789999


Q ss_pred             EEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCC
Q 028826           79 ILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKT  158 (203)
Q Consensus        79 ~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (203)
                      ++|+||||.+++.||.++++.+.+++|+..|.++.|||+++++..+.+.++++|+++.+..++              ...
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            999999999999999999999999999999999999999999999999999999999998774              457


Q ss_pred             CCceeEEEEEcCCCCcHHHHHHHHhc-CCCCeEEEEeccCCcccC
Q 028826          159 PLGLHLEYLECESDKKPSQLVDLLIK-NKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       159 ~~~i~~~~~~~~~~~k~~~l~~ll~~-~~~~~~lIF~ns~~~~e~  202 (203)
                      +.++.|+++.|.+++|+-.++.+++- .-.+++|||+||-.+|.+
T Consensus       239 ~dqL~Qy~v~cse~DKflllyallKL~LI~gKsliFVNtIdr~Yr  283 (569)
T KOG0346|consen  239 PDQLTQYQVKCSEEDKFLLLYALLKLRLIRGKSLIFVNTIDRCYR  283 (569)
T ss_pred             cccceEEEEEeccchhHHHHHHHHHHHHhcCceEEEEechhhhHH
Confidence            78999999999999999999999984 456799999999888753

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=100.00  E-value=4.1e-33  Score=243.33  Aligned_cols=185  Identities=29%  Similarity=0.523  Sum_probs=170.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ++|||+||||||.|+.+.+.++....+++++..++||.+...+.+.+ ..+++|||+||+++.+++.. +.+++++++++
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            47999999999999999999998887789999999999988888877 56899999999999999988 88999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||.|++++|.+++..++..+|..+|+++||||+|+.+..+.+.++.+|..+.+...               ....+
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            999999999999999999999999999999999999999999999999999998888766               45667


Q ss_pred             ceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          161 GLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       161 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      .+.+.|+.+...+|...|..++......++||||||+..|++
T Consensus       219 ~i~q~~~~v~~~~k~~~L~~~L~~~~~~~~IVF~~tk~~a~~  260 (629)
T PRK11634        219 DISQSYWTVWGMRKNEALVRFLEAEDFDAAIIFVRTKNATLE  260 (629)
T ss_pred             ceEEEEEEechhhHHHHHHHHHHhcCCCCEEEEeccHHHHHH
Confidence            888999988888999999999998888899999999987753

>PTZ00110 helicase; Provisional

Probab=100.00  E-value=9.3e-33  Score=238.54  Aligned_cols=185  Identities=31%  Similarity=0.514  Sum_probs=164.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ++|||+||||||.|+++++++++... ++++..++||.....+...+ ..+++|+|+||++|.+++.. +..++++++++
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            37999999999999999999998877 89999999999988888777 46899999999999999988 78899999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCC-CCeEEEeccCcccccccchhhhhccCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLR-NPVRIEVRAESKSHHASASSQQLASSKTP  159 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (203)
                      |+||||+|++++|.+.++.++..+++.+|+++||||+|..+..+++.++. +++.+.+....              ....
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            99999999999999999999999999999999999999999999998886 57777775541              2345


Q ss_pred             CceeEEEEEcCCCCcHHHHHHHHhcC--CCCeEEEEeccCCcccC
Q 028826          160 LGLHLEYLECESDKKPSQLVDLLIKN--KSKKIIMYVQHGNFSED  202 (203)
Q Consensus       160 ~~i~~~~~~~~~~~k~~~l~~ll~~~--~~~~~lIF~ns~~~~e~  202 (203)
                      .++.+.+..+++.+|...|..++...  ..+++||||||++.|++
T Consensus       348 ~~i~q~~~~~~~~~k~~~L~~ll~~~~~~~~k~LIF~~t~~~a~~  392 (545)
T PTZ00110        348 HNIKQEVFVVEEHEKRGKLKMLLQRIMRDGDKILIFVETKKGADF  392 (545)
T ss_pred             CCeeEEEEEEechhHHHHHHHHHHHhcccCCeEEEEecChHHHHH
Confidence            67889998888889999999999865  56799999999998863

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=1.2e-32  Score=232.09  Aligned_cols=184  Identities=33%  Similarity=0.516  Sum_probs=165.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +||||+||||||.|+++++..+++.. ++++..++||.....+...+ ..++||+||||+++.+++.. +.+++++++++
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            48999999999999999999999887 89999999999888887777 56899999999999999988 88999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCC--CCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPK--LRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKT  158 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~--~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (203)
                      |+||||++++++|..++..++..++.  .+|.++||||++..+..++..++.+|..+.+...               ...
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            99999999999999999999999974  5678999999999999999999999998888766               445


Q ss_pred             CCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          159 PLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       159 ~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      ..++.+.++.....+|...|..++.....+++|||||+++.|++
T Consensus       227 ~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lVF~~t~~~~~~  270 (423)
T PRK04837        227 GHRIKEELFYPSNEEKMRLLQTLIEEEWPDRAIIFANTKHRCEE  270 (423)
T ss_pred             CCceeEEEEeCCHHHHHHHHHHHHHhcCCCeEEEEECCHHHHHH
Confidence            56788888877778899999999988878899999999988763

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

Probab=100.00  E-value=9.2e-34  Score=233.61  Aligned_cols=200  Identities=32%  Similarity=0.528  Sum_probs=169.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ||||+|||||||.|+|+.+++|.+.+.=|-.+.+.||.....+...| .+|++|||||||||.+++.+..++.+++++|+
T Consensus       213 ~ALVivPTREL~~Q~y~~~qKLl~~~hWIVPg~lmGGEkkKSEKARL-RKGiNILIgTPGRLvDHLknT~~i~~s~LRwl  291 (708)
T KOG0348|consen  213 YALVIVPTRELALQIYETVQKLLKPFHWIVPGVLMGGEKKKSEKARL-RKGINILIGTPGRLVDHLKNTKSIKFSRLRWL  291 (708)
T ss_pred             eEEEEechHHHHHHHHHHHHHHhcCceEEeeceeecccccccHHHHH-hcCceEEEcCchHHHHHHhccchheeeeeeEE
Confidence            69999999999999999999998877567778899999988888888 57999999999999999999889999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCC-------------CCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCccccc--
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLP-------------KLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHH--  145 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~-------------~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~--  145 (203)
                      |+||+|++++.||.+++..|+..+.             ...|.+++|||+++.|.++++.-+.||+.|..+.....-.  
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            9999999999999999999998872             2368999999999999999999999999998433211000  


Q ss_pred             ------c--cchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhc----CCCCeEEEEeccCCccc
Q 028826          146 ------A--SASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIK----NKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       146 ------~--~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~----~~~~~~lIF~ns~~~~e  201 (203)
                            .  .+.....+....|+++.|+|..++.+-+.-.|..+|..    ...+++|||.++.+.+|
T Consensus       372 ~~a~~ev~~~~~~~~l~~~~iPeqL~qry~vVPpKLRLV~Laa~L~~~~k~~~~qk~iVF~S~~d~Ve  439 (708)
T KOG0348|consen  372 DKAVQEVDDGPAGDKLDSFAIPEQLLQRYTVVPPKLRLVALAALLLNKVKFEEKQKMIVFFSCSDSVE  439 (708)
T ss_pred             hhhhhhcCCcccccccccccCcHHhhhceEecCCchhHHHHHHHHHHHhhhhhhceeEEEEechhHHH
Confidence                  0  01112235578899999999999999999888888863    45679999999987765

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

Probab=100.00  E-value=7e-33  Score=228.55  Aligned_cols=183  Identities=36%  Similarity=0.553  Sum_probs=167.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||||||.|++++++++.-.. .++++..+||.+...+.+.+ .+++||+|+||+||.+++.. +.+.+++++++
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            37999999999999999999997665 89999999999998888888 57999999999999999999 99999999999


Q ss_pred             EEcchhHhhh-hchHHHHHHHHHhCC----CCCcEEEEeeecChhHHHHHHhcCCC-CeEEEeccCcccccccchhhhhc
Q 028826           81 VLDEADRLLD-MGFQKQISYIISRLP----KLRRTGLFSATQTEAVEELSKAGLRN-PVRIEVRAESKSHHASASSQQLA  154 (203)
Q Consensus        81 ViDEad~l~~-~~~~~~~~~il~~~~----~~~q~i~~SAT~~~~v~~~~~~~l~~-~~~i~~~~~~~~~~~~~~~~~~~  154 (203)
                      |+||||+|+| .+|.+++++|+....    .++|.++||||+|..+..++..++.+ +..+.+...              
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 899999999999885    47899999999999999999999997 888888887              


Q ss_pred             cCCCCCceeEEEEEcCCCCcHHHHHHHHhcCC---------CCeEEEEeccCCccc
Q 028826          155 SSKTPLGLHLEYLECESDKKPSQLVDLLIKNK---------SKKIIMYVQHGNFSE  201 (203)
Q Consensus       155 ~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~---------~~~~lIF~ns~~~~e  201 (203)
                       .....++.|.+.++.+.+|...|+++|....         +++++|||++++.|.
T Consensus       297 -g~~~~ni~q~i~~V~~~~kr~~Lldll~~~~~~~~~~~~~~e~tlvFvEt~~~~d  351 (482)
T KOG0335|consen  297 -GSTSENITQKILFVNEMEKRSKLLDLLNKDDGPPSDGEPKWEKTLVFVETKRGAD  351 (482)
T ss_pred             -ccccccceeEeeeecchhhHHHHHHHhhcccCCcccCCcccceEEEEeeccchhh
Confidence             6789999999999999999999999997432         238999999998774

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=100.00  E-value=2.1e-32  Score=232.47  Aligned_cols=183  Identities=31%  Similarity=0.556  Sum_probs=167.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+|||+||||||.|+.+.++++.... ++++..++||.+...+...+ ..+++|+|+||++|++++.. +.++++++++|
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            38999999999999999999998887 89999999999988887777 56899999999999999988 78899999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||+|++++|...++.++..++...|+++||||+++++..++.+++.++..+.+...               .....
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            999999999999999999999999999999999999999999999999999998887665               45667


Q ss_pred             ceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          161 GLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      ++.+++..++...|...+..++.....+++|||||+++.|+
T Consensus       219 ~i~~~~~~~~~~~k~~~l~~l~~~~~~~~~lVF~~t~~~~~  259 (456)
T PRK10590        219 QVTQHVHFVDKKRKRELLSQMIGKGNWQQVLVFTRTKHGAN  259 (456)
T ss_pred             ceeEEEEEcCHHHHHHHHHHHHHcCCCCcEEEEcCcHHHHH
Confidence            88899988888889999999998888889999999998775

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

Probab=100.00  E-value=1.4e-33  Score=214.62  Aligned_cols=182  Identities=26%  Similarity=0.462  Sum_probs=171.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +|++|.|||||.||.++..++++++|++++..++||...+.+...+. +-|+|+||||+|++.+.++ +.+++++++.+|
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 4899999999999999999 999999999999


Q ss_pred             EcchhHhhhh-chHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           82 LDEADRLLDM-GFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        82 iDEad~l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      +||+|.|+++ ..+.++..|.+..|...|+.+||||++++++...++++.+|..+.++.+.              ..+.-
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            9999999964 58999999999999999999999999999999999999999999998875              45778


Q ss_pred             ceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCc
Q 028826          161 GLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNF  199 (203)
Q Consensus       161 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~  199 (203)
                      +++|+|..+.+.+|...+.++|......+++||+.|.++
T Consensus       257 GLqQ~YvkLke~eKNrkl~dLLd~LeFNQVvIFvKsv~R  295 (387)
T KOG0329|consen  257 GLQQYYVKLKENEKNRKLNDLLDVLEFNQVVIFVKSVQR  295 (387)
T ss_pred             hHHHHHHhhhhhhhhhhhhhhhhhhhhcceeEeeehhhh
Confidence            899999999999999999999999999999999998765

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=100.00  E-value=4e-32  Score=235.49  Aligned_cols=185  Identities=32%  Similarity=0.546  Sum_probs=165.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ++|||+||||||.|+++.+.+++... ++++..++||.+...+...+ ..++||||+||++|++++...+.++++++++|
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            48999999999999999999998887 89999999999988887777 56799999999999999987345789999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCC--CCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPK--LRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKT  158 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~--~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (203)
                      ||||||.|++++|..++..++..++.  .+|+++||||++..+..+...++.++..+.+...               ...
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  7899999999999999999999999887776555               345


Q ss_pred             CCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          159 PLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       159 ~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      ...+.|.++.+...+|...|..++......++||||||++.|++
T Consensus       229 ~~~i~q~~~~~~~~~k~~~L~~ll~~~~~~k~LVF~nt~~~ae~  272 (572)
T PRK04537        229 AARVRQRIYFPADEEKQTLLLGLLSRSEGARTMVFVNTKAFVER  272 (572)
T ss_pred             ccceeEEEEecCHHHHHHHHHHHHhcccCCcEEEEeCCHHHHHH
Confidence            67788998888888999999999998888899999999988763

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

Probab=100.00  E-value=2.2e-31  Score=229.10  Aligned_cols=182  Identities=28%  Similarity=0.486  Sum_probs=162.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .||||+||||||.|++++++.++... ++++..++||.....+...+ ..+++|+|+||++|.+++.. +.+.+++++++
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            48999999999999999999998887 79999999999988888777 56899999999999999998 78899999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||+|+++||++.+..++..++ .+|+++||||+++++..+++.++.++..+.+...               .....
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            9999999999999999999999985 6899999999999999999999999998888765               44556


Q ss_pred             ceeEEEEEcCCCCcHHHHHHHHhcCC--CCeEEEEeccCCccc
Q 028826          161 GLHLEYLECESDKKPSQLVDLLIKNK--SKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~~~k~~~l~~ll~~~~--~~~~lIF~ns~~~~e  201 (203)
                      .+.+.+..++..+|...|.+++....  .+++||||||+..|+
T Consensus       339 ~v~q~~~~~~~~~k~~~l~~~l~~~~~~~~~~iVFv~s~~~a~  381 (518)
T PLN00206        339 AVKQLAIWVETKQKKQKLFDILKSKQHFKPPAVVFVSSRLGAD  381 (518)
T ss_pred             ceeEEEEeccchhHHHHHHHHHHhhcccCCCEEEEcCCchhHH
Confidence            78888888988889999999997543  368999999998775

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

Probab=100.00  E-value=2e-32  Score=218.05  Aligned_cols=182  Identities=31%  Similarity=0.532  Sum_probs=170.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +||+++||||||+|+..+.+.++... ++++..+.||.....+...+....++|+||||+|+.++++. +.+....++++
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            57899999999999999999999887 89999999999988777777677899999999999999999 78889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||.|++.||.+.+..+++++|++.|++++|||+|+++....++++++|+.+.+...               ..+..
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               46789


Q ss_pred             ceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          161 GLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      .++|+|..+.+++|...|.++.+  ..++.+||||+++.+.
T Consensus       239 gikq~~i~v~k~~k~~~l~dl~~--~~~q~~if~nt~r~v~  277 (397)
T KOG0327|consen  239 GIKQFYINVEKEEKLDTLCDLYR--RVTQAVIFCNTRRKVD  277 (397)
T ss_pred             heeeeeeeccccccccHHHHHHH--hhhcceEEecchhhHH
Confidence            99999999999999999999999  6679999999998754

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=99.98  E-value=3.8e-31  Score=225.91  Aligned_cols=185  Identities=31%  Similarity=0.490  Sum_probs=166.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ++|||+||||||.|+++.++.+.+.. ++++..++||.+...+.+.+..++++|+|+||++|+.+... +...+++++++
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            47999999999999999999998877 89999999999988888887667899999999999999887 78889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCC--CCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPK--LRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKT  158 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~--~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (203)
                      ||||+|.+++.+|...++++++.++.  .+|++++|||++.++..+++.++.++..+.+...               ...
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  5799999999999999999999999998888766               345


Q ss_pred             CCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          159 PLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       159 ~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      ..++.+.++.+...+|...|..++.....+++|||||+++.|+.
T Consensus       307 ~~~~~~~~~~~~~~~k~~~l~~ll~~~~~~~~IVF~~s~~~~~~  350 (475)
T PRK01297        307 SDTVEQHVYAVAGSDKYKLLYNLVTQNPWERVMVFANRKDEVRR  350 (475)
T ss_pred             CCcccEEEEEecchhHHHHHHHHHHhcCCCeEEEEeCCHHHHHH
Confidence            56677888888888999999999998888899999999988763

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=99.97  E-value=1.7e-30  Score=219.70  Aligned_cols=183  Identities=29%  Similarity=0.485  Sum_probs=164.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++||+|||.|+++.++.++... ++++..++||.....+...+ ..+++|+|+||++|++++.. +.+++++++++|
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            7999999999999999999999887 89999999999988877766 56899999999999999988 888999999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecCh-hHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE-AVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~-~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      +||||+|++++|...+..+...++...|+++||||++. .+..+.+.++.++..+.....               .....
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 588899999999998888766               45667


Q ss_pred             ceeEEEEEcCC-CCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          161 GLHLEYLECES-DKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       161 ~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      ++.++++.++. ..|...|..+++.....++|||||+++.|++
T Consensus       218 ~i~~~~~~~~~~~~k~~~l~~l~~~~~~~~~lVF~~s~~~~~~  260 (434)
T PRK11192        218 KIHQWYYRADDLEHKTALLCHLLKQPEVTRSIVFVRTRERVHE  260 (434)
T ss_pred             CceEEEEEeCCHHHHHHHHHHHHhcCCCCeEEEEeCChHHHHH
Confidence            78888888765 6789999999988778899999999988763

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

Probab=99.97  E-value=6.8e-31  Score=211.16  Aligned_cols=183  Identities=28%  Similarity=0.445  Sum_probs=165.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ..|+++||||||.|+.-++.+++-+  +++.++++||....++...+ +++.+|+|+||+||.++... +.+++.++.++
T Consensus       296 ~~lvl~ptreLalqie~e~~kysyn--g~ksvc~ygggnR~eqie~l-krgveiiiatPgrlndL~~~-n~i~l~siTYl  371 (629)
T KOG0336|consen  296 GVLVLTPTRELALQIEGEVKKYSYN--GLKSVCVYGGGNRNEQIEDL-KRGVEIIIATPGRLNDLQMD-NVINLASITYL  371 (629)
T ss_pred             ceEEEeccHHHHHHHHhHHhHhhhc--CcceEEEecCCCchhHHHHH-hcCceEEeeCCchHhhhhhc-CeeeeeeeEEE
Confidence            3689999999999999999999655  89999999999999999999 67999999999999999998 99999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||+|++.||.+.++.|+--+.+.+|+++.|||+|+.|..++..|+++|..+.+..-.              .....
T Consensus       372 VlDEADrMLDMgFEpqIrkilldiRPDRqtvmTSATWP~~VrrLa~sY~Kep~~v~vGsLd--------------L~a~~  437 (629)
T KOG0336|consen  372 VLDEADRMLDMGFEPQIRKILLDIRPDRQTVMTSATWPEGVRRLAQSYLKEPMIVYVGSLD--------------LVAVK  437 (629)
T ss_pred             EecchhhhhcccccHHHHHHhhhcCCcceeeeecccCchHHHHHHHHhhhCceEEEecccc--------------eeeee
Confidence            9999999999999999999999999999999999999999999999999999999987752              33456


Q ss_pred             ceeEEEEEcCCCCcHHHHHHHHhcC-CCCeEEEEeccCCccc
Q 028826          161 GLHLEYLECESDKKPSQLVDLLIKN-KSKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lIF~ns~~~~e  201 (203)
                      +++|.++.-.+.+|...+..++... ...++||||.++..|+
T Consensus       438 sVkQ~i~v~~d~~k~~~~~~f~~~ms~ndKvIiFv~~K~~AD  479 (629)
T KOG0336|consen  438 SVKQNIIVTTDSEKLEIVQFFVANMSSNDKVIIFVSRKVMAD  479 (629)
T ss_pred             eeeeeEEecccHHHHHHHHHHHHhcCCCceEEEEEechhhhh
Confidence            7888887667778888888888754 5679999999987765

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

Probab=99.97  E-value=1.6e-31  Score=215.00  Aligned_cols=182  Identities=35%  Similarity=0.552  Sum_probs=170.5

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      |+|++||||||.|+.++.+.++.+. ++++.+++||.+.+++...+ ..+||||++||+++.++.-. -.+.++.+.++|
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            7999999999999999999999988 89999999999999999988 57899999999999988877 558999999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCc
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLG  161 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (203)
                      +||||.+++.||.+.+..++..+|.++|+++||||+|..+-++++..+.+|..+.++.+               ....+.
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            99999999999999999999999999999999999999999999999999999998888               678899


Q ss_pred             eeEEEEEcCCCCcHHHHHHHHhcC-CCCeEEEEeccCCccc
Q 028826          162 LHLEYLECESDKKPSQLVDLLIKN-KSKKIIMYVQHGNFSE  201 (203)
Q Consensus       162 i~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lIF~ns~~~~e  201 (203)
                      ++..|..+.+.+|...|+.++... ..++++|||.|+.-+|
T Consensus       235 lk~~f~~~~~a~K~aaLl~il~~~~~~~~t~vf~~tk~hve  275 (529)
T KOG0337|consen  235 LKVRFFRVRKAEKEAALLSILGGRIKDKQTIVFVATKHHVE  275 (529)
T ss_pred             hhhheeeeccHHHHHHHHHHHhccccccceeEEecccchHH
Confidence            999999999999999999999865 4578999999987665

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

Probab=99.97  E-value=2.7e-32  Score=218.05  Aligned_cols=183  Identities=30%  Similarity=0.560  Sum_probs=163.8

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhh-----cCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFIS-----TLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFR   75 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~-----~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~   75 (203)
                      ++||+||+||||.|+++.+..+..     .+|.+|+..+.||.+..++...+ ..+.||+|+||+||.+++.. +.+++.
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            589999999999999999999875     45789999999999999998888 67999999999999999998 889999


Q ss_pred             CccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhcc
Q 028826           76 NLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLAS  155 (203)
Q Consensus        76 ~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~  155 (203)
                      -++++.+||||+|++.||.++++.++..+...+|+++||||+|..+..|++.-+-.|+.+.+...+              
T Consensus       326 ~CRyL~lDEADRmiDmGFEddir~iF~~FK~QRQTLLFSATMP~KIQ~FAkSALVKPvtvNVGRAG--------------  391 (610)
T KOG0341|consen  326 ACRYLTLDEADRMIDMGFEDDIRTIFSFFKGQRQTLLFSATMPKKIQNFAKSALVKPVTVNVGRAG--------------  391 (610)
T ss_pred             HHHHhhhhhHHHHhhccchhhHHHHHHHHhhhhheeeeeccccHHHHHHHHhhcccceEEeccccc--------------
Confidence            999999999999999999999999999999999999999999999999999999999999998873              


Q ss_pred             CCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          156 SKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       156 ~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                       ...-++-|.+-++..+.|+-.|++-|.+.. .|++|||..+.+++
T Consensus       392 -AAsldViQevEyVkqEaKiVylLeCLQKT~-PpVLIFaEkK~DVD  435 (610)
T KOG0341|consen  392 -AASLDVIQEVEYVKQEAKIVYLLECLQKTS-PPVLIFAEKKADVD  435 (610)
T ss_pred             -ccchhHHHHHHHHHhhhhhhhHHHHhccCC-CceEEEeccccChH
Confidence             344455566666778888888888886654 48999999988764

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

Probab=99.97  E-value=1.5e-30  Score=205.54  Aligned_cols=184  Identities=30%  Similarity=0.411  Sum_probs=163.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhC---CCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM---DVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~---~~~~l~~v   77 (203)
                      ||+|++||||||.|+.+++..+++.. ++++..++||.+.-.+...| ..+||++|+||||+.+++..+   ..+.++++
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            79999999999999999999999888 99999999999988887777 678999999999999999874   34568999


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCC--CeEEEeccCcccccccchhhhhcc
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRN--PVRIEVRAESKSHHASASSQQLAS  155 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~--~~~i~~~~~~~~~~~~~~~~~~~~  155 (203)
                      +++|+||||.+++.+|-+.+.-+.+.+|..+|+++||||+++.+.++..-....  ........+               
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            999999999999999999999999999999999999999999999888766665  444444444               


Q ss_pred             CCCCCceeEEEEEcCCCCcHHHHHHHHhcCC---CCeEEEEeccCCccc
Q 028826          156 SKTPLGLHLEYLECESDKKPSQLVDLLIKNK---SKKIIMYVQHGNFSE  201 (203)
Q Consensus       156 ~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~---~~~~lIF~ns~~~~e  201 (203)
                      ...++.+.|.|+.|+..-|-..|..+|+...   .+.++||+|+...|+
T Consensus       220 vstvetL~q~yI~~~~~vkdaYLv~~Lr~~~~~~~~simIFvnttr~cQ  268 (442)
T KOG0340|consen  220 VSTVETLYQGYILVSIDVKDAYLVHLLRDFENKENGSIMIFVNTTRECQ  268 (442)
T ss_pred             CCchhhhhhheeecchhhhHHHHHHHHhhhhhccCceEEEEeehhHHHH
Confidence            6788999999999999999999999998553   568999999988776

>KOG0347 consensus RNA helicase [RNA processing and modification]

Probab=99.97  E-value=1.6e-30  Score=215.10  Aligned_cols=182  Identities=25%  Similarity=0.459  Sum_probs=153.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCC--ccCCCcc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDV--LDFRNLV   78 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~--~~l~~v~   78 (203)
                      +|||++||||||.|+.+.+..++++. ++++..++||.+...|.+.| +..|||+|+|||||+.++...+.  -++++++
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-QIRVASITGGLAVQKQQRLL-NQRPDIVVATPGRLWELIEEDNTHLGNFKKVK  342 (731)
T ss_pred             eeEEecChHHHHHHHHHHHHHhcccc-CeEEEEeechhHHHHHHHHH-hcCCCEEEecchHHHHHHHhhhhhhhhhhhce
Confidence            58999999999999999999998876 99999999999999999888 55899999999999999998322  2588999


Q ss_pred             EEEEcchhHhhhhchHHHHHHHHHhCC-----CCCcEEEEeeecCh---------------------hHHHHHHh--cCC
Q 028826           79 ILVLDEADRLLDMGFQKQISYIISRLP-----KLRRTGLFSATQTE---------------------AVEELSKA--GLR  130 (203)
Q Consensus        79 ~lViDEad~l~~~~~~~~~~~il~~~~-----~~~q~i~~SAT~~~---------------------~v~~~~~~--~l~  130 (203)
                      ++|+||+|+|++.|+.+.+..|+..+.     ..+|+++||||++-                     .++.++++  +..
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     46799999999752                     23344443  233


Q ss_pred             CCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcc
Q 028826          131 NPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFS  200 (203)
Q Consensus       131 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~  200 (203)
                      .|.+|..++.               ......+....+.|+..+|--.|+.+|..+++ ++|||||+-..+
T Consensus       423 kpkiiD~t~q---------------~~ta~~l~Es~I~C~~~eKD~ylyYfl~ryPG-rTlVF~NsId~v  476 (731)
T KOG0347|consen  423 KPKIIDLTPQ---------------SATASTLTESLIECPPLEKDLYLYYFLTRYPG-RTLVFCNSIDCV  476 (731)
T ss_pred             CCeeEecCcc---------------hhHHHHHHHHhhcCCccccceeEEEEEeecCC-ceEEEechHHHH
Confidence            6788888887               55677788888889999999899988888874 899999996544

>KOG0334 consensus RNA helicase [RNA processing and modification]

Probab=99.96  E-value=1.7e-29  Score=221.81  Aligned_cols=184  Identities=33%  Similarity=0.547  Sum_probs=165.7

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhC--CCccCCCcc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM--DVLDFRNLV   78 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~--~~~~l~~v~   78 (203)
                      +|||++||||||.||++++++|+... ++++++++||....+++..+. .++.|+|+||+|.++++-..  +..++.++.
T Consensus       440 i~li~aPtrela~QI~r~~~kf~k~l-~ir~v~vygg~~~~~qiaelk-Rg~eIvV~tpGRmiD~l~~n~grvtnlrR~t  517 (997)
T KOG0334|consen  440 IALILAPTRELAMQIHREVRKFLKLL-GIRVVCVYGGSGISQQIAELK-RGAEIVVCTPGRMIDILCANSGRVTNLRRVT  517 (997)
T ss_pred             eEEEEcCCHHHHHHHHHHHHHHHhhc-CceEEEecCCccHHHHHHHHh-cCCceEEeccchhhhhHhhcCCccccccccc
Confidence            48999999999999999999999997 999999999999999999995 56999999999999988761  234566667


Q ss_pred             EEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCC
Q 028826           79 ILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKT  158 (203)
Q Consensus        79 ~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (203)
                      ++|+||||+|++.||.+.+..|+..++..+|+++||||+|..++.+++..+..|+.+.+...               ...
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            99999999999999999999999999999999999999999999999999999999888766               567


Q ss_pred             CCceeEEEEEcC-CCCcHHHHHHHHhcC-CCCeEEEEeccCCccc
Q 028826          159 PLGLHLEYLECE-SDKKPSQLVDLLIKN-KSKKIIMYVQHGNFSE  201 (203)
Q Consensus       159 ~~~i~~~~~~~~-~~~k~~~l~~ll~~~-~~~~~lIF~ns~~~~e  201 (203)
                      ...+++.+..|+ +.+|+..|..||... ...++||||.+...|.
T Consensus       583 ~k~V~q~v~V~~~e~eKf~kL~eLl~e~~e~~~tiiFv~~qe~~d  627 (997)
T KOG0334|consen  583 CKEVTQVVRVCAIENEKFLKLLELLGERYEDGKTIIFVDKQEKAD  627 (997)
T ss_pred             eccceEEEEEecCchHHHHHHHHHHHHHhhcCCEEEEEcCchHHH
Confidence            788999999998 789999999999753 5679999999887764

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

Probab=99.96  E-value=4.1e-29  Score=204.78  Aligned_cols=189  Identities=26%  Similarity=0.402  Sum_probs=167.7

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCC----eEEEeccHHHHHHHHhCCCccCCC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGA----NLLIGTPGRLYDIMERMDVLDFRN   76 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~----~ilV~Tp~~l~~~~~~~~~~~l~~   76 (203)
                      .||||+|||+|+.|+++.+.+++... ++.|+.+.|..+.+.+.++|...++    ||+|+||+||.+++.++.++++++
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            48999999999999999999999988 8999999999999999999987777    999999999999999779999999


Q ss_pred             ccEEEEcchhHhhhhchHHHHHHHHHhCCC----------------------------------CCcEEEEeeecChhHH
Q 028826           77 LVILVLDEADRLLDMGFQKQISYIISRLPK----------------------------------LRRTGLFSATQTEAVE  122 (203)
Q Consensus        77 v~~lViDEad~l~~~~~~~~~~~il~~~~~----------------------------------~~q~i~~SAT~~~~v~  122 (203)
                      ++++||||||+|++..|.+++..++..+..                                  ..+.++||||++....
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            999999999999999888888877766632                                  1268899999999989


Q ss_pred             HHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          123 ELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       123 ~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      .+...-+..|..+.+...           ..+.++.|+.+.|++..++...|.-.+..+++..+..++|+|+||..++.
T Consensus       376 Kl~~l~l~~Prl~~v~~~-----------~~~ryslp~~l~~~~vv~~~~~kpl~~~~lI~~~k~~r~lcf~~S~~sa~  443 (620)
T KOG0350|consen  376 KLKDLTLHIPRLFHVSKP-----------LIGRYSLPSSLSHRLVVTEPKFKPLAVYALITSNKLNRTLCFVNSVSSAN  443 (620)
T ss_pred             HHhhhhcCCCceEEeecc-----------cceeeecChhhhhceeecccccchHhHHHHHHHhhcceEEEEecchHHHH
Confidence            999988899977776532           13348899999999999999999999999999999999999999987764

>PTZ00424 helicase 45; Provisional

Probab=99.96  E-value=1.2e-27  Score=200.47  Aligned_cols=183  Identities=33%  Similarity=0.548  Sum_probs=160.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+|||+||+||+.|+++.++.++... ++++..+.||.....+...+ ..+++|+|+||+++.+++.. +...+++++++
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            37999999999999999999998776 78999999998877777666 46789999999999999988 77889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||+|.+++.+|...+..+++.++...|++++|||+|+.+..+...++.++..+.+...               .....
T Consensus       175 ViDEah~~~~~~~~~~~~~i~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~---------------~~~~~  239 (401)
T PTZ00424        175 ILDEADEMLSRGFKGQIYDVFKKLPPDVQVALFSATMPNEILELTTKFMRDPKRILVKKD---------------ELTLE  239 (401)
T ss_pred             EEecHHHHHhcchHHHHHHHHhhCCCCcEEEEEEecCCHHHHHHHHHHcCCCEEEEeCCC---------------CcccC
Confidence            999999999999999999999999999999999999999999999999999988776654               34566


Q ss_pred             ceeEEEEEcCC-CCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          161 GLHLEYLECES-DKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      ++.+++..++. +.+...+..+++.....++||||||++.|+
T Consensus       240 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ivF~~t~~~~~  281 (401)
T PTZ00424        240 GIRQFYVAVEKEEWKFDTLCDLYETLTITQAIIYCNTRRKVD  281 (401)
T ss_pred             CceEEEEecChHHHHHHHHHHHHHhcCCCeEEEEecCcHHHH
Confidence            78888877765 457888889888888889999999998775

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

Probab=99.94  E-value=4.8e-27  Score=186.89  Aligned_cols=181  Identities=28%  Similarity=0.408  Sum_probs=161.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +|+.|+||||||.|+.+++.+.+++. +++..+...|....+- ..+   ..+|+||||+-+.+++...+-++++.++.+
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-ELTASYAIRGSKAKRG-NKL---TEQIVIGTPGTVLDLMLKLKCIDLEKIKVF  236 (477)
T ss_pred             CceeeCchHHHHHHHHHHHHHhcCce-eeeEEEEecCcccccC-Ccc---hhheeeCCCccHHHHHHHHHhhChhhceEE
Confidence            57889999999999999999999998 8999998888733211 112   258999999999998877677899999999


Q ss_pred             EEcchhHhhh-hchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCC
Q 028826           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTP  159 (203)
Q Consensus        81 ViDEad~l~~-~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (203)
                      |+||||.|++ .||.+.-.+|...+|++.|.++||||+...+..|+...++++..+.+..+               ....
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            9999999996 57999999999999999999999999999999999999999999999888               5688


Q ss_pred             CceeEEEEEcCC-CCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          160 LGLHLEYLECES-DKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       160 ~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      .+++|+|..|.. .+|++.|..++....-+++||||.|+++|+
T Consensus       302 ~~IkQlyv~C~~~~~K~~~l~~lyg~~tigqsiIFc~tk~ta~  344 (477)
T KOG0332|consen  302 DNIKQLYVLCACRDDKYQALVNLYGLLTIGQSIIFCHTKATAM  344 (477)
T ss_pred             cchhhheeeccchhhHHHHHHHHHhhhhhhheEEEEeehhhHH
Confidence            999999999976 589999999998888889999999998874

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

Probab=99.93  E-value=1e-24  Score=192.63  Aligned_cols=177  Identities=17%  Similarity=0.187  Sum_probs=136.6

Q ss_pred             EEE-EcCcHHHHHHHHHHHHHhhhcCC----------------------CceEEEEEcCcchHHHHHHHHhCCCeEEEec
Q 028826            2 GMI-ISPTRELSAQIYHVAQPFISTLP----------------------DVKSMLLVGGVEVKADVKKIEEEGANLLIGT   58 (203)
Q Consensus         2 ali-l~PtreLa~Qi~~~~~~l~~~~~----------------------~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~T   58 (203)
                      +|| ++||||||.|+++.++++++.++                      ++++..++||.+...+...+ ..+|+|||||
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            455 66999999999999999998652                      48999999999999898887 5789999999


Q ss_pred             cHHHHHHHHhCCCcc----------------CCCccEEEEcchhHhhhhchHHHHHHHHHhC--CCC---CcEEEEeeec
Q 028826           59 PGRLYDIMERMDVLD----------------FRNLVILVLDEADRLLDMGFQKQISYIISRL--PKL---RRTGLFSATQ  117 (203)
Q Consensus        59 p~~l~~~~~~~~~~~----------------l~~v~~lViDEad~l~~~~~~~~~~~il~~~--~~~---~q~i~~SAT~  117 (203)
                      +    +++.. +.++                +++++++|+||||  ++.+|.+.+..|++.+  ++.   +|+++||||+
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    45544 4442                7899999999999  6889999999999975  432   6999999999


Q ss_pred             ChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHH---hcCCCCeEEEEe
Q 028826          118 TEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLL---IKNKSKKIIMYV  194 (203)
Q Consensus       118 ~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll---~~~~~~~~lIF~  194 (203)
                      +..+..+...++.++..+.+...               .....++.++ +.++.+.|...+...+   .....+++||||
T Consensus       216 p~ei~~l~~~~~~~p~~i~V~~~---------------~l~a~ki~q~-v~v~~e~Kl~~lv~~L~~ll~e~g~~vLVF~  279 (844)
T TIGR02621       216 RTDGPDRTTLLSAEDYKHPVLKK---------------RLAAKKIVKL-VPPSDEKFLSTMVKELNLLMKDSGGAILVFC  279 (844)
T ss_pred             CccHHHHHHHHccCCceeecccc---------------cccccceEEE-EecChHHHHHHHHHHHHHHHhhCCCcEEEEE
Confidence            99999888888888776666544               3344566664 3445555554444332   123557899999


Q ss_pred             ccCCcccC
Q 028826          195 QHGNFSED  202 (203)
Q Consensus       195 ns~~~~e~  202 (203)
                      ||++.|++
T Consensus       280 NTv~~Aq~  287 (844)
T TIGR02621       280 RTVKHVRK  287 (844)
T ss_pred             CCHHHHHH
Confidence            99998764

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.

>PRK09401 reverse gyrase; Reviewed

Probab=99.93  E-value=1.8e-24  Score=198.90  Aligned_cols=174  Identities=18%  Similarity=0.196  Sum_probs=136.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcch-----HHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEV-----KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFR   75 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~-----~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~   75 (203)
                      ++|||+|||||+.|+++.+++++... ++++..+.||...     .++...+.++.++|+|+||++|.+++.   .+...
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            48999999999999999999999877 7888888877542     233344544679999999999998875   35667


Q ss_pred             CccEEEEcchhHhhh-----------hchH-HHHHHHHHhCCC------------------------CCcEEEEeeecCh
Q 028826           76 NLVILVLDEADRLLD-----------MGFQ-KQISYIISRLPK------------------------LRRTGLFSATQTE  119 (203)
Q Consensus        76 ~v~~lViDEad~l~~-----------~~~~-~~~~~il~~~~~------------------------~~q~i~~SAT~~~  119 (203)
                      +++++|+||||+|++           .||. +++..+++.++.                        ..|+++||||+++
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           5674 678888877764                        6899999999987


Q ss_pred             h-HHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCC
Q 028826          120 A-VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGN  198 (203)
Q Consensus       120 ~-v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~  198 (203)
                      . +..   ..++++..+.+...               .....++.|.|..++  +|...|..+++..+ .++|||||+++
T Consensus       281 ~~~~~---~l~~~ll~~~v~~~---------------~~~~rnI~~~yi~~~--~k~~~L~~ll~~l~-~~~LIFv~t~~  339 (1176)
T PRK09401        281 RGNRV---KLFRELLGFEVGSP---------------VFYLRNIVDSYIVDE--DSVEKLVELVKRLG-DGGLIFVPSDK  339 (1176)
T ss_pred             cchHH---HHhhccceEEecCc---------------ccccCCceEEEEEcc--cHHHHHHHHHHhcC-CCEEEEEeccc
Confidence            5 332   23345555666554               346688999998766  78888999998765 57999999988


Q ss_pred             c
Q 028826          199 F  199 (203)
Q Consensus       199 ~  199 (203)
                      .
T Consensus       340 ~  340 (1176)
T PRK09401        340 G  340 (1176)
T ss_pred             C
Confidence            7

>PRK14701 reverse gyrase; Provisional

Probab=99.90  E-value=6.9e-23  Score=192.36  Aligned_cols=179  Identities=22%  Similarity=0.216  Sum_probs=136.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCC-CceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLP-DVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRN   76 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~-~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~   76 (203)
                      ++|||+||+||+.|+++.++.++.... ++++..++||.+..++..   .+.++.++|+|+||++|.+++..  ... .+
T Consensus       124 ~aLVl~PTreLa~Qi~~~l~~l~~~~~~~v~v~~~~g~~s~~e~~~~~~~l~~g~~dILV~TPgrL~~~~~~--l~~-~~  200 (1638)
T PRK14701        124 KCYIILPTTLLVKQTVEKIESFCEKANLDVRLVYYHSNLRKKEKEEFLERIENGDFDILVTTAQFLARNFPE--MKH-LK  200 (1638)
T ss_pred             eEEEEECHHHHHHHHHHHHHHHHhhcCCceeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECCchhHHhHHH--Hhh-CC
Confidence            489999999999999999999987652 578888999988776643   34445699999999999987764  222 78


Q ss_pred             ccEEEEcchhHhhh-----------hchHHHHHH----HHH----------------------hCCCCCc-EEEEeeecC
Q 028826           77 LVILVLDEADRLLD-----------MGFQKQISY----IIS----------------------RLPKLRR-TGLFSATQT  118 (203)
Q Consensus        77 v~~lViDEad~l~~-----------~~~~~~~~~----il~----------------------~~~~~~q-~i~~SAT~~  118 (203)
                      ++++|+||||+|++           .||.+++..    ++.                      .+++.+| .++||||++
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            99999999999987           378877764    332                      3455666 577999999


Q ss_pred             hhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCC
Q 028826          119 EAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGN  198 (203)
Q Consensus       119 ~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~  198 (203)
                      +.-. . ..+++++..+.+...               .....++.|.|..++..+| ..|.++++.. ++++||||||++
T Consensus       281 ~r~~-~-~~l~~~~l~f~v~~~---------------~~~lr~i~~~yi~~~~~~k-~~L~~ll~~~-g~~gIVF~~t~~  341 (1638)
T PRK14701        281 AKGD-R-VKLYRELLGFEVGSG---------------RSALRNIVDVYLNPEKIIK-EHVRELLKKL-GKGGLIFVPIDE  341 (1638)
T ss_pred             chhH-H-HHHhhcCeEEEecCC---------------CCCCCCcEEEEEECCHHHH-HHHHHHHHhC-CCCeEEEEeccc
Confidence            6411 1 234467777777666               4577889999987765555 6788888876 468999999998


Q ss_pred             ccc
Q 028826          199 FSE  201 (203)
Q Consensus       199 ~~e  201 (203)
                      .+|
T Consensus       342 ~~e  344 (1638)
T PRK14701        342 GAE  344 (1638)
T ss_pred             cch
Confidence            764

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

Probab=99.90  E-value=7.6e-23  Score=182.09  Aligned_cols=177  Identities=18%  Similarity=0.220  Sum_probs=121.8

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHH-hCC--CccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIME-RMD--VLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~-~~~--~~~l~~v   77 (203)
                      .||||+||||||.|+...+++++ . .++++..+.|+... ++...+ ..+++|+|+||+++...+- ...  ...++++
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            48999999999999999999997 3 37888887777664 344555 4579999999999874322 101  1237899


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHH-------hCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchh
Q 028826           78 VILVLDEADRLLDMGFQKQISYIIS-------RLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASS  150 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~-------~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~  150 (203)
                      +++|+||||.|.+ .|...+..+++       ..+..+|++++|||+++..+ +++.++..+..+ +..+          
T Consensus       159 ~~vViDEah~~~g-~fg~~~~~il~rL~ri~~~~g~~~q~i~~SATi~n~~~-~~~~l~g~~~~~-i~~~----------  225 (742)
T TIGR03817       159 RYVVIDECHSYRG-VFGSHVALVLRRLRRLCARYGASPVFVLASATTADPAA-AASRLIGAPVVA-VTED----------  225 (742)
T ss_pred             CEEEEeChhhccC-ccHHHHHHHHHHHHHHHHhcCCCCEEEEEecCCCCHHH-HHHHHcCCCeEE-ECCC----------
Confidence            9999999999865 35555444443       34677899999999998855 567777777544 3322          


Q ss_pred             hhhccCCCCCceeEEEEEcCC-----------------CCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          151 QQLASSKTPLGLHLEYLECES-----------------DKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       151 ~~~~~~~~~~~i~~~~~~~~~-----------------~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                            ..+....+..++.+.                 .++...+..+++.  ..++||||||++.||.
T Consensus       226 ------~~~~~~~~~~~~~p~~~~~~~~~~~~~r~~~~~~~~~~l~~l~~~--~~~~IVF~~sr~~ae~  286 (742)
T TIGR03817       226 ------GSPRGARTVALWEPPLTELTGENGAPVRRSASAEAADLLADLVAE--GARTLTFVRSRRGAEL  286 (742)
T ss_pred             ------CCCcCceEEEEecCCccccccccccccccchHHHHHHHHHHHHHC--CCCEEEEcCCHHHHHH
Confidence                  112222222222221                 1355667777764  4699999999998873

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.

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=99.90  E-value=1.8e-22  Score=187.20  Aligned_cols=133  Identities=17%  Similarity=0.197  Sum_probs=104.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhh-----------hcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFI-----------STLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM   69 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~-----------~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~   69 (203)
                      .+|||+|+|||++|+++.++...           ....++++...+|+.+..++.+.+ .++|||||+||++|..++...
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            37999999999999999887522           122378999999999888776665 568999999999999988752


Q ss_pred             CCccCCCccEEEEcchhHhhhhc----hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCC-CCeEE
Q 028826           70 DVLDFRNLVILVLDEADRLLDMG----FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLR-NPVRI  135 (203)
Q Consensus        70 ~~~~l~~v~~lViDEad~l~~~~----~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~-~~~~i  135 (203)
                      ....++++++|||||+|.|.+..    +...+.++...++...|+|++|||+++ .++++++... .++.+
T Consensus       118 ~r~~L~~Vr~VIVDE~H~L~g~kRG~~Lel~LeRL~~l~~~~~QrIgLSATI~n-~eevA~~L~g~~pv~I  187 (1490)
T PRK09751        118 ARETLRGVETVIIDEVHAVAGSKRGAHLALSLERLDALLHTSAQRIGLSATVRS-ASDVAAFLGGDRPVTV  187 (1490)
T ss_pred             hhhhhccCCEEEEecHHHhcccccccHHHHHHHHHHHhCCCCCeEEEEEeeCCC-HHHHHHHhcCCCCEEE
Confidence            33468999999999999998653    455667777777788999999999987 4666664433 35554

>TIGR01054 rgy reverse gyrase

Probab=99.88  E-value=7.8e-22  Score=181.73  Aligned_cols=175  Identities=23%  Similarity=0.260  Sum_probs=127.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEE---EEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSM---LLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDF   74 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~---~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l   74 (203)
                      .+|||+||||||.|+++.+++++... ++++.   .++||.+..++..   .+.+++++|+||||++|.+++..   +..
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            48999999999999999999998876 55543   4678887665533   34445699999999999988765   222


Q ss_pred             CCccEEEEcchhHhhh-----------hchHHH-HHHHH----------------------HhCCCCCc--EEEEeee-c
Q 028826           75 RNLVILVLDEADRLLD-----------MGFQKQ-ISYII----------------------SRLPKLRR--TGLFSAT-Q  117 (203)
Q Consensus        75 ~~v~~lViDEad~l~~-----------~~~~~~-~~~il----------------------~~~~~~~q--~i~~SAT-~  117 (203)
                       +++++|+||||.|++           .||.++ +..++                      +.+++.+|  .++|||| .
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           567654 44433                      34455555  5779999 5


Q ss_pred             ChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccC
Q 028826          118 TEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHG  197 (203)
Q Consensus       118 ~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~  197 (203)
                      |..+..   .++++...+.+...               .....++.|.|..++.  +...|.++++... .++|||||++
T Consensus       278 p~~~~~---~l~r~ll~~~v~~~---------------~~~~r~I~~~~~~~~~--~~~~L~~ll~~l~-~~~IVFv~t~  336 (1171)
T TIGR01054       278 PRGKRA---KLFRELLGFEVGGG---------------SDTLRNVVDVYVEDED--LKETLLEIVKKLG-TGGIVYVSID  336 (1171)
T ss_pred             ccccHH---HHcccccceEecCc---------------cccccceEEEEEeccc--HHHHHHHHHHHcC-CCEEEEEecc
Confidence            655432   34456656666555               4567889999875543  3567888887664 5799999998


Q ss_pred             ---Cccc
Q 028826          198 ---NFSE  201 (203)
Q Consensus       198 ---~~~e  201 (203)
                         +.|+
T Consensus       337 ~~~~~a~  343 (1171)
T TIGR01054       337 YGKEKAE  343 (1171)
T ss_pred             ccHHHHH
Confidence               5554

Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.

>cd00268 DEADc DEAD-box helicases

Probab=99.87  E-value=4.3e-21  Score=146.52  Aligned_cols=131  Identities=46%  Similarity=0.760  Sum_probs=119.5

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ++|++||++|+.|+...++.+.... ++++..+.||.+..+....+ ..+++|+|+||+++..++.. +..++.+++++|
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            7999999999999999999998765 89999999998877766665 46899999999999999987 778899999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEE
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRI  135 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i  135 (203)
                      +||+|.+.+.++...+..+.+.++..+|++++|||+++.+..++..++.+|+.+
T Consensus       149 vDE~h~~~~~~~~~~~~~~~~~l~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~  202 (203)
T cd00268         149 LDEADRMLDMGFEDQIREILKLLPKDRQTLLFSATMPKEVRDLARKFLRNPVRI  202 (203)
T ss_pred             EeChHHhhccChHHHHHHHHHhCCcccEEEEEeccCCHHHHHHHHHHCCCCEEe
Confidence            999999998889999999999999999999999999999999999999998876

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.

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

Probab=99.87  E-value=7.7e-23  Score=170.92  Aligned_cols=184  Identities=26%  Similarity=0.319  Sum_probs=155.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhh--hcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCC--ccCCC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFI--STLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDV--LDFRN   76 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~--~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~--~~l~~   76 (203)
                      +|+|+.||||||.|++.+++++.  ... +.++..+............+.....|++|+||.++..++.. +.  ++++.
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            48999999999999999999998  555 56666665554433333344445689999999999999987 44  78999


Q ss_pred             ccEEEEcchhHhhhh-chHHHHHHHHHhCC-CCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhc
Q 028826           77 LVILVLDEADRLLDM-GFQKQISYIISRLP-KLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLA  154 (203)
Q Consensus        77 v~~lViDEad~l~~~-~~~~~~~~il~~~~-~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~  154 (203)
                      |.++|+||||.+++. +|...+..|++.+. +...+-+||||++..++++++....++..+.++..              
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 89999999988774 56678899999999999999999999999999887              


Q ss_pred             cCCCCCceeEEEEEcCC-CCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          155 SSKTPLGLHLEYLECES-DKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       155 ~~~~~~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                       .+....+.|...+|.+ ..|+-++.+++...-.+|++||+.+.++|.
T Consensus       355 -~sa~~~V~QelvF~gse~~K~lA~rq~v~~g~~PP~lIfVQs~eRak  401 (593)
T KOG0344|consen  355 -NSANETVDQELVFCGSEKGKLLALRQLVASGFKPPVLIFVQSKERAK  401 (593)
T ss_pred             -hhHhhhhhhhheeeecchhHHHHHHHHHhccCCCCeEEEEecHHHHH
Confidence             5567788888888855 579999999999998889999999987764

>PRK00254 ski2-like helicase; Provisional

Probab=99.87  E-value=2.4e-21  Score=172.87  Aligned_cols=119  Identities=14%  Similarity=0.219  Sum_probs=101.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +|||+|+++|+.|+++.+.++.. . ++++..++|+.+...+  .+  +.++|+|+||+++..+++. +...+++++++|
T Consensus        71 ~l~l~P~~aLa~q~~~~~~~~~~-~-g~~v~~~~Gd~~~~~~--~~--~~~~IiV~Tpe~~~~ll~~-~~~~l~~l~lvV  143 (720)
T PRK00254         71 AVYLVPLKALAEEKYREFKDWEK-L-GLRVAMTTGDYDSTDE--WL--GKYDIIIATAEKFDSLLRH-GSSWIKDVKLVV  143 (720)
T ss_pred             EEEEeChHHHHHHHHHHHHHHhh-c-CCEEEEEeCCCCCchh--hh--ccCCEEEEcHHHHHHHHhC-CchhhhcCCEEE
Confidence            79999999999999999998753 4 8999999998765432  22  4689999999999999887 666789999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhc
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAG  128 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~  128 (203)
                      +||+|.+.+.++...+..++..++...|++++|||+++ ...+.++.
T Consensus       144 iDE~H~l~~~~rg~~le~il~~l~~~~qiI~lSATl~n-~~~la~wl  189 (720)
T PRK00254        144 ADEIHLIGSYDRGATLEMILTHMLGRAQILGLSATVGN-AEELAEWL  189 (720)
T ss_pred             EcCcCccCCccchHHHHHHHHhcCcCCcEEEEEccCCC-HHHHHHHh
Confidence            99999998888899999999999999999999999986 46666643

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

Probab=99.86  E-value=2.9e-21  Score=157.03  Aligned_cols=185  Identities=25%  Similarity=0.471  Sum_probs=150.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcC--CCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTL--PDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~--~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      .|+|+-|+||||.|+++.+++|-.+.  |.+|...+.||.....|.+++ ..+.||+||||+|+.+++.. +.+.+..++
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 EAVIVEPSRELAEQTHNQIEEFKMHTSNPEVRSLLMIGGVLKRTQCKQL-KDGTHIVVGTPGRLLQPISK-GLVTLTHCR  365 (725)
T ss_pred             ceeEecCcHHHHHHHHhhHHHHHhhcCChhhhhhhhhhhHHhHHHHHHh-hcCceeeecCchhhhhhhhc-cceeeeeeE
Confidence            47999999999999999888886544  467777999999999999998 56899999999999999998 999999999


Q ss_pred             EEEEcchhHhhhhchHHHHHHHHHhCCC------CCcEEEEeeecCh-hHHHHHHhcCCCCeEEEeccCcccccccchhh
Q 028826           79 ILVLDEADRLLDMGFQKQISYIISRLPK------LRRTGLFSATQTE-AVEELSKAGLRNPVRIEVRAESKSHHASASSQ  151 (203)
Q Consensus        79 ~lViDEad~l~~~~~~~~~~~il~~~~~------~~q~i~~SAT~~~-~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~  151 (203)
                      ++|+||+|.++..++.+.+.++..++|+      ..|.+++|||+.. +|..+.+..+.-|.++....+           
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            9999999999999999999999988863      5699999999965 577788889999999998776           


Q ss_pred             hhccCCCCCceeEEEEEcCC------------------------------CCcHHHHHHH---------HhcCCCCeEEE
Q 028826          152 QLASSKTPLGLHLEYLECES------------------------------DKKPSQLVDL---------LIKNKSKKIIM  192 (203)
Q Consensus       152 ~~~~~~~~~~i~~~~~~~~~------------------------------~~k~~~l~~l---------l~~~~~~~~lI  192 (203)
                          ...|+.++|....+..                              .+....-..+         ++++...++||
T Consensus       435 ----D~vpetvHhvv~lv~p~~d~sw~~lr~~i~td~vh~kdn~~pg~~Spe~~s~a~kilkgEy~v~ai~~h~mdkaii  510 (725)
T KOG0349|consen  435 ----DLVPETVHHVVKLVCPSVDGSWCDLRQFIETDKVHTKDNLLPGQVSPENPSSATKILKGEYGVVAIRRHAMDKAII  510 (725)
T ss_pred             ----cccchhhccceeecCCccCccHHHHhhhhccCCcccccccccccCCCCChhhhhHHhcCchhhhhhhhhccCceEE
Confidence                4555555555544321                              1112222233         34567789999


Q ss_pred             EeccCCcccC
Q 028826          193 YVQHGNFSED  202 (203)
Q Consensus       193 F~ns~~~~e~  202 (203)
                      ||.|+.+|++
T Consensus       511 fcrtk~dcDn  520 (725)
T KOG0349|consen  511 FCRTKQDCDN  520 (725)
T ss_pred             EEeccccchH
Confidence            9999999864

>PRK13767 ATP-dependent helicase; Provisional

Probab=99.85  E-value=1.2e-20  Score=171.03  Aligned_cols=117  Identities=18%  Similarity=0.219  Sum_probs=91.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHH-------hh----hcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhC
Q 028826            1 MGMIISPTRELSAQIYHVAQP-------FI----STLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM   69 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~-------l~----~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~   69 (203)
                      ++||++|||+|+.|+++.+..       ++    ...+++++...+|+.+..++.+.+ .++|+|+|+||+++..++.. 
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            389999999999999876542       22    233478999999998877776666 56899999999999888865 


Q ss_pred             CCc--cCCCccEEEEcchhHhhhhchHHH----HHHHHHhCCCCCcEEEEeeecCh
Q 028826           70 DVL--DFRNLVILVLDEADRLLDMGFQKQ----ISYIISRLPKLRRTGLFSATQTE  119 (203)
Q Consensus        70 ~~~--~l~~v~~lViDEad~l~~~~~~~~----~~~il~~~~~~~q~i~~SAT~~~  119 (203)
                      ..+  .+++++++|+||+|.+.+..+...    +.++....+...|++++|||+++
T Consensus       164 ~~~~~~l~~l~~VVIDE~H~l~~~~RG~~l~~~L~rL~~l~~~~~q~IglSATl~~  219 (876)
T PRK13767        164 PKFREKLRTVKWVIVDEIHSLAENKRGVHLSLSLERLEELAGGEFVRIGLSATIEP  219 (876)
T ss_pred             hhHHHHHhcCCEEEEechhhhccCccHHHHHHHHHHHHHhcCCCCeEEEEecccCC
Confidence            333  478999999999999987654444    34444444567899999999986

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=99.85  E-value=3.6e-20  Score=158.18  Aligned_cols=176  Identities=18%  Similarity=0.201  Sum_probs=121.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCc-cCCC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVL-DFRN   76 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~-~l~~   76 (203)
                      .+|||+||+||+.|..+.++.+     ++++..+.|+....+...   .+..+.++|+++||+++.........+ ...+
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            3799999999999888877654     688888887766553332   334567999999999986422110123 5688


Q ss_pred             ccEEEEcchhHhhhhc--hHHHHHHH---HHhCCCCCcEEEEeeecChhHHHHHHhcC--CCCeEEEeccCcccccccch
Q 028826           77 LVILVLDEADRLLDMG--FQKQISYI---ISRLPKLRRTGLFSATQTEAVEELSKAGL--RNPVRIEVRAESKSHHASAS  149 (203)
Q Consensus        77 v~~lViDEad~l~~~~--~~~~~~~i---l~~~~~~~q~i~~SAT~~~~v~~~~~~~l--~~~~~i~~~~~~~~~~~~~~  149 (203)
                      ++++||||||++.+||  |++.+..+   ...+ ++.|++++|||+++.+...+...+  .++..+.....         
T Consensus       128 i~~iViDEaH~i~~~g~~fr~~~~~l~~l~~~~-~~~~~l~lTAT~~~~~~~di~~~l~l~~~~~~~~s~~---------  197 (470)
T TIGR00614       128 ITLIAVDEAHCISQWGHDFRPDYKALGSLKQKF-PNVPIMALTATASPSVREDILRQLNLKNPQIFCTSFD---------  197 (470)
T ss_pred             cCEEEEeCCcccCccccccHHHHHHHHHHHHHc-CCCceEEEecCCCHHHHHHHHHHcCCCCCcEEeCCCC---------
Confidence            9999999999999887  67776554   3444 578899999999998876555443  35555433222         


Q ss_pred             hhhhccCCCCCceeEEEEEcCCC-CcHHHHHHHHh-cCCCCeEEEEeccCCcccC
Q 028826          150 SQQLASSKTPLGLHLEYLECESD-KKPSQLVDLLI-KNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~~~~~~-~k~~~l~~ll~-~~~~~~~lIF~ns~~~~e~  202 (203)
                               .+++..  ...... +....+...+. ....+++||||+|++.|++
T Consensus       198 ---------r~nl~~--~v~~~~~~~~~~l~~~l~~~~~~~~~IIF~~s~~~~e~  241 (470)
T TIGR00614       198 ---------RPNLYY--EVRRKTPKILEDLLRFIRKEFKGKSGIIYCPSRKKSEQ  241 (470)
T ss_pred             ---------CCCcEE--EEEeCCccHHHHHHHHHHHhcCCCceEEEECcHHHHHH
Confidence                     234332  222222 55667777776 4566677999999998874

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

>PRK02362 ski2-like helicase; Provisional

Probab=99.85  E-value=1.6e-20  Score=168.06  Aligned_cols=119  Identities=16%  Similarity=0.259  Sum_probs=96.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++|||+||.|+++.++++.+ . ++++..++|+.+...+  .+  ..++|+|+||+++..++++ +...+++++++
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            379999999999999999998864 3 7999999998764432  22  4689999999999999987 55668999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhC---CCCCcEEEEeeecChhHHHHHHh
Q 028826           81 VLDEADRLLDMGFQKQISYIISRL---PKLRRTGLFSATQTEAVEELSKA  127 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~---~~~~q~i~~SAT~~~~v~~~~~~  127 (203)
                      |+||+|.+.+.++...++.++..+   +...|++++|||+++. .++.++
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            999999998877877777776555   5678999999999863 445543

>PRK10689 transcription-repair coupling factor; Provisional

Probab=99.84  E-value=6.9e-20  Score=168.55  Aligned_cols=169  Identities=18%  Similarity=0.224  Sum_probs=124.3

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      +++||+||++||.|+++.+++..... ++++..++|+.+..++...+   ..+++||+||||+.+    .  ..+.++++
T Consensus       651 qvlvLvPT~eLA~Q~~~~f~~~~~~~-~v~i~~l~g~~s~~e~~~il~~l~~g~~dIVVgTp~lL----~--~~v~~~~L  723 (1147)
T PRK10689        651 QVAVLVPTTLLAQQHYDNFRDRFANW-PVRIEMLSRFRSAKEQTQILAEAAEGKIDILIGTHKLL----Q--SDVKWKDL  723 (1147)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHhhccC-CceEEEEECCCCHHHHHHHHHHHHhCCCCEEEECHHHH----h--CCCCHhhC
Confidence            58999999999999999999877766 68998999988876665543   336799999999643    2  45678899


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCC
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSK  157 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~  157 (203)
                      +++||||+|++   |+..  ...+..++.++|+++||||.++.+..+....++++..+.....                 
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            99999999997   4322  3446778889999999999999888888888899988876544                 


Q ss_pred             CCCceeEEEEEcCCC-CcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          158 TPLGLHLEYLECESD-KKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       158 ~~~~i~~~~~~~~~~-~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      ....+++++...... .|...+..+.   ++++++||||+.+.++
T Consensus       782 ~r~~v~~~~~~~~~~~~k~~il~el~---r~gqv~vf~n~i~~ie  823 (1147)
T PRK10689        782 RRLAVKTFVREYDSLVVREAILREIL---RGGQVYYLYNDVENIQ  823 (1147)
T ss_pred             CCCCceEEEEecCcHHHHHHHHHHHh---cCCeEEEEECCHHHHH
Confidence            122355554433221 1222222332   4568999999987654

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

Probab=99.84  E-value=9.8e-20  Score=164.14  Aligned_cols=177  Identities=20%  Similarity=0.203  Sum_probs=121.3

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHh-----CCCeEEEeccHHHHH---HHHhCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEE-----EGANLLIGTPGRLYD---IMERMDVL   72 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~-----~~~~ilV~Tp~~l~~---~~~~~~~~   72 (203)
                      .+|||+|+++|+.+....+..   .  +++...+.|+.+..++...+..     ++++||++||++|..   ++.....+
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            479999999999743333333   2  7999999999887776654432     578999999999863   22221111


Q ss_pred             -cCCCccEEEEcchhHhhhhc--hHHHHHHH--HHhCCCCCcEEEEeeecChhHHHHHHhcCC--CCeEEEeccCccccc
Q 028826           73 -DFRNLVILVLDEADRLLDMG--FQKQISYI--ISRLPKLRRTGLFSATQTEAVEELSKAGLR--NPVRIEVRAESKSHH  145 (203)
Q Consensus        73 -~l~~v~~lViDEad~l~~~~--~~~~~~~i--l~~~~~~~q~i~~SAT~~~~v~~~~~~~l~--~~~~i~~~~~~~~~~  145 (203)
                       ....+.+|||||||++++||  |+++++.+  +....+..|++++|||+++.+...+...+.  ++..+....      
T Consensus       577 ~~~~~LslIVIDEAHcVSqWGhDFRpdYr~L~~Lr~~fp~vPilALTATAT~~V~eDI~~~L~l~~~~vfr~Sf------  650 (1195)
T PLN03137        577 NSRGLLARFVIDEAHCVSQWGHDFRPDYQGLGILKQKFPNIPVLALTATATASVKEDVVQALGLVNCVVFRQSF------  650 (1195)
T ss_pred             hhccccceeccCcchhhhhcccchHHHHHHHHHHHHhCCCCCeEEEEecCCHHHHHHHHHHcCCCCcEEeeccc------
Confidence             23568999999999999998  88888763  444445789999999999998875554443  333332221      


Q ss_pred             ccchhhhhccCCCCCceeEEEEEcCCCCc-HHHHHHHHhcC-CCCeEEEEeccCCcccC
Q 028826          146 ASASSQQLASSKTPLGLHLEYLECESDKK-PSQLVDLLIKN-KSKKIIMYVQHGNFSED  202 (203)
Q Consensus       146 ~~~~~~~~~~~~~~~~i~~~~~~~~~~~k-~~~l~~ll~~~-~~~~~lIF~ns~~~~e~  202 (203)
                                  ..+++  +|..++...+ ...+..++... ..+++||||+|++.||+
T Consensus       651 ------------~RpNL--~y~Vv~k~kk~le~L~~~I~~~~~~esgIIYC~SRke~E~  695 (1195)
T PLN03137        651 ------------NRPNL--WYSVVPKTKKCLEDIDKFIKENHFDECGIIYCLSRMDCEK  695 (1195)
T ss_pred             ------------Cccce--EEEEeccchhHHHHHHHHHHhcccCCCceeEeCchhHHHH
Confidence                        23344  4444444433 46677777644 35689999999998874

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

Probab=99.83  E-value=1.3e-19  Score=134.12  Aligned_cols=120  Identities=33%  Similarity=0.521  Sum_probs=103.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ++|++|+++|+.|..+.+.++.... ++++..++||.....+.......+++|+|+||+++..++.. +..++.+++++|
T Consensus        47 ~lii~P~~~l~~q~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ilv~T~~~l~~~~~~-~~~~~~~~~~iV  124 (169)
T PF00270_consen   47 VLIIVPTRALAEQQFERLRKFFSNT-NVRVVLLHGGQSISEDQREVLSNQADILVTTPEQLLDLISN-GKINISRLSLIV  124 (169)
T ss_dssp             EEEEESSHHHHHHHHHHHHHHTTTT-TSSEEEESTTSCHHHHHHHHHHTTSSEEEEEHHHHHHHHHT-TSSTGTTESEEE
T ss_pred             EEEEeeccccccccccccccccccc-ccccccccccccccccccccccccccccccCcchhhccccc-cccccccceeec
Confidence            7999999999999999999998874 79999999998866343333356899999999999999998 666888899999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCC--CCCcEEEEeeecChhHHH
Q 028826           82 LDEADRLLDMGFQKQISYIISRLP--KLRRTGLFSATQTEAVEE  123 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~--~~~q~i~~SAT~~~~v~~  123 (203)
                      +||+|.+.++++...+..++..+.  .+.|++++|||+++.++.
T Consensus       125 iDE~h~l~~~~~~~~~~~i~~~~~~~~~~~~i~~SAT~~~~~~~  168 (169)
T PF00270_consen  125 IDEAHHLSDETFRAMLKSILRRLKRFKNIQIILLSATLPSNVEK  168 (169)
T ss_dssp             EETHHHHHHTTHHHHHHHHHHHSHTTTTSEEEEEESSSTHHHHH
T ss_pred             cCcccccccccHHHHHHHHHHHhcCCCCCcEEEEeeCCChhHhh
Confidence            999999998888889999998884  368999999999977665

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 ....

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=99.83  E-value=2.4e-19  Score=162.00  Aligned_cols=171  Identities=19%  Similarity=0.220  Sum_probs=121.7

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      +++|++||++||.|+++.++++.+.+ ++++..++|+.+..++..   .+..+.+|||||||..    + . +.+.++++
T Consensus       502 qvlvLvPT~~LA~Q~~~~f~~~~~~~-~i~v~~Lsg~~~~~e~~~~~~~l~~g~~dIVIGTp~l----l-~-~~v~f~~L  574 (926)
T TIGR00580       502 QVAVLVPTTLLAQQHFETFKERFANF-PVTIELLSRFRSAKEQNEILKELASGKIDILIGTHKL----L-Q-KDVKFKDL  574 (926)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHHhccC-CcEEEEEeccccHHHHHHHHHHHHcCCceEEEchHHH----h-h-CCCCcccC
Confidence            58999999999999999999988877 799999988876544433   4444579999999943    2 2 56789999


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCC
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSK  157 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~  157 (203)
                      +++||||+|++   |  ...+..+..++.+.|++++|||.++....+....+.++..+.....                 
T Consensus       575 ~llVIDEahrf---g--v~~~~~L~~~~~~~~vL~~SATpiprtl~~~l~g~~d~s~I~~~p~-----------------  632 (926)
T TIGR00580       575 GLLIIDEEQRF---G--VKQKEKLKELRTSVDVLTLSATPIPRTLHMSMSGIRDLSIIATPPE-----------------  632 (926)
T ss_pred             CEEEeeccccc---c--hhHHHHHHhcCCCCCEEEEecCCCHHHHHHHHhcCCCcEEEecCCC-----------------
Confidence            99999999985   2  2334556777788999999999888877777667778877765443                 


Q ss_pred             CCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          158 TPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       158 ~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      ....+.+++...+...-...+..-+  ..+++++||||+.+.+++
T Consensus       633 ~R~~V~t~v~~~~~~~i~~~i~~el--~~g~qv~if~n~i~~~e~  675 (926)
T TIGR00580       633 DRLPVRTFVMEYDPELVREAIRREL--LRGGQVFYVHNRIESIEK  675 (926)
T ss_pred             CccceEEEEEecCHHHHHHHHHHHH--HcCCeEEEEECCcHHHHH
Confidence            1223555554322211112222222  245789999999877653

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.

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=99.82  E-value=2.3e-19  Score=157.19  Aligned_cols=174  Identities=19%  Similarity=0.227  Sum_probs=128.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      ++|++|+++|+.|..+.++.+     ++.+..+.|+.+..+...   .+..+..+|+++||+++...... +.+...+++
T Consensus        56 ~lVisPl~sL~~dq~~~l~~~-----gi~~~~~~s~~~~~~~~~~~~~l~~~~~~il~~tpe~l~~~~~~-~~l~~~~l~  129 (591)
T TIGR01389        56 TVVISPLISLMKDQVDQLRAA-----GVAAAYLNSTLSAKEQQDIEKALVNGELKLLYVAPERLEQDYFL-NMLQRIPIA  129 (591)
T ss_pred             EEEEcCCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHhCCCCCEEEEChhHhcChHHH-HHHhcCCCC
Confidence            799999999999888887775     688888888877665443   34457899999999999753333 345667899


Q ss_pred             EEEEcchhHhhhhc--hHHHHHHH---HHhCCCCCcEEEEeeecChhHHHHHHhcCC--CCeEEEeccCcccccccchhh
Q 028826           79 ILVLDEADRLLDMG--FQKQISYI---ISRLPKLRRTGLFSATQTEAVEELSKAGLR--NPVRIEVRAESKSHHASASSQ  151 (203)
Q Consensus        79 ~lViDEad~l~~~~--~~~~~~~i---l~~~~~~~q~i~~SAT~~~~v~~~~~~~l~--~~~~i~~~~~~~~~~~~~~~~  151 (203)
                      ++||||||++.+||  |++.+..+   ...++ ..+++++|||.++.+...+..++.  ++..+....            
T Consensus       130 ~iViDEaH~i~~~g~~frp~y~~l~~l~~~~~-~~~vi~lTAT~~~~~~~~i~~~l~~~~~~~~~~~~------------  196 (591)
T TIGR01389       130 LVAVDEAHCVSQWGHDFRPEYQRLGSLAERFP-QVPRIALTATADAETRQDIRELLRLADANEFITSF------------  196 (591)
T ss_pred             EEEEeCCcccccccCccHHHHHHHHHHHHhCC-CCCEEEEEeCCCHHHHHHHHHHcCCCCCCeEecCC------------
Confidence            99999999999887  77776655   34454 445999999999998876665554  343332111            


Q ss_pred             hhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          152 QLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       152 ~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                            ..+++  .|......++...+.+.+.....+++||||+|++.|++
T Consensus       197 ------~r~nl--~~~v~~~~~~~~~l~~~l~~~~~~~~IIf~~sr~~~e~  239 (591)
T TIGR01389       197 ------DRPNL--RFSVVKKNNKQKFLLDYLKKHRGQSGIIYASSRKKVEE  239 (591)
T ss_pred             ------CCCCc--EEEEEeCCCHHHHHHHHHHhcCCCCEEEEECcHHHHHH
Confidence                  22333  34444566788889999988778899999999998864

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.

>COG1204 Superfamily II helicase [General function prediction only]

Probab=99.81  E-value=1.7e-19  Score=160.09  Aligned_cols=179  Identities=17%  Similarity=0.224  Sum_probs=129.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ++|+||+|+||.|+++++.++...  |+++...+|+.+...+  .+  .+++|+|+|||++-.++++ ...-+.+++++|
T Consensus        79 ~vYivPlkALa~Ek~~~~~~~~~~--GirV~~~TgD~~~~~~--~l--~~~~ViVtT~EK~Dsl~R~-~~~~~~~V~lvV  151 (766)
T COG1204          79 VVYIVPLKALAEEKYEEFSRLEEL--GIRVGISTGDYDLDDE--RL--ARYDVIVTTPEKLDSLTRK-RPSWIEEVDLVV  151 (766)
T ss_pred             EEEEeChHHHHHHHHHHhhhHHhc--CCEEEEecCCcccchh--hh--ccCCEEEEchHHhhHhhhc-CcchhhcccEEE
Confidence            799999999999999999977554  9999999999885542  22  5799999999999999988 555778999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCC---CCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCC
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPK---LRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKT  158 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~---~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (203)
                      |||+|.+-+....+.+..++..+..   ..|++.+|||+|+ ..+++.+.-.++..-......              ...
T Consensus       152 iDEiH~l~d~~RG~~lE~iv~r~~~~~~~~rivgLSATlpN-~~evA~wL~a~~~~~~~rp~~--------------l~~  216 (766)
T COG1204         152 IDEIHLLGDRTRGPVLESIVARMRRLNELIRIVGLSATLPN-AEEVADWLNAKLVESDWRPVP--------------LRR  216 (766)
T ss_pred             EeeeeecCCcccCceehhHHHHHHhhCcceEEEEEeeecCC-HHHHHHHhCCcccccCCCCcc--------------ccc
Confidence            9999998777566666666666643   4799999999996 477777665555522222221              223


Q ss_pred             CCceeEEEEEcCCCCc-------HHHHHHHHhcC-CCCeEEEEeccCCcccC
Q 028826          159 PLGLHLEYLECESDKK-------PSQLVDLLIKN-KSKKIIMYVQHGNFSED  202 (203)
Q Consensus       159 ~~~i~~~~~~~~~~~k-------~~~l~~ll~~~-~~~~~lIF~ns~~~~e~  202 (203)
                      +....+.++..+...|       ...+...+... .++++||||+|++.++.
T Consensus       217 ~v~~~~~~~~~~~~~k~~~~~~~~~~~~~v~~~~~~~~qvLvFv~sR~~a~~  268 (766)
T COG1204         217 GVPYVGAFLGADGKKKTWPLLIDNLALELVLESLAEGGQVLVFVHSRKEAEK  268 (766)
T ss_pred             CCccceEEEEecCccccccccchHHHHHHHHHHHhcCCeEEEEEecCchHHH
Confidence            3344555555554443       33333333333 56799999999998753

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=99.81  E-value=6.9e-19  Score=154.29  Aligned_cols=175  Identities=19%  Similarity=0.167  Sum_probs=124.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||++|+++|+.|..+.++.+     ++.+..+.++....+...   .+..+..+++++||+++...... ..+...++
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            3799999999999988888765     677888888776655433   23346789999999998732211 23445679


Q ss_pred             cEEEEcchhHhhhhc--hHHHHHHH---HHhCCCCCcEEEEeeecChhHHHHHHhc--CCCCeEEEeccCcccccccchh
Q 028826           78 VILVLDEADRLLDMG--FQKQISYI---ISRLPKLRRTGLFSATQTEAVEELSKAG--LRNPVRIEVRAESKSHHASASS  150 (203)
Q Consensus        78 ~~lViDEad~l~~~~--~~~~~~~i---l~~~~~~~q~i~~SAT~~~~v~~~~~~~--l~~~~~i~~~~~~~~~~~~~~~  150 (203)
                      +++||||||++.+||  |++.+..+   ...+ +..|++++|||.++.+...+...  +.+|.......           
T Consensus       141 ~~iVIDEaH~i~~~G~~fr~~y~~L~~l~~~~-p~~~~v~lTAT~~~~~~~di~~~l~l~~~~~~~~~~-----------  208 (607)
T PRK11057        141 ALLAVDEAHCISQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQISSF-----------  208 (607)
T ss_pred             CEEEEeCccccccccCcccHHHHHHHHHHHhC-CCCcEEEEecCCChhHHHHHHHHhCCCCeEEEECCC-----------
Confidence            999999999999887  66665544   3444 57899999999999876643333  34554332221           


Q ss_pred             hhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          151 QQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       151 ~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                             ..+++  .|..+....+...+...+.....+++||||||++.||+
T Consensus       209 -------~r~nl--~~~v~~~~~~~~~l~~~l~~~~~~~~IIFc~tr~~~e~  251 (607)
T PRK11057        209 -------DRPNI--RYTLVEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVED  251 (607)
T ss_pred             -------CCCcc--eeeeeeccchHHHHHHHHHhcCCCCEEEEECcHHHHHH
Confidence                   22333  34445556677888888888888899999999998874

>PRK01172 ski2-like helicase; Provisional

Probab=99.80  E-value=4.1e-19  Score=157.76  Aligned_cols=119  Identities=20%  Similarity=0.240  Sum_probs=95.1

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++|+++||.|+++.+.++.. . +.++...+|+.+....  .+  ..+||+|+||+++..++.+ ....+++++++|
T Consensus        68 ~v~i~P~raLa~q~~~~~~~l~~-~-g~~v~~~~G~~~~~~~--~~--~~~dIiv~Tpek~~~l~~~-~~~~l~~v~lvV  140 (674)
T PRK01172         68 SIYIVPLRSLAMEKYEELSRLRS-L-GMRVKISIGDYDDPPD--FI--KRYDVVILTSEKADSLIHH-DPYIINDVGLIV  140 (674)
T ss_pred             EEEEechHHHHHHHHHHHHHHhh-c-CCeEEEEeCCCCCChh--hh--ccCCEEEECHHHHHHHHhC-ChhHHhhcCEEE
Confidence            79999999999999999998754 4 7899888888664332  22  4689999999999998876 555689999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHh---CCCCCcEEEEeeecChhHHHHHHhc
Q 028826           82 LDEADRLLDMGFQKQISYIISR---LPKLRRTGLFSATQTEAVEELSKAG  128 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~---~~~~~q~i~~SAT~~~~v~~~~~~~  128 (203)
                      +||+|.+.+.++...++.++..   ++...|++++|||+++ ..++.+++
T Consensus       141 iDEaH~l~d~~rg~~le~ll~~~~~~~~~~riI~lSATl~n-~~~la~wl  189 (674)
T PRK01172        141 ADEIHIIGDEDRGPTLETVLSSARYVNPDARILALSATVSN-ANELAQWL  189 (674)
T ss_pred             EecchhccCCCccHHHHHHHHHHHhcCcCCcEEEEeCccCC-HHHHHHHh
Confidence            9999999877776667666544   4567899999999986 46666643

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=99.79  E-value=4.7e-18  Score=150.69  Aligned_cols=169  Identities=17%  Similarity=0.242  Sum_probs=113.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      +++|++||++||.|+++.++++.+.. ++++..++||.+..+...   .+.++.++|+||||+++.      ....++++
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            48999999999999999999999887 899999999988654433   444557999999998874      34567899


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCC
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSK  157 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~  157 (203)
                      +++|+||+|++- .    ..+..+...+..+|++++|||..+....+......+...+.....                 
T Consensus       385 ~lvVIDE~Hrfg-~----~qr~~l~~~~~~~~iL~~SATp~prtl~~~~~g~~~~s~i~~~p~-----------------  442 (681)
T PRK10917        385 GLVIIDEQHRFG-V----EQRLALREKGENPHVLVMTATPIPRTLAMTAYGDLDVSVIDELPP-----------------  442 (681)
T ss_pred             ceEEEechhhhh-H----HHHHHHHhcCCCCCEEEEeCCCCHHHHHHHHcCCCceEEEecCCC-----------------
Confidence            999999999862 2    222334444567999999999877655554422223333221111                 


Q ss_pred             CCCceeEEEEEcCCCCcHHHHHHHHhc--CCCCeEEEEeccCCccc
Q 028826          158 TPLGLHLEYLECESDKKPSQLVDLLIK--NKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       158 ~~~~i~~~~~~~~~~~k~~~l~~ll~~--~~~~~~lIF~ns~~~~e  201 (203)
                      ....+...+..  . ++...+.+.+..  ..+++++|||++.+.++
T Consensus       443 ~r~~i~~~~~~--~-~~~~~~~~~i~~~~~~g~q~~v~~~~ie~s~  485 (681)
T PRK10917        443 GRKPITTVVIP--D-SRRDEVYERIREEIAKGRQAYVVCPLIEESE  485 (681)
T ss_pred             CCCCcEEEEeC--c-ccHHHHHHHHHHHHHcCCcEEEEEccccccc
Confidence            12234444432  2 223333344432  35669999999766543

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

Probab=99.78  E-value=2.1e-18  Score=152.17  Aligned_cols=176  Identities=18%  Similarity=0.208  Sum_probs=131.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCc--cCCCcc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL--DFRNLV   78 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~--~l~~v~   78 (203)
                      +|||++|.|+|++.+.+-++..+..+ |+.+..-+|+....+..+++ .++|||+|+|||.|.-++.. +..  .+++++
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            48999999999999999999999988 99998888888877777776 68999999999999988865 332  489999


Q ss_pred             EEEEcchhHhhhhchHHH----HHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCC--Ce-EEEeccCcccccccchhh
Q 028826           79 ILVLDEADRLLDMGFQKQ----ISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRN--PV-RIEVRAESKSHHASASSQ  151 (203)
Q Consensus        79 ~lViDEad~l~~~~~~~~----~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~--~~-~i~~~~~~~~~~~~~~~~  151 (203)
                      ++|+||+|.+.+.....+    +.++....+ ..|.|++|||..+ ....+++....  +. .+.+...           
T Consensus       152 ~VIVDEiHel~~sKRG~~Lsl~LeRL~~l~~-~~qRIGLSATV~~-~~~varfL~g~~~~~~Iv~~~~~-----------  218 (814)
T COG1201         152 YVIVDEIHALAESKRGVQLALSLERLRELAG-DFQRIGLSATVGP-PEEVAKFLVGFGDPCEIVDVSAA-----------  218 (814)
T ss_pred             EEEeehhhhhhccccchhhhhhHHHHHhhCc-ccEEEeehhccCC-HHHHHHHhcCCCCceEEEEcccC-----------
Confidence            999999999986554333    345555555 8999999999985 45666655554  33 3333333           


Q ss_pred             hhccCCCCCceeEEEEEcCC---------CCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          152 QLASSKTPLGLHLEYLECES---------DKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       152 ~~~~~~~~~~i~~~~~~~~~---------~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                              ....+.......         ..-+..+.+++++++  .+|||+|||..+|+
T Consensus       219 --------k~~~i~v~~p~~~~~~~~~~~~~~~~~i~~~v~~~~--ttLIF~NTR~~aE~  268 (814)
T COG1201         219 --------KKLEIKVISPVEDLIYDEELWAALYERIAELVKKHR--TTLIFTNTRSGAER  268 (814)
T ss_pred             --------CcceEEEEecCCccccccchhHHHHHHHHHHHhhcC--cEEEEEeChHHHHH
Confidence                    222333332211         125677777777777  89999999998874

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=99.77  E-value=9.1e-18  Score=150.47  Aligned_cols=169  Identities=13%  Similarity=0.119  Sum_probs=121.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHh-hhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccE
Q 028826            1 MGMIISPTRELSAQIYHVAQPF-ISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVI   79 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l-~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~   79 (203)
                      .++|+.|||++|.|+.+.+.+. +... +..+++..++.+..       ....+|+|+||++|++++..  ...++++++
T Consensus        50 ~ilvlqPrR~aA~qia~rva~~l~~~~-g~~VGy~vr~~~~~-------~~~t~I~v~T~G~Llr~l~~--d~~L~~v~~  119 (812)
T PRK11664         50 KIIMLEPRRLAARNVAQRLAEQLGEKP-GETVGYRMRAESKV-------GPNTRLEVVTEGILTRMIQR--DPELSGVGL  119 (812)
T ss_pred             eEEEECChHHHHHHHHHHHHHHhCccc-CceEEEEecCcccc-------CCCCcEEEEChhHHHHHHhh--CCCcCcCcE
Confidence            3799999999999999988544 3344 77888888776532       34568999999999998875  468999999


Q ss_pred             EEEcchhH-hhhhch-HHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCC
Q 028826           80 LVLDEADR-LLDMGF-QKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSK  157 (203)
Q Consensus        80 lViDEad~-l~~~~~-~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~  157 (203)
                      +|+||+|. .++.++ ...+..+++.+++..|++++|||++.+  .+ ..++.++..+.+...                 
T Consensus       120 IIlDEaHER~l~~Dl~L~ll~~i~~~lr~~lqlilmSATl~~~--~l-~~~~~~~~~I~~~gr-----------------  179 (812)
T PRK11664        120 VILDEFHERSLQADLALALLLDVQQGLRDDLKLLIMSATLDND--RL-QQLLPDAPVIVSEGR-----------------  179 (812)
T ss_pred             EEEcCCCccccccchHHHHHHHHHHhCCccceEEEEecCCCHH--HH-HHhcCCCCEEEecCc-----------------
Confidence            99999996 444332 334456677788899999999999865  23 456666555544322                 


Q ss_pred             CCCceeEEEEEcCCCCcHH-----HHHHHHhcCCCCeEEEEeccCCccc
Q 028826          158 TPLGLHLEYLECESDKKPS-----QLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       158 ~~~~i~~~~~~~~~~~k~~-----~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                       ...++++|..++..++..     .+..+++. ..+.+|||||+.+.++
T Consensus       180 -~~pV~~~y~~~~~~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~ei~  226 (812)
T PRK11664        180 -SFPVERRYQPLPAHQRFDEAVARATAELLRQ-ESGSLLLFLPGVGEIQ  226 (812)
T ss_pred             -cccceEEeccCchhhhHHHHHHHHHHHHHHh-CCCCEEEEcCCHHHHH
Confidence             124778887776665553     44555543 3578999999987765

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=99.77  E-value=1.4e-17  Score=149.17  Aligned_cols=169  Identities=15%  Similarity=0.151  Sum_probs=120.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHh-hhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccE
Q 028826            1 MGMIISPTRELSAQIYHVAQPF-ISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVI   79 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l-~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~   79 (203)
                      .++|+.|+|++|.|+.+.+.+. +... +..+++.+++.+.      . ....+|+|+||++|++++..  ..+++++++
T Consensus        47 ~ilvlqPrR~aA~qiA~rva~~~~~~~-g~~VGy~vr~~~~------~-s~~t~I~v~T~G~Llr~l~~--d~~L~~v~~  116 (819)
T TIGR01970        47 KIIMLEPRRLAARSAAQRLASQLGEAV-GQTVGYRVRGENK------V-SRRTRLEVVTEGILTRMIQD--DPELDGVGA  116 (819)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHHhCCCc-CcEEEEEEccccc------c-CCCCcEEEECCcHHHHHHhh--CcccccCCE
Confidence            3799999999999999988544 3333 6677766665432      1 35689999999999999876  468999999


Q ss_pred             EEEcchh-HhhhhchH-HHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCC
Q 028826           80 LVLDEAD-RLLDMGFQ-KQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSK  157 (203)
Q Consensus        80 lViDEad-~l~~~~~~-~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~  157 (203)
                      +||||+| ++++.++. ..+..+...+++..|++++|||++...   ...++.++..+.+...                 
T Consensus       117 VIiDEaHER~L~~Dl~L~ll~~i~~~lr~dlqlIlmSATl~~~~---l~~~l~~~~vI~~~gr-----------------  176 (819)
T TIGR01970       117 LIFDEFHERSLDADLGLALALDVQSSLREDLKILAMSATLDGER---LSSLLPDAPVVESEGR-----------------  176 (819)
T ss_pred             EEEeccchhhhccchHHHHHHHHHHhcCCCceEEEEeCCCCHHH---HHHHcCCCcEEEecCc-----------------
Confidence            9999999 47766543 334566677788999999999999753   3456666555554332                 


Q ss_pred             CCCceeEEEEEcCCCCcH-----HHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          158 TPLGLHLEYLECESDKKP-----SQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       158 ~~~~i~~~~~~~~~~~k~-----~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                       ...+.++|..++..++.     ..+..+++. ..+++||||+++.+++
T Consensus       177 -~~pVe~~y~~~~~~~~~~~~v~~~l~~~l~~-~~g~iLVFlpg~~eI~  223 (819)
T TIGR01970       177 -SFPVEIRYLPLRGDQRLEDAVSRAVEHALAS-ETGSILVFLPGQAEIR  223 (819)
T ss_pred             -ceeeeeEEeecchhhhHHHHHHHHHHHHHHh-cCCcEEEEECCHHHHH
Confidence             12467778776655543     344455544 3568999999987664

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=99.77  E-value=6e-18  Score=148.45  Aligned_cols=172  Identities=15%  Similarity=0.137  Sum_probs=118.8

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhc--CCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFIST--LPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~--~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +++|++||||||.|+...+.+..++  .++.++...+||... ...... ....+++|+|++.        ...++++++
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            3789999999999999998876543  346778888999773 221211 2468999999752        223578899


Q ss_pred             EEEEcchhHhhhhchHHHHHHHHHhC-CCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCC
Q 028826           79 ILVLDEADRLLDMGFQKQISYIISRL-PKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSK  157 (203)
Q Consensus        79 ~lViDEad~l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~  157 (203)
                      ++|+||||.+...+  +.+..++... ++.+|+++||||+++++..+ ..+++++..+.+...                 
T Consensus       294 ~VVIDEaHEr~~~~--DllL~llk~~~~~~rq~ILmSATl~~dv~~l-~~~~~~p~~I~I~gr-----------------  353 (675)
T PHA02653        294 TVIIDEVHEHDQIG--DIIIAVARKHIDKIRSLFLMTATLEDDRDRI-KEFFPNPAFVHIPGG-----------------  353 (675)
T ss_pred             EEEccccccCccch--hHHHHHHHHhhhhcCEEEEEccCCcHhHHHH-HHHhcCCcEEEeCCC-----------------
Confidence            99999999986654  3444555444 34569999999999988877 568889888877532                 


Q ss_pred             CCCceeEEEEEcCC----------CCcHHHHHHHHhc--CCCCeEEEEeccCCcccC
Q 028826          158 TPLGLHLEYLECES----------DKKPSQLVDLLIK--NKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       158 ~~~~i~~~~~~~~~----------~~k~~~l~~ll~~--~~~~~~lIF~ns~~~~e~  202 (203)
                      ....++++|.....          .++...+..+...  ...+++||||+++..|++
T Consensus       354 t~~pV~~~yi~~~~~~~~~~~y~~~~k~~~l~~L~~~~~~~~g~iLVFlpg~~ei~~  410 (675)
T PHA02653        354 TLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKYTPPKGSSGIVFVASVSQCEE  410 (675)
T ss_pred             cCCCeEEEEeecCcccccchhhhHHHHHHHHHHHHHhhcccCCcEEEEECcHHHHHH
Confidence            34567777764331          1232333333322  234689999999987764

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=99.75  E-value=5.9e-17  Score=142.72  Aligned_cols=170  Identities=18%  Similarity=0.250  Sum_probs=110.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHH---HHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKAD---VKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~---~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      +++|++||++||.|+++.++++.+.. ++++..++||....+.   ...+.++.++|+||||+++.      ....++++
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            58999999999999999999998877 8999999999876653   33444567999999998874      34667899


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCC--CCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhcc
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLP--KLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLAS  155 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~--~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~  155 (203)
                      +++|+||+|++-. ..+..   +.....  ..+|++++|||..+....+......+...+.....               
T Consensus       359 ~lvVIDEaH~fg~-~qr~~---l~~~~~~~~~~~~l~~SATp~prtl~l~~~~~l~~~~i~~~p~---------------  419 (630)
T TIGR00643       359 ALVIIDEQHRFGV-EQRKK---LREKGQGGFTPHVLVMSATPIPRTLALTVYGDLDTSIIDELPP---------------  419 (630)
T ss_pred             ceEEEechhhccH-HHHHH---HHHhcccCCCCCEEEEeCCCCcHHHHHHhcCCcceeeeccCCC---------------
Confidence            9999999998622 12222   223322  26899999999876544433211111111111111               


Q ss_pred             CCCCCceeEEEEEcCCCCcHHHHHHHHhc--CCCCeEEEEeccCCccc
Q 028826          156 SKTPLGLHLEYLECESDKKPSQLVDLLIK--NKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       156 ~~~~~~i~~~~~~~~~~~k~~~l~~ll~~--~~~~~~lIF~ns~~~~e  201 (203)
                        ....+..++.  ...++ ..++..+..  ..+++++|||++.+.++
T Consensus       420 --~r~~i~~~~~--~~~~~-~~~~~~i~~~l~~g~q~~v~~~~i~~s~  462 (630)
T TIGR00643       420 --GRKPITTVLI--KHDEK-DIVYEFIEEEIAKGRQAYVVYPLIEESE  462 (630)
T ss_pred             --CCCceEEEEe--CcchH-HHHHHHHHHHHHhCCcEEEEEccccccc
Confidence              1123333332  33333 444444443  25678999999876543

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=99.74  E-value=1.5e-16  Score=131.43  Aligned_cols=200  Identities=13%  Similarity=0.080  Sum_probs=120.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcC---CCceEEEEEcCcchH--HH-----------------HHHHHhCCCeEEEecc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTL---PDVKSMLLVGGVEVK--AD-----------------VKKIEEEGANLLIGTP   59 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~---~~i~~~~~~~g~~~~--~~-----------------~~~l~~~~~~ilV~Tp   59 (203)
                      +++++|+++|+.|+++.++++...+   .+.++..+.|....+  ..                 .+.+..++|+|+++||
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   255666655542111  00                 0111235799999999


Q ss_pred             HHHHHHHHhC---CC-c---cCCCccEEEEcchhHhhhhc-----hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHh
Q 028826           60 GRLYDIMERM---DV-L---DFRNLVILVLDEADRLLDMG-----FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (203)
Q Consensus        60 ~~l~~~~~~~---~~-~---~l~~v~~lViDEad~l~~~~-----~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~  127 (203)
                      +.+..+++..   +. .   .+.+++++|+||+|.+-.++     +......+++......+++++|||+++.+...+..
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   11 1   25799999999999975332     11233344444444679999999999998887776


Q ss_pred             c--CCCCeEEEeccCccc-c--cccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHh-------cCCCCeEEEEec
Q 028826          128 G--LRNPVRIEVRAESKS-H--HASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLI-------KNKSKKIIMYVQ  195 (203)
Q Consensus       128 ~--l~~~~~i~~~~~~~~-~--~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~-------~~~~~~~lIF~n  195 (203)
                      .  +..+..+.-+..... +  +.......++.....+.+++.+.. ....|...+..+++       ...++++|||||
T Consensus       202 ~~~~~~~~~~v~g~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~-~~~~~~~~l~~l~~~i~~~~~~~~~~k~LIf~n  280 (357)
T TIGR03158       202 AKQAGVKIAPIDGEKYQFPDNPELEADNKTQSFRPVLPPVELELIP-APDFKEEELSELAEEVIERFRQLPGERGAIILD  280 (357)
T ss_pred             ccccCceeeeecCcccccCCChhhhccccccccceeccceEEEEEe-CCchhHHHHHHHHHHHHHHHhccCCCeEEEEEC
Confidence            5  445543322221000 0  000000111112233477777766 44445544433332       235679999999


Q ss_pred             cCCcccC
Q 028826          196 HGNFSED  202 (203)
Q Consensus       196 s~~~~e~  202 (203)
                      |++.|++
T Consensus       281 t~~~~~~  287 (357)
T TIGR03158       281 SLDEVNR  287 (357)
T ss_pred             CHHHHHH
Confidence            9988763

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=99.74  E-value=1.5e-17  Score=137.59  Aligned_cols=180  Identities=16%  Similarity=0.081  Sum_probs=112.1

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchH------------HHHHHHHh-----CCCeEEEeccHHHHH
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVK------------ADVKKIEE-----EGANLLIGTPGRLYD   64 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~------------~~~~~l~~-----~~~~ilV~Tp~~l~~   64 (203)
                      ++|++|+++|+.|+++.+..+.+.    +++.++|+....            ........     ...+|+|+||+.+..
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    344445443211            11111101     236799999999987


Q ss_pred             HHHh-CC--CccCC--CccEEEEcchhHhhhhchHHHHHHHHHhCC-CCCcEEEEeeecChhHHHHHHhcCCCCeEEEec
Q 028826           65 IMER-MD--VLDFR--NLVILVLDEADRLLDMGFQKQISYIISRLP-KLRRTGLFSATQTEAVEELSKAGLRNPVRIEVR  138 (203)
Q Consensus        65 ~~~~-~~--~~~l~--~v~~lViDEad~l~~~~~~~~~~~il~~~~-~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~  138 (203)
                      .+.. .+  ...+.  ..+++|+||+|.+.+.++.. +..+++.++ .+.|++++|||+|+.+.++...+...+......
T Consensus       108 ~~~~~~~~~~~~~~~~~~~~iViDE~h~~~~~~~~~-l~~~l~~l~~~~~~~i~~SATlp~~l~~~~~~~~~~~~~~~~~  186 (358)
T TIGR01587       108 SVFGEFGHYEFTLASIANSLLIFDEVHFYDEYTLAL-ILAVLEVLKDNDVPILLMSATLPKFLKEYAEKIGYVEFNEPLD  186 (358)
T ss_pred             HHhcccchHHHHHHHhcCCEEEEeCCCCCCHHHHHH-HHHHHHHHHHcCCCEEEEecCchHHHHHHHhcCCCcccccCCC
Confidence            7654 01  11122  23799999999998765433 555555554 478999999999988877777654432211111


Q ss_pred             cCcccccccchhhhhccCCCCCceeEEEEEcC--CCCcHHHHHHHHhcC-CCCeEEEEeccCCcccC
Q 028826          139 AESKSHHASASSQQLASSKTPLGLHLEYLECE--SDKKPSQLVDLLIKN-KSKKIIMYVQHGNFSED  202 (203)
Q Consensus       139 ~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~--~~~k~~~l~~ll~~~-~~~~~lIF~ns~~~~e~  202 (203)
                      ..                .......+.+..+.  ...+...+.++++.. .++++||||||++.|++
T Consensus       187 ~~----------------~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~lVf~~t~~~~~~  237 (358)
T TIGR01587       187 LK----------------EERRFERHRFIKIESDKVGEISSLERLLEFIKKGGKIAIIVNTVDRAQE  237 (358)
T ss_pred             Cc----------------cccccccccceeeccccccCHHHHHHHHHHhhCCCeEEEEECCHHHHHH
Confidence            11                00011233333222  245677777777643 56799999999988764

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.

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

Probab=99.71  E-value=4.8e-16  Score=139.86  Aligned_cols=183  Identities=19%  Similarity=0.204  Sum_probs=128.7

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCC-CceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHh-C--CCccCCC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLP-DVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMER-M--DVLDFRN   76 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~-~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~-~--~~~~l~~   76 (203)
                      .||+|.||++||+...+.++++.+..+ +++...+.|.....+.. .+..++||||++||..|..++-. .  -.+.+++
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            489999999999999999999999885 57777767666655443 44478999999999999885543 1  1234788


Q ss_pred             ccEEEEcchhHhhhhchHHHHHHHHHhC-------CCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccch
Q 028826           77 LVILVLDEADRLLDMGFQKQISYIISRL-------PKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASAS  149 (203)
Q Consensus        77 v~~lViDEad~l~~~~~~~~~~~il~~~-------~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~  149 (203)
                      +++||+||+|.. ...|..++..+++++       +...|+|+.|||+... .+++..+........+...         
T Consensus       196 Lk~lVvDElHtY-rGv~GS~vA~llRRL~~~~~~~~~~~q~i~~SAT~~np-~e~~~~l~~~~f~~~v~~~---------  264 (851)
T COG1205         196 LKYLVVDELHTY-RGVQGSEVALLLRRLLRRLRRYGSPLQIICTSATLANP-GEFAEELFGRDFEVPVDED---------  264 (851)
T ss_pred             CcEEEEecceec-cccchhHHHHHHHHHHHHHhccCCCceEEEEeccccCh-HHHHHHhcCCcceeeccCC---------
Confidence            999999999976 333555554444433       4688999999999876 4455555554444434333         


Q ss_pred             hhhhccCCCCCceeEEEEEcC---------CCCcHHHHHHHHhc--CCCCeEEEEeccCCcccC
Q 028826          150 SQQLASSKTPLGLHLEYLECE---------SDKKPSQLVDLLIK--NKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~~~~---------~~~k~~~l~~ll~~--~~~~~~lIF~ns~~~~e~  202 (203)
                             ..+....+++..-+         ...+...+..+...  ..+-++|+|+.|++.+|.
T Consensus       265 -------g~~~~~~~~~~~~p~~~~~~~~~r~s~~~~~~~~~~~~~~~~~~tL~F~~sr~~~e~  321 (851)
T COG1205         265 -------GSPRGLRYFVRREPPIRELAESIRRSALAELATLAALLVRNGIQTLVFFRSRKQVEL  321 (851)
T ss_pred             -------CCCCCceEEEEeCCcchhhhhhcccchHHHHHHHHHHHHHcCceEEEEEehhhhhhh
Confidence                   24555566655555         23555555555543  256699999999998875

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

Probab=99.67  E-value=2.6e-16  Score=132.16  Aligned_cols=176  Identities=19%  Similarity=0.215  Sum_probs=126.7

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCccE
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLVI   79 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~   79 (203)
                      |+|+|.-+||+|-|+.+++=-+++ ++++..-+|...........   ....+||||||-+-+..+++. + -++.++..
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            799999999999999997655666 78887777765444332211   124589999999999999986 4 78999999


Q ss_pred             EEEcchhHhhhhchHHHHHHH---HHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccC
Q 028826           80 LVLDEADRLLDMGFQKQISYI---ISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASS  156 (203)
Q Consensus        80 lViDEad~l~~~~~~~~~~~i---l~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~  156 (203)
                      +||||+|.+-+....+.+.-+   ++.+.+..|+|.+|||..++ .++++.+-...+...                    
T Consensus       342 VVIDEiHtL~deERG~RLdGLI~RLr~l~~~AQ~i~LSATVgNp-~elA~~l~a~lV~y~--------------------  400 (830)
T COG1202         342 VVIDEIHTLEDEERGPRLDGLIGRLRYLFPGAQFIYLSATVGNP-EELAKKLGAKLVLYD--------------------  400 (830)
T ss_pred             EEeeeeeeccchhcccchhhHHHHHHHhCCCCeEEEEEeecCCh-HHHHHHhCCeeEeec--------------------
Confidence            999999988664433333333   33344689999999999865 677776655544332                    


Q ss_pred             CCCCceeEEEEEc-CCCCcHHHHHHHHhcC--------CCCeEEEEeccCCcccC
Q 028826          157 KTPLGLHLEYLEC-ESDKKPSQLVDLLIKN--------KSKKIIMYVQHGNFSED  202 (203)
Q Consensus       157 ~~~~~i~~~~~~~-~~~~k~~~l~~ll~~~--------~~~~~lIF~ns~~~~e~  202 (203)
                      ..|-.+.....++ ++.+|.+.+..+.+..        -.++||||+||++.|++
T Consensus       401 ~RPVplErHlvf~~~e~eK~~ii~~L~k~E~~~~sskg~rGQtIVFT~SRrr~h~  455 (830)
T COG1202         401 ERPVPLERHLVFARNESEKWDIIARLVKREFSTESSKGYRGQTIVFTYSRRRCHE  455 (830)
T ss_pred             CCCCChhHeeeeecCchHHHHHHHHHHHHHHhhhhccCcCCceEEEecchhhHHH
Confidence            1344444444445 4778999999988632        13589999999999874

>PRK12898 secA preprotein translocase subunit SecA; Reviewed

Probab=99.64  E-value=1.9e-15  Score=131.53  Aligned_cols=179  Identities=18%  Similarity=0.155  Sum_probs=128.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHH-HHHHHhCCC--------
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMDV--------   71 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l-~~~~~~~~~--------   71 (203)
                      +++|++||++||.|.++++.++...+ ++++++++||.+..  .+.. ..++||++||...+ .++++. +-        
T Consensus       146 ~v~VvTptreLA~qdae~~~~l~~~l-Glsv~~i~gg~~~~--~r~~-~y~~dIvygT~~e~~FDyLrd-~~~~~~~~~~  220 (656)
T PRK12898        146 PVHVITVNDYLAERDAELMRPLYEAL-GLTVGCVVEDQSPD--ERRA-AYGADITYCTNKELVFDYLRD-RLALGQRASD  220 (656)
T ss_pred             eEEEEcCcHHHHHHHHHHHHHHHhhc-CCEEEEEeCCCCHH--HHHH-HcCCCEEEECCCchhhhhccc-cccccccccc
Confidence            48999999999999999999999988 89999999997643  3333 35799999999998 466654 10        


Q ss_pred             -----------------ccCCCccEEEEcchhHhh-hh-----------------chHHHHHHHHHhCCCC---------
Q 028826           72 -----------------LDFRNLVILVLDEADRLL-DM-----------------GFQKQISYIISRLPKL---------  107 (203)
Q Consensus        72 -----------------~~l~~v~~lViDEad~l~-~~-----------------~~~~~~~~il~~~~~~---------  107 (203)
                                       .-...+.+.||||+|.++ |.                 ........+...+...         
T Consensus       221 ~~~~~~~l~~~~~~~~~~v~r~~~~aIvDEvDSiLiDeartpliis~~~~~~~~~~~y~~~~~~~~~l~~~~~y~~d~~~  300 (656)
T PRK12898        221 ARLALESLHGRSSRSTQLLLRGLHFAIVDEADSVLIDEARTPLIISAPAKEADEAEVYRQALELAAQLKEGEDYTIDAAE  300 (656)
T ss_pred             hhhhhhhhccccCchhhhcccccceeEeecccceeeccCCCceEEECCCCCCchhHHHHHHHHHHHhcCCCCceEEECCC
Confidence                             113567899999999975 31                 0111111222211100         


Q ss_pred             --------------------------------------------------------------------------------
Q 028826          108 --------------------------------------------------------------------------------  107 (203)
Q Consensus       108 --------------------------------------------------------------------------------  107 (203)
                                                                                                      
T Consensus       301 ~~v~lt~~g~~~~e~~~~~l~~~~~~~~~~~~~i~~Al~A~~l~~~d~dYiV~d~~V~ivD~~TGR~~~gr~w~~GLhQa  380 (656)
T PRK12898        301 KRIELTEAGRARIAELAESLPPAWRGAVRREELVRQALSALHLFRRDEHYIVRDGKVVIVDEFTGRVMPDRSWEDGLHQM  380 (656)
T ss_pred             CeEEEcHHHHHHHHHHhCcchhhcccchHHHHHHHHHHHHHHHHhcCCceEEECCeEEEEECCCCeECCCCCcChHHHHH
Confidence                                                                                            


Q ss_pred             ----------------------------CcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCC
Q 028826          108 ----------------------------RRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTP  159 (203)
Q Consensus       108 ----------------------------~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (203)
                                                  ....++|+|.+....++.+.|..+++.|.....                 ..
T Consensus       381 ieaKE~v~i~~e~~t~a~It~q~~Fr~Y~kl~GmTGTa~~~~~El~~~y~l~vv~IPt~kp-----------------~~  443 (656)
T PRK12898        381 IEAKEGCELTDPRETLARITYQRFFRRYLRLAGMTGTAREVAGELWSVYGLPVVRIPTNRP-----------------SQ  443 (656)
T ss_pred             HHHhcCCCCCcCceeeeeehHHHHHHhhHHHhcccCcChHHHHHHHHHHCCCeEEeCCCCC-----------------cc
Confidence                                        056778999988888888888888766555443                 23


Q ss_pred             CceeEEEEEcCCCCcHHHHHHHHhcC--CCCeEEEEeccCCccc
Q 028826          160 LGLHLEYLECESDKKPSQLVDLLIKN--KSKKIIMYVQHGNFSE  201 (203)
Q Consensus       160 ~~i~~~~~~~~~~~k~~~l~~ll~~~--~~~~~lIF~ns~~~~e  201 (203)
                      ....+.++.++..+|...|.++++..  .++++||||+|.+.||
T Consensus       444 r~~~~~~v~~t~~~K~~aL~~~i~~~~~~~~pvLIft~t~~~se  487 (656)
T PRK12898        444 RRHLPDEVFLTAAAKWAAVAARVRELHAQGRPVLVGTRSVAASE  487 (656)
T ss_pred             ceecCCEEEeCHHHHHHHHHHHHHHHHhcCCCEEEEeCcHHHHH
Confidence            33556667778888999999999764  3578999999998876

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

Probab=99.63  E-value=2.1e-15  Score=129.23  Aligned_cols=175  Identities=18%  Similarity=0.203  Sum_probs=121.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +|||+|--.|.....+.++..     |+++..+.++.+.++...   .+..+..+++.-+||++..---. ..+.-..+.
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            689999888876555555554     799999999877665444   44456789999999999743222 234467789


Q ss_pred             EEEEcchhHhhhhc--hHHHHHHHH---HhCCCCCcEEEEeeecChhHHHHHHhcCC--CCeEEEeccCcccccccchhh
Q 028826           79 ILVLDEADRLLDMG--FQKQISYII---SRLPKLRRTGLFSATQTEAVEELSKAGLR--NPVRIEVRAESKSHHASASSQ  151 (203)
Q Consensus        79 ~lViDEad~l~~~~--~~~~~~~il---~~~~~~~q~i~~SAT~~~~v~~~~~~~l~--~~~~i~~~~~~~~~~~~~~~~  151 (203)
                      ++|||||||+.+||  |++++.++-   ..+| +..++.+|||.++.+..-+...+.  ++..+.....           
T Consensus       134 l~vIDEAHCiSqWGhdFRP~Y~~lg~l~~~~~-~~p~~AlTATA~~~v~~DI~~~L~l~~~~~~~~sfd-----------  201 (590)
T COG0514         134 LVAIDEAHCISQWGHDFRPDYRRLGRLRAGLP-NPPVLALTATATPRVRDDIREQLGLQDANIFRGSFD-----------  201 (590)
T ss_pred             eEEechHHHHhhcCCccCHhHHHHHHHHhhCC-CCCEEEEeCCCChHHHHHHHHHhcCCCcceEEecCC-----------
Confidence            99999999999998  999988664   4444 789999999999999986665544  4444444333           


Q ss_pred             hhccCCCCCceeEEEEEcC-CCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          152 QLASSKTPLGLHLEYLECE-SDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       152 ~~~~~~~~~~i~~~~~~~~-~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                             .+|+........ ...+...+.. ......++.||||.|++.||+
T Consensus       202 -------RpNi~~~v~~~~~~~~q~~fi~~-~~~~~~~~GIIYc~sRk~~E~  245 (590)
T COG0514         202 -------RPNLALKVVEKGEPSDQLAFLAT-VLPQLSKSGIIYCLTRKKVEE  245 (590)
T ss_pred             -------CchhhhhhhhcccHHHHHHHHHh-hccccCCCeEEEEeeHHhHHH
Confidence                   455544443332 1233332222 125566789999999999885

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

Probab=99.59  E-value=5.7e-15  Score=130.85  Aligned_cols=174  Identities=18%  Similarity=0.279  Sum_probs=118.6

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCC---ccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDV---LDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~---~~l~~v~   78 (203)
                      .+|++|+|+||..+.+.+.+=...+ |++|..++|+....+.+  +  ..++|||+|||++--.-++ ..   --++.|+
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            4899999999998877666555555 89999999998876555  3  2589999999997544333 22   2368999


Q ss_pred             EEEEcchhHhhhhchHHHHHHHHHhC-------CCCCcEEEEeeecChhHHHHHHhcCCCC--eEEEeccCcccccccch
Q 028826           79 ILVLDEADRLLDMGFQKQISYIISRL-------PKLRRTGLFSATQTEAVEELSKAGLRNP--VRIEVRAESKSHHASAS  149 (203)
Q Consensus        79 ~lViDEad~l~~~~~~~~~~~il~~~-------~~~~q~i~~SAT~~~~v~~~~~~~l~~~--~~i~~~~~~~~~~~~~~  149 (203)
                      ++|+||+|.|-+. ..+.++.|+.+.       -....++++|||+|+ .++++.+.--+|  -.+..+.          
T Consensus       241 LviIDEVHlLhd~-RGpvlEtiVaRtlr~vessqs~IRivgLSATlPN-~eDvA~fL~vn~~~glfsFd~----------  308 (1230)
T KOG0952|consen  241 LVIIDEVHLLHDD-RGPVLETIVARTLRLVESSQSMIRIVGLSATLPN-YEDVARFLRVNPYAGLFSFDQ----------  308 (1230)
T ss_pred             eEEeeeehhhcCc-ccchHHHHHHHHHHHHHhhhhheEEEEeeccCCC-HHHHHHHhcCCCccceeeecc----------
Confidence            9999999977543 455555555444       245689999999996 455555332232  2333333          


Q ss_pred             hhhhccCCCCCceeEEEEEcCCCC-----------cHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          150 SQQLASSKTPLGLHLEYLECESDK-----------KPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       150 ~~~~~~~~~~~~i~~~~~~~~~~~-----------k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                            .-.|-.+.+.++..+..+           ..+...+.+  ..+.+++|||.+|.++-
T Consensus       309 ------~yRPvpL~~~~iG~k~~~~~~~~~~~d~~~~~kv~e~~--~~g~qVlvFvhsR~~Ti  363 (1230)
T KOG0952|consen  309 ------RYRPVPLTQGFIGIKGKKNRQQKKNIDEVCYDKVVEFL--QEGHQVLVFVHSRNETI  363 (1230)
T ss_pred             ------cccccceeeeEEeeecccchhhhhhHHHHHHHHHHHHH--HcCCeEEEEEecChHHH
Confidence                  346778888888876651           123333333  25669999999998764

>PHA02558 uvsW UvsW helicase; Provisional

Probab=99.58  E-value=5.8e-15  Score=127.10  Aligned_cols=103  Identities=15%  Similarity=0.136  Sum_probs=80.7

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+|||+||+||+.|+.+.+++++... +..+..+.+|....        ..++|+|+||+++.....    ..+++++++
T Consensus       160 ~vLilvpt~eL~~Q~~~~l~~~~~~~-~~~~~~i~~g~~~~--------~~~~I~VaT~qsl~~~~~----~~~~~~~~i  226 (501)
T PHA02558        160 KVLIIVPTTSLVTQMIDDFVDYRLFP-REAMHKIYSGTAKD--------TDAPIVVSTWQSAVKQPK----EWFDQFGMV  226 (501)
T ss_pred             eEEEEECcHHHHHHHHHHHHHhcccc-ccceeEEecCcccC--------CCCCEEEeeHHHHhhchh----hhccccCEE
Confidence            37999999999999999999986432 45666677775431        357999999999876442    246789999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChh
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~  120 (203)
                      |+||||++.+.    .+..++..+++.+|+++||||+++.
T Consensus       227 IvDEaH~~~~~----~~~~il~~~~~~~~~lGLTATp~~~  262 (501)
T PHA02558        227 IVDECHLFTGK----SLTSIITKLDNCKFKFGLTGSLRDG  262 (501)
T ss_pred             EEEchhcccch----hHHHHHHhhhccceEEEEeccCCCc
Confidence            99999999754    4566777787788999999999754

>TIGR00963 secA preprotein translocase, SecA subunit

Probab=99.57  E-value=2.5e-14  Score=125.48  Aligned_cols=84  Identities=15%  Similarity=0.215  Sum_probs=73.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHH-HHHHHhCC------Ccc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMD------VLD   73 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l-~~~~~~~~------~~~   73 (203)
                      ++.|++||++||.|.++++.++..++ |++++++.||.+..++...   ..+||++|||++| .++++. +      .+.
T Consensus        99 ~V~VvTpt~~LA~qdae~~~~l~~~L-GLsv~~i~g~~~~~~r~~~---y~~dIvyGT~~rlgfDyLrd-~~~~~~~~~~  173 (745)
T TIGR00963        99 GVHVVTVNDYLAQRDAEWMGQVYRFL-GLSVGLILSGMSPEERREA---YACDITYGTNNELGFDYLRD-NMAHSKEEKV  173 (745)
T ss_pred             CEEEEcCCHHHHHHHHHHHHHHhccC-CCeEEEEeCCCCHHHHHHh---cCCCEEEECCCchhhHHHhc-ccccchhhhh
Confidence            47899999999999999999999998 8999999999887655433   3589999999999 899887 4      356


Q ss_pred             CCCccEEEEcchhHhh
Q 028826           74 FRNLVILVLDEADRLL   89 (203)
Q Consensus        74 l~~v~~lViDEad~l~   89 (203)
                      ++++.++|+||+|.++
T Consensus       174 ~r~l~~aIIDEaDs~L  189 (745)
T TIGR00963       174 QRPFHFAIIDEVDSIL  189 (745)
T ss_pred             ccccceeEeecHHHHh
Confidence            8999999999999987

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.

>smart00487 DEXDc DEAD-like helicases superfamily

Probab=99.56  E-value=3.8e-13  Score=100.94  Aligned_cols=136  Identities=37%  Similarity=0.572  Sum_probs=110.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ++|++||++++.|+...+.++.... ........++....+....+.....+++++||+.+...+.. ......+++++|
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            6899999999999999999987654 33455566666545555555444349999999999999887 556788899999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEecc
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRA  139 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~  139 (203)
                      +||+|.+....+...+..++..+++..+++++|||.++........+..+...+....
T Consensus       135 iDE~h~~~~~~~~~~~~~~~~~~~~~~~~v~~saT~~~~~~~~~~~~~~~~~~~~~~~  192 (201)
T smart00487      135 LDEAHRLLDGGFGDQLEKLLKLLPKNVQLLLLSATPPEEIENLLELFLNDPVFIDVGP  192 (201)
T ss_pred             EECHHHHhcCCcHHHHHHHHHhCCccceEEEEecCCchhHHHHHHHhcCCCEEEeCCc
Confidence            9999999765788889999998888999999999999999999998888777766554

>PRK09200 preprotein translocase subunit SecA; Reviewed

Probab=99.55  E-value=6.1e-14  Score=124.51  Aligned_cols=86  Identities=19%  Similarity=0.181  Sum_probs=70.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHH-HHHHHhC-----CCccC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERM-----DVLDF   74 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l-~~~~~~~-----~~~~l   74 (203)
                      +++|++||++||.|.+.++.++...+ |++++++.||.+..++.+..  .++||++|||+++ .++++..     ....+
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            47899999999999999999999998 99999999998843333332  4699999999999 5666541     11346


Q ss_pred             CCccEEEEcchhHhh
Q 028826           75 RNLVILVLDEADRLL   89 (203)
Q Consensus        75 ~~v~~lViDEad~l~   89 (203)
                      ..+.++|+||||.++
T Consensus       198 r~~~~~IvDEaDsiL  212 (790)
T PRK09200        198 RPLNYAIIDEIDSIL  212 (790)
T ss_pred             cccceEEEeccccce
Confidence            889999999999986

>TIGR03714 secA2 accessory Sec system translocase SecA2

Probab=99.55  E-value=8.5e-14  Score=122.77  Aligned_cols=86  Identities=19%  Similarity=0.206  Sum_probs=67.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcc---hHHHHHHHHhCCCeEEEeccHHH-HHHHHhC-----CCc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVE---VKADVKKIEEEGANLLIGTPGRL-YDIMERM-----DVL   72 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~---~~~~~~~l~~~~~~ilV~Tp~~l-~~~~~~~-----~~~   72 (203)
                      ++|++||++||.|..+++..+...+ |+++..+++|..   ...+.+.. ..++||++|||+++ .+++...     ...
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            7899999999999999999999988 899998887632   22223333 35799999999999 5666431     234


Q ss_pred             cCCCccEEEEcchhHhh
Q 028826           73 DFRNLVILVLDEADRLL   89 (203)
Q Consensus        73 ~l~~v~~lViDEad~l~   89 (203)
                      .+.++.++|+||||.|+
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.

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

Probab=99.54  E-value=8.2e-14  Score=125.42  Aligned_cols=128  Identities=23%  Similarity=0.238  Sum_probs=102.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ++|.+|+|+|.+|.++.+....... .=.++.++|+.+.        +....++|.|.+-|..|+.. ++..+.++.++|
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            6899999999999999887764322 1234677777664        57789999999999999999 888999999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcC---CCCeEEEeccC
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGL---RNPVRIEVRAE  140 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l---~~~~~i~~~~~  140 (203)
                      +||+|.+-+......++.++-.+|...|++++|||+|+. .+|..|.-   ..|..+.....
T Consensus       235 FDEvHyi~D~eRG~VWEE~Ii~lP~~v~~v~LSATv~N~-~EF~~Wi~~~~~~~~~vv~t~~  295 (1041)
T COG4581         235 FDEVHYIGDRERGVVWEEVIILLPDHVRFVFLSATVPNA-EEFAEWIQRVHSQPIHVVSTEH  295 (1041)
T ss_pred             EEeeeeccccccchhHHHHHHhcCCCCcEEEEeCCCCCH-HHHHHHHHhccCCCeEEEeecC
Confidence            999999988877888889999999999999999999976 55555433   34555554443

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

Probab=99.54  E-value=1.5e-14  Score=124.56  Aligned_cols=169  Identities=19%  Similarity=0.203  Sum_probs=128.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||-+|.++|.+|-|+++..=.+.     |+..+|+.+.        +..+..+|.|.+.|..|+.+ ++--+..+.|+|
T Consensus       175 VIYTSPIKALSNQKYREl~~EF~D-----VGLMTGDVTI--------nP~ASCLVMTTEILRsMLYR-GSEvmrEVaWVI  240 (1041)
T KOG0948|consen  175 VIYTSPIKALSNQKYRELLEEFKD-----VGLMTGDVTI--------NPDASCLVMTTEILRSMLYR-GSEVMREVAWVI  240 (1041)
T ss_pred             EEeeChhhhhcchhHHHHHHHhcc-----cceeecceee--------CCCCceeeeHHHHHHHHHhc-cchHhheeeeEE
Confidence            688899999999999988775433     4566776654        45678999999999999999 877789999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhc---CCCCeEEEeccCcccccccchhhhhccCCC
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAG---LRNPVRIEVRAESKSHHASASSQQLASSKT  158 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~---l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (203)
                      +||+|.|=|....-.++.-+-.+|.+...+++|||+|++ .+|++|.   -..|..|..++.                 .
T Consensus       241 FDEIHYMRDkERGVVWEETIIllP~~vr~VFLSATiPNA-~qFAeWI~~ihkQPcHVVYTdy-----------------R  302 (1041)
T KOG0948|consen  241 FDEIHYMRDKERGVVWEETIILLPDNVRFVFLSATIPNA-RQFAEWICHIHKQPCHVVYTDY-----------------R  302 (1041)
T ss_pred             eeeehhccccccceeeeeeEEeccccceEEEEeccCCCH-HHHHHHHHHHhcCCceEEeecC-----------------C
Confidence            999999977665556666677889999999999999986 5666653   346777766555                 6


Q ss_pred             CCceeEEEEEcC---------CC-----Cc--------------------------------------HHHHHHHHhcCC
Q 028826          159 PLGLHLEYLECE---------SD-----KK--------------------------------------PSQLVDLLIKNK  186 (203)
Q Consensus       159 ~~~i~~~~~~~~---------~~-----~k--------------------------------------~~~l~~ll~~~~  186 (203)
                      |..++||.+...         ++     +.                                      +-.+...+-..+
T Consensus       303 PTPLQHyifP~ggdGlylvVDek~~FrednF~~am~~l~~~~~~~~~~~~~~k~~kG~~~~~~~~~s~i~kiVkmi~~~~  382 (1041)
T KOG0948|consen  303 PTPLQHYIFPAGGDGLYLVVDEKGKFREDNFQKAMSVLRKAGESDGKKKANKKGRKGGTGGKGPGDSDIYKIVKMIMERN  382 (1041)
T ss_pred             CCcceeeeecCCCCeeEEEEecccccchHHHHHHHHHhhccCCCccccccccccccCCcCCCCCCcccHHHHHHHHHhhc
Confidence            777888855532         11     11                                      123444444556


Q ss_pred             CCeEEEEeccCCcccC
Q 028826          187 SKKIIMYVQHGNFSED  202 (203)
Q Consensus       187 ~~~~lIF~ns~~~~e~  202 (203)
                      +.|+|||+-|++.||.
T Consensus       383 ~~PVIvFSFSkkeCE~  398 (1041)
T KOG0948|consen  383 YLPVIVFSFSKKECEA  398 (1041)
T ss_pred             CCceEEEEecHhHHHH
Confidence            7799999999999984

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

Probab=99.54  E-value=4e-14  Score=124.61  Aligned_cols=114  Identities=25%  Similarity=0.240  Sum_probs=97.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ++|-+|.++|.+|-++.++.-....     ..++|+...        +..+.++|+|.+.|..|+++ +.--+.++.++|
T Consensus       343 ~iYTSPIKALSNQKfRDFk~tF~Dv-----gLlTGDvqi--------nPeAsCLIMTTEILRsMLYr-gadliRDvE~VI  408 (1248)
T KOG0947|consen  343 TIYTSPIKALSNQKFRDFKETFGDV-----GLLTGDVQI--------NPEASCLIMTTEILRSMLYR-GADLIRDVEFVI  408 (1248)
T ss_pred             eEecchhhhhccchHHHHHHhcccc-----ceeecceee--------CCCcceEeehHHHHHHHHhc-ccchhhccceEE
Confidence            6889999999999999998865443     267777553        45678999999999999998 777789999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCC
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLR  130 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~  130 (203)
                      +||+|.+-|......++.++-++|+..++|++|||.|+. .+|+.|.-+
T Consensus       409 FDEVHYiND~eRGvVWEEViIMlP~HV~~IlLSATVPN~-~EFA~WIGR  456 (1248)
T KOG0947|consen  409 FDEVHYINDVERGVVWEEVIIMLPRHVNFILLSATVPNT-LEFADWIGR  456 (1248)
T ss_pred             EeeeeecccccccccceeeeeeccccceEEEEeccCCCh-HHHHHHhhh
Confidence            999999988888888899999999999999999999975 667776544

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=99.52  E-value=2e-13  Score=125.91  Aligned_cols=159  Identities=18%  Similarity=0.234  Sum_probs=105.0

Q ss_pred             cHHHHHHHHHHHHH-hhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchh
Q 028826            8 TRELSAQIYHVAQP-FISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEAD   86 (203)
Q Consensus         8 treLa~Qi~~~~~~-l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad   86 (203)
                      +++||.|+.+++.. ++... |+++    ...+   +.    ..+++|+|+||++|++.+.. + ..+++++++||||||
T Consensus       131 ArsLA~RVA~El~~~lG~~V-GY~v----rf~~---~~----s~~t~I~v~TpG~LL~~l~~-d-~~Ls~~~~IIIDEAH  196 (1294)
T PRK11131        131 ARTVANRIAEELETELGGCV-GYKV----RFND---QV----SDNTMVKLMTDGILLAEIQQ-D-RLLMQYDTIIIDEAH  196 (1294)
T ss_pred             HHHHHHHHHHHHhhhhccee-ceee----cCcc---cc----CCCCCEEEEChHHHHHHHhc-C-CccccCcEEEecCcc
Confidence            68999999998875 43332 3332    1111   11    35789999999999999876 3 459999999999999


Q ss_pred             -HhhhhchHH-HHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCceeE
Q 028826           87 -RLLDMGFQK-QISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHL  164 (203)
Q Consensus        87 -~l~~~~~~~-~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~  164 (203)
                       ++++.+|.. .++.++... ++.|+|++|||++.  ..+.+.+...|. +.+...                  ...+.+
T Consensus       197 ERsLn~DfLLg~Lk~lL~~r-pdlKvILmSATid~--e~fs~~F~~apv-I~V~Gr------------------~~pVei  254 (1294)
T PRK11131        197 ERSLNIDFILGYLKELLPRR-PDLKVIITSATIDP--ERFSRHFNNAPI-IEVSGR------------------TYPVEV  254 (1294)
T ss_pred             ccccccchHHHHHHHhhhcC-CCceEEEeeCCCCH--HHHHHHcCCCCE-EEEcCc------------------cccceE
Confidence             578877654 344544433 46799999999975  467776655553 444332                  123566


Q ss_pred             EEEEcCCCC---cHHHHHHHH---h---cCCCCeEEEEeccCCcccC
Q 028826          165 EYLECESDK---KPSQLVDLL---I---KNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       165 ~~~~~~~~~---k~~~l~~ll---~---~~~~~~~lIF~ns~~~~e~  202 (203)
                      +|......+   +.+.+..++   .   ....+.+|||||+...+++
T Consensus       255 ~y~p~~~~~~~~~~d~l~~ll~~V~~l~~~~~GdILVFLpg~~EIe~  301 (1294)
T PRK11131        255 RYRPIVEEADDTERDQLQAIFDAVDELGREGPGDILIFMSGEREIRD  301 (1294)
T ss_pred             EEeecccccchhhHHHHHHHHHHHHHHhcCCCCCEEEEcCCHHHHHH
Confidence            776654322   233333333   2   3456789999999887653

>PRK05580 primosome assembly protein PriA; Validated

Probab=99.52  E-value=1.1e-12  Score=116.37  Aligned_cols=113  Identities=18%  Similarity=0.259  Sum_probs=81.3

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      ++||++||++|+.|+.+.+++..    +.++..++||.+..++..   .+..+.++|+||||+.+.        ..++++
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            48999999999999999888753    578999999987654433   334567899999998763        346889


Q ss_pred             cEEEEcchhHhhhhc-----h-HHHHHHHHHhCCCCCcEEEEeeecChhHHHHHH
Q 028826           78 VILVLDEADRLLDMG-----F-QKQISYIISRLPKLRRTGLFSATQTEAVEELSK  126 (203)
Q Consensus        78 ~~lViDEad~l~~~~-----~-~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~  126 (203)
                      +++|+||+|...-..     | ..++. +.+....+.|++++|||.+.+....+.
T Consensus       260 ~liVvDEeh~~s~~~~~~p~y~~r~va-~~ra~~~~~~~il~SATps~~s~~~~~  313 (679)
T PRK05580        260 GLIIVDEEHDSSYKQQEGPRYHARDLA-VVRAKLENIPVVLGSATPSLESLANAQ  313 (679)
T ss_pred             CEEEEECCCccccccCcCCCCcHHHHH-HHHhhccCCCEEEEcCCCCHHHHHHHh
Confidence            999999999753211     1 12222 223334688999999998766555443

>PRK12904 preprotein translocase subunit SecA; Reviewed

Probab=99.50  E-value=2.9e-13  Score=120.20  Aligned_cols=83  Identities=17%  Similarity=0.285  Sum_probs=72.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHH-HHHHHhCCC------ccC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMDV------LDF   74 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l-~~~~~~~~~------~~l   74 (203)
                      +-|++||.+||.|.++++..+...+ |++++++.||.+..++....   .+||++|||+++ .++++. +.      ...
T Consensus       125 V~IvTpn~yLA~rd~e~~~~l~~~L-Glsv~~i~~~~~~~er~~~y---~~dI~ygT~~elgfDyLrd-~~~~~~~~~~~  199 (830)
T PRK12904        125 VHVVTVNDYLAKRDAEWMGPLYEFL-GLSVGVILSGMSPEERREAY---AADITYGTNNEFGFDYLRD-NMVFSLEERVQ  199 (830)
T ss_pred             EEEEecCHHHHHHHHHHHHHHHhhc-CCeEEEEcCCCCHHHHHHhc---CCCeEEECCcchhhhhhhc-ccccchhhhcc
Confidence            4589999999999999999999998 99999999998887766554   489999999999 889986 32      236


Q ss_pred             CCccEEEEcchhHhh
Q 028826           75 RNLVILVLDEADRLL   89 (203)
Q Consensus        75 ~~v~~lViDEad~l~   89 (203)
                      ..+.++|+||||.++
T Consensus       200 r~~~~aIvDEaDsiL  214 (830)
T PRK12904        200 RGLNYAIVDEVDSIL  214 (830)
T ss_pred             cccceEEEechhhhe
Confidence            789999999999986

>TIGR00595 priA primosomal protein N'

Probab=99.49  E-value=3.1e-12  Score=110.05  Aligned_cols=112  Identities=19%  Similarity=0.249  Sum_probs=79.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      ++||++|+++|+.|+++.+++..    +.++..++|+.+..+..+   .+..+.++|+|||+..+.        ..++++
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            48999999999999999888753    567888899876554433   334467899999998763        246789


Q ss_pred             cEEEEcchhHhhhh---c--h-HHHHHHHHHhCCCCCcEEEEeeecChhHHHHH
Q 028826           78 VILVLDEADRLLDM---G--F-QKQISYIISRLPKLRRTGLFSATQTEAVEELS  125 (203)
Q Consensus        78 ~~lViDEad~l~~~---~--~-~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~  125 (203)
                      +++||||.|...-+   +  | ..++....+.. .+.+++++|||.+.+....+
T Consensus        95 ~lIIVDEeh~~sykq~~~p~y~ar~~a~~ra~~-~~~~vil~SATPsles~~~~  147 (505)
T TIGR00595        95 GLIIVDEEHDSSYKQEEGPRYHARDVAVYRAKK-FNCPVVLGSATPSLESYHNA  147 (505)
T ss_pred             CEEEEECCCccccccccCCCCcHHHHHHHHHHh-cCCCEEEEeCCCCHHHHHHH
Confidence            99999999976422   1  1 12333344444 57899999999665444333

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).

>PRK12899 secA preprotein translocase subunit SecA; Reviewed

Probab=99.49  E-value=1.1e-13  Score=123.32  Aligned_cols=83  Identities=16%  Similarity=0.309  Sum_probs=74.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHH-HHHHHhCCCccCC-----
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMDVLDFR-----   75 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l-~~~~~~~~~~~l~-----   75 (203)
                      ++||+||+|||.|+.+++..+.+++ ++++.+++||.+..++...+   +|||+||||++| .++++. +.+.++     
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            6899999999999999999999988 89999999999988876554   599999999999 999998 667766     


Q ss_pred             --CccEEEEcchhHhh
Q 028826           76 --NLVILVLDEADRLL   89 (203)
Q Consensus        76 --~v~~lViDEad~l~   89 (203)
                        .+.++|+||||.|+
T Consensus       213 qr~~~~~IIDEADsmL  228 (970)
T PRK12899        213 GRGFYFAIIDEVDSIL  228 (970)
T ss_pred             cccccEEEEechhhhh
Confidence              45899999999987

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

Probab=99.43  E-value=4e-12  Score=114.79  Aligned_cols=178  Identities=19%  Similarity=0.173  Sum_probs=123.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhC--CCeEEEeccHHHHHHHHhC-CCccCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEE--GANLLIGTPGRLYDIMERM-DVLDFR   75 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~--~~~ilV~Tp~~l~~~~~~~-~~~~l~   75 (203)
                      .|||.|-..|..   +++.+|.+.  +++...+.++....++..   .+..+  ..+|+..|||++..--... ...++.
T Consensus       307 tvVISPL~SLm~---DQv~~L~~~--~I~a~~L~s~q~~~~~~~i~q~l~~~~~~ikilYvtPE~v~~~~~l~~~~~~L~  381 (941)
T KOG0351|consen  307 TVVISPLISLMQ---DQVTHLSKK--GIPACFLSSIQTAAERLAILQKLANGNPIIKILYVTPEKVVASEGLLESLADLY  381 (941)
T ss_pred             eEEeccHHHHHH---HHHHhhhhc--CcceeeccccccHHHHHHHHHHHhCCCCeEEEEEeCHHHhhcccchhhHHHhcc
Confidence            589999777665   666666443  899999999888764433   34344  6899999999986422110 222344


Q ss_pred             C---ccEEEEcchhHhhhhc--hHHHHHHHHHhC--CCCCcEEEEeeecChhHHHHHHh--cCCCCeEEEeccCcccccc
Q 028826           76 N---LVILVLDEADRLLDMG--FQKQISYIISRL--PKLRRTGLFSATQTEAVEELSKA--GLRNPVRIEVRAESKSHHA  146 (203)
Q Consensus        76 ~---v~~lViDEad~l~~~~--~~~~~~~il~~~--~~~~q~i~~SAT~~~~v~~~~~~--~l~~~~~i~~~~~~~~~~~  146 (203)
                      .   +.++||||||+...||  |+++++++-...  .....++.+|||.+..+..-+-.  .++++.++..         
T Consensus       382 ~~~~lal~vIDEAHCVSqWgHdFRp~Yk~l~~l~~~~~~vP~iALTATAT~~v~~DIi~~L~l~~~~~~~~---------  452 (941)
T KOG0351|consen  382 ARGLLALFVIDEAHCVSQWGHDFRPSYKRLGLLRIRFPGVPFIALTATATERVREDVIRSLGLRNPELFKS---------  452 (941)
T ss_pred             CCCeeEEEEecHHHHhhhhcccccHHHHHHHHHHhhCCCCCeEEeehhccHHHHHHHHHHhCCCCcceecc---------
Confidence            4   8999999999999998  888887664333  23478999999999998874443  4456664433         


Q ss_pred             cchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHh-cCCCCeEEEEeccCCcccC
Q 028826          147 SASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLI-KNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       147 ~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~-~~~~~~~lIF~ns~~~~e~  202 (203)
                               ...++|+...+..-...+....+...++ .+..+.+||||.++++||+
T Consensus       453 ---------sfnR~NL~yeV~~k~~~~~~~~~~~~~~~~~~~~s~IIYC~sr~~ce~  500 (941)
T KOG0351|consen  453 ---------SFNRPNLKYEVSPKTDKDALLDILEESKLRHPDQSGIIYCLSRKECEQ  500 (941)
T ss_pred             ---------cCCCCCceEEEEeccCccchHHHHHHhhhcCCCCCeEEEeCCcchHHH
Confidence                     3356777666655443344444444444 4577899999999999984

>PRK13766 Hef nuclease; Provisional

Probab=99.38  E-value=2.1e-11  Score=110.27  Aligned_cols=115  Identities=18%  Similarity=0.217  Sum_probs=87.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +|||+||++|+.|+.+.++++.... +.++..+.|+.+..+... + ..+++|+|+||+.+...+.. +.+++.+++++|
T Consensus        61 vLvl~Pt~~L~~Q~~~~~~~~~~~~-~~~v~~~~g~~~~~~r~~-~-~~~~~iiv~T~~~l~~~l~~-~~~~~~~~~liV  136 (773)
T PRK13766         61 VLILAPTKPLVEQHAEFFRKFLNIP-EEKIVVFTGEVSPEKRAE-L-WEKAKVIVATPQVIENDLIA-GRISLEDVSLLI  136 (773)
T ss_pred             EEEEeCcHHHHHHHHHHHHHHhCCC-CceEEEEeCCCCHHHHHH-H-HhCCCEEEECHHHHHHHHHc-CCCChhhCcEEE
Confidence            7999999999999999999986432 467888888877654332 2 24689999999999877666 778899999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChh
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~  120 (203)
                      +||||++........+........+.++++++|||....
T Consensus       137 vDEaH~~~~~~~~~~i~~~~~~~~~~~~il~lTaTP~~~  175 (773)
T PRK13766        137 FDEAHRAVGNYAYVYIAERYHEDAKNPLVLGLTASPGSD  175 (773)
T ss_pred             EECCccccccccHHHHHHHHHhcCCCCEEEEEEcCCCCC
Confidence            999999875443344444444445677899999997543

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

Probab=99.38  E-value=3.4e-12  Score=115.23  Aligned_cols=175  Identities=16%  Similarity=0.194  Sum_probs=118.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCc-cCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL-DFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~-~l~~v~~l   80 (203)
                      .+|++|.++|++.+...+.+-.+.+ |++|...+|+.....+.    -.+.+|+||||++.-..-++.+.. ..+-++.+
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            4799999999987766554444555 89999999987754333    146789999999975554442222 24578999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCC-------CCCcEEEEeeecChh--HHHHHHhcCCCCeEEEeccCcccccccchhh
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLP-------KLRRTGLFSATQTEA--VEELSKAGLRNPVRIEVRAESKSHHASASSQ  151 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~-------~~~q~i~~SAT~~~~--v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~  151 (203)
                      |+||.|.+-| ...+.++.+..+..       ..+..+++|||+|+=  |..|+.-.  .+-.+..+.+           
T Consensus       442 IIDEIHLLhD-dRGpvLESIVaRt~r~ses~~e~~RlVGLSATLPNy~DV~~Fl~v~--~~glf~fd~s-----------  507 (1674)
T KOG0951|consen  442 IIDEIHLLHD-DRGPVLESIVARTFRRSESTEEGSRLVGLSATLPNYEDVASFLRVD--PEGLFYFDSS-----------  507 (1674)
T ss_pred             hhhhhhhccc-ccchHHHHHHHHHHHHhhhcccCceeeeecccCCchhhhHHHhccC--cccccccCcc-----------
Confidence            9999997643 35666666655442       367899999999973  33333321  2344444444           


Q ss_pred             hhccCCCCCceeEEEEEcCCCCcHHH--------HHHHHhcCCCCeEEEEeccCCcc
Q 028826          152 QLASSKTPLGLHLEYLECESDKKPSQ--------LVDLLIKNKSKKIIMYVQHGNFS  200 (203)
Q Consensus       152 ~~~~~~~~~~i~~~~~~~~~~~k~~~--------l~~ll~~~~~~~~lIF~ns~~~~  200 (203)
                           -.|..+.|.|+.+.+++....        ..+.++.-+.+++||||.||+.+
T Consensus       508 -----yRpvPL~qq~Igi~ek~~~~~~qamNe~~yeKVm~~agk~qVLVFVHsRkET  559 (1674)
T KOG0951|consen  508 -----YRPVPLKQQYIGITEKKPLKRFQAMNEACYEKVLEHAGKNQVLVFVHSRKET  559 (1674)
T ss_pred             -----cCcCCccceEeccccCCchHHHHHHHHHHHHHHHHhCCCCcEEEEEEechHH
Confidence                 367889999999887653333        23344455668999999999875

>PRK13104 secA preprotein translocase subunit SecA; Reviewed

Probab=99.36  E-value=4.2e-12  Score=113.30  Aligned_cols=84  Identities=18%  Similarity=0.298  Sum_probs=73.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHH-HHHHHhCC-CccC----
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMD-VLDF----   74 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l-~~~~~~~~-~~~l----   74 (203)
                      .++|++||++||.|.++++..+...+ |+++.+++||.+..++....   .+||++|||++| .++++. + .+++    
T Consensus       125 ~V~VvTpn~yLA~qd~e~m~~l~~~l-GLtv~~i~gg~~~~~r~~~y---~~dIvygT~grlgfDyLrd-~~~~~~~~~v  199 (896)
T PRK13104        125 GVHIVTVNDYLAKRDSQWMKPIYEFL-GLTVGVIYPDMSHKEKQEAY---KADIVYGTNNEYGFDYLRD-NMAFSLTDKV  199 (896)
T ss_pred             CEEEEcCCHHHHHHHHHHHHHHhccc-CceEEEEeCCCCHHHHHHHh---CCCEEEECChhhhHHHHhc-CCccchHhhh
Confidence            37899999999999999999999988 89999999998877665443   689999999999 899987 4 4555    


Q ss_pred             -CCccEEEEcchhHhh
Q 028826           75 -RNLVILVLDEADRLL   89 (203)
Q Consensus        75 -~~v~~lViDEad~l~   89 (203)
                       ..+.++|+||||.|+
T Consensus       200 ~r~l~~~IvDEaDsiL  215 (896)
T PRK13104        200 QRELNFAIVDEVDSIL  215 (896)
T ss_pred             ccccceEEeccHhhhh
Confidence             589999999999986

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

Probab=99.35  E-value=5e-11  Score=99.43  Aligned_cols=135  Identities=16%  Similarity=0.177  Sum_probs=102.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +|+++||+-|+.|-...++++..- |.-.++.++|....++....-  ...+|+|+||.-+..=+.. |.+|+.++.++|
T Consensus        61 vlfLAPTKPLV~Qh~~~~~~v~~i-p~~~i~~ltGev~p~~R~~~w--~~~kVfvaTPQvveNDl~~-Grid~~dv~~li  136 (542)
T COG1111          61 VLFLAPTKPLVLQHAEFCRKVTGI-PEDEIAALTGEVRPEEREELW--AKKKVFVATPQVVENDLKA-GRIDLDDVSLLI  136 (542)
T ss_pred             EEEecCCchHHHHHHHHHHHHhCC-ChhheeeecCCCChHHHHHHH--hhCCEEEeccHHHHhHHhc-CccChHHceEEE
Confidence            799999999999999999999643 467888999988876544432  3578999999999877777 899999999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHH---HHHhcCCCCeEEEeccC
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEE---LSKAGLRNPVRIEVRAE  140 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~---~~~~~l~~~~~i~~~~~  140 (203)
                      +||||+-....-...+.+..-...+++.++++|||..+..+.   .++..--+.+.+....+
T Consensus       137 fDEAHRAvGnyAYv~Va~~y~~~~k~~~ilgLTASPGs~~ekI~eV~~nLgIe~vevrTE~d  198 (542)
T COG1111         137 FDEAHRAVGNYAYVFVAKEYLRSAKNPLILGLTASPGSDLEKIQEVVENLGIEKVEVRTEED  198 (542)
T ss_pred             echhhhccCcchHHHHHHHHHHhccCceEEEEecCCCCCHHHHHHHHHhCCcceEEEecCCC
Confidence            999999866554444444444445788999999998776554   44444445555555544

>cd00046 DEXDc DEAD-like helicases superfamily

Probab=99.34  E-value=6.1e-11  Score=83.97  Aligned_cols=112  Identities=38%  Similarity=0.588  Sum_probs=84.5

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ++|++|++.++.|..+.+.+....  +..+..+.++.......... ..+.+|+++|++.+...... .........++|
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            689999999999999999888654  57777777776655444333 46899999999999987776 444566788999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeec
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ  117 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  117 (203)
                      +||+|.+....................+++++|||.
T Consensus       109 iDE~h~~~~~~~~~~~~~~~~~~~~~~~~i~~saTp  144 (144)
T cd00046         109 LDEAHRLLNQGFGLLGLKILLKLPKDRQVLLLSATP  144 (144)
T ss_pred             EeCHHHHhhcchHHHHHHHHhhCCccceEEEEeccC
Confidence            999999876544433223334446788999999994

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

>PRK09694 helicase Cas3; Provisional

Probab=99.25  E-value=2.3e-10  Score=103.44  Aligned_cols=126  Identities=13%  Similarity=0.119  Sum_probs=81.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhc-CCCceEEEEEcCcchHHHH---------------------HHHHh--C---CCeE
Q 028826            2 GMIISPTRELSAQIYHVAQPFIST-LPDVKSMLLVGGVEVKADV---------------------KKIEE--E---GANL   54 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~-~~~i~~~~~~~g~~~~~~~---------------------~~l~~--~---~~~i   54 (203)
                      .+|..||++.++|+++.+.++... +++..+...+|+.......                     .++.+  +   -.+|
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            578899999999999999876543 2245677777765422111                     12211  1   1689


Q ss_pred             EEeccHHHHHHHHhCCCccCCC----ccEEEEcchhHhhhhchHHHHHHHHHhCC-CCCcEEEEeeecChhHHH-HHHhc
Q 028826           55 LIGTPGRLYDIMERMDVLDFRN----LVILVLDEADRLLDMGFQKQISYIISRLP-KLRRTGLFSATQTEAVEE-LSKAG  128 (203)
Q Consensus        55 lV~Tp~~l~~~~~~~~~~~l~~----v~~lViDEad~l~~~~~~~~~~~il~~~~-~~~q~i~~SAT~~~~v~~-~~~~~  128 (203)
                      +|||+..++..+-..+...+..    =+.|||||+|.+ +......+..+++.+. ....+|++|||+|....+ +.+.+
T Consensus       414 ~V~TiDQlL~a~l~~kh~~lR~~~La~svvIiDEVHAy-D~ym~~lL~~~L~~l~~~g~~vIllSATLP~~~r~~L~~a~  492 (878)
T PRK09694        414 GVCTIDQVLISVLPVKHRFIRGFGLGRSVLIVDEVHAY-DAYMYGLLEAVLKAQAQAGGSVILLSATLPATLKQKLLDTY  492 (878)
T ss_pred             EEcCHHHHHHHHHccchHHHHHHhhccCeEEEechhhC-CHHHHHHHHHHHHHHHhcCCcEEEEeCCCCHHHHHHHHHHh
Confidence            9999999885433212222222    258999999987 4444555666666553 356799999999988765 44433

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

Probab=99.22  E-value=1.3e-10  Score=94.09  Aligned_cols=181  Identities=18%  Similarity=0.184  Sum_probs=127.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHH--hCCCeEEEeccHHHHH---HHHh-CCC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIE--EEGANLLIGTPGRLYD---IMER-MDV   71 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~--~~~~~ilV~Tp~~l~~---~~~~-~~~   71 (203)
                      ++||++|.-.|.....-+++.|     |+....+....+.++..+   .+.  +....+|..||+++..   ++.+ -+.
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            6899999888876555666666     666666666655543322   121  2567899999999864   2222 146


Q ss_pred             ccCCCccEEEEcchhHhhhhc--hHHHHHH--HHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCccccccc
Q 028826           72 LDFRNLVILVLDEADRLLDMG--FQKQISY--IISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHAS  147 (203)
Q Consensus        72 ~~l~~v~~lViDEad~l~~~~--~~~~~~~--il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~  147 (203)
                      +....++.+.+||+|+-..||  |++++..  ++.+-.+...++.++||.++++..-++..+--..-+....        
T Consensus       211 ~~~~~~~~iaidevhccsqwghdfr~dy~~l~ilkrqf~~~~iigltatatn~vl~d~k~il~ie~~~tf~a--------  282 (695)
T KOG0353|consen  211 LEAGFFKLIAIDEVHCCSQWGHDFRPDYKALGILKRQFKGAPIIGLTATATNHVLDDAKDILCIEAAFTFRA--------  282 (695)
T ss_pred             hhcceeEEEeecceeehhhhCcccCcchHHHHHHHHhCCCCceeeeehhhhcchhhHHHHHHhHHhhheeec--------
Confidence            778899999999999998887  8888764  4555557889999999999998887776655322222222        


Q ss_pred             chhhhhccCCCCCceeEEEEEcCC--CCcHHHHHHHHh-cCCCCeEEEEeccCCcccC
Q 028826          148 ASSQQLASSKTPLGLHLEYLECES--DKKPSQLVDLLI-KNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       148 ~~~~~~~~~~~~~~i~~~~~~~~~--~~k~~~l~~ll~-~~~~~~~lIF~ns~~~~e~  202 (203)
                              ....+++...+..-++  ++=++.+.++++ .+.++..||||-|+++||.
T Consensus       283 --------~fnr~nl~yev~qkp~n~dd~~edi~k~i~~~f~gqsgiiyc~sq~d~ek  332 (695)
T KOG0353|consen  283 --------GFNRPNLKYEVRQKPGNEDDCIEDIAKLIKGDFAGQSGIIYCFSQKDCEK  332 (695)
T ss_pred             --------ccCCCCceeEeeeCCCChHHHHHHHHHHhccccCCCcceEEEeccccHHH
Confidence                    2345666666655544  345667777776 5678899999999999984

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=99.16  E-value=1e-09  Score=102.13  Aligned_cols=130  Identities=18%  Similarity=0.221  Sum_probs=88.1

Q ss_pred             hCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchh-HhhhhchHHH-HHHHHHhCCCCCcEEEEeeecChhHHHHHH
Q 028826           49 EEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEAD-RLLDMGFQKQ-ISYIISRLPKLRRTGLFSATQTEAVEELSK  126 (203)
Q Consensus        49 ~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad-~l~~~~~~~~-~~~il~~~~~~~q~i~~SAT~~~~v~~~~~  126 (203)
                      .....|.++|||+|+..+..  ...+++++++|||||| ++++.++.-. ++.++... +..|++++|||++.  ..+.+
T Consensus       154 s~~T~I~~~TdGiLLr~l~~--d~~L~~~~~IIIDEaHERsL~~D~LL~lLk~il~~r-pdLKlIlmSATld~--~~fa~  228 (1283)
T TIGR01967       154 SSNTLVKLMTDGILLAETQQ--DRFLSRYDTIIIDEAHERSLNIDFLLGYLKQLLPRR-PDLKIIITSATIDP--ERFSR  228 (1283)
T ss_pred             CCCceeeeccccHHHHHhhh--CcccccCcEEEEcCcchhhccchhHHHHHHHHHhhC-CCCeEEEEeCCcCH--HHHHH
Confidence            35688999999999998875  3458999999999999 5888776543 66666554 47899999999974  56777


Q ss_pred             hcCCCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCC------CcHHHHHHHHh---cCCCCeEEEEeccC
Q 028826          127 AGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESD------KKPSQLVDLLI---KNKSKKIIMYVQHG  197 (203)
Q Consensus       127 ~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~------~k~~~l~~ll~---~~~~~~~lIF~ns~  197 (203)
                      .+...|+ +.+...                  ...+..+|......      ++.+.+...+.   ....+.+|||+++.
T Consensus       229 ~F~~apv-I~V~Gr------------------~~PVev~Y~~~~~~~~~~~~~~~~~i~~~I~~l~~~~~GdILVFLpg~  289 (1283)
T TIGR01967       229 HFNNAPI-IEVSGR------------------TYPVEVRYRPLVEEQEDDDLDQLEAILDAVDELFAEGPGDILIFLPGE  289 (1283)
T ss_pred             HhcCCCE-EEECCC------------------cccceeEEecccccccchhhhHHHHHHHHHHHHHhhCCCCEEEeCCCH
Confidence            6655554 444322                  12344555544321      24444444443   23457899999998


Q ss_pred             CcccC
Q 028826          198 NFSED  202 (203)
Q Consensus       198 ~~~e~  202 (203)
                      ..+++
T Consensus       290 ~EI~~  294 (1283)
T TIGR01967       290 REIRD  294 (1283)
T ss_pred             HHHHH
Confidence            77653

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.

>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=99.11  E-value=8.3e-09  Score=86.55  Aligned_cols=138  Identities=17%  Similarity=0.244  Sum_probs=91.5

Q ss_pred             CCeEEEeccHHHHHHHHh----CC-CccCCCccEEEEcchhHhhh--hchHHHHHHHHHhCCC-----------------
Q 028826           51 GANLLIGTPGRLYDIMER----MD-VLDFRNLVILVLDEADRLLD--MGFQKQISYIISRLPK-----------------  106 (203)
Q Consensus        51 ~~~ilV~Tp~~l~~~~~~----~~-~~~l~~v~~lViDEad~l~~--~~~~~~~~~il~~~~~-----------------  106 (203)
                      .+||||++|--|...+..    .+ .-.|+++.++|+|.||.|+-  |.+...+-.-+...|+                 
T Consensus       131 ~SDIIiASPLGLr~~i~~~~~~~~d~DFLSSIEv~iiD~ad~l~MQNW~Hv~~v~~~lN~~P~~~~~~DfsRVR~w~Ldg  210 (442)
T PF06862_consen  131 SSDIIIASPLGLRMIIGEEGEKKRDYDFLSSIEVLIIDQADVLLMQNWEHVLHVFEHLNLQPKKSHDTDFSRVRPWYLDG  210 (442)
T ss_pred             cCCEEEEChHHHHHHhccccccccccchhheeeeEeechhhHHHHhhHHHHHHHHHHhccCCCCCCCCCHHHHHHHHHcC
Confidence            489999999999888873    11 23389999999999999863  4444444334444443                 


Q ss_pred             ----CCcEEEEeeecChhHHHHHHhcCCCCe-EEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCC-------c
Q 028826          107 ----LRRTGLFSATQTEAVEELSKAGLRNPV-RIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDK-------K  174 (203)
Q Consensus       107 ----~~q~i~~SAT~~~~v~~~~~~~l~~~~-~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~-------k  174 (203)
                          -+|++++|+..++++..+.+.++.+.. .+.+......        .+.......++.|.|...+..+       +
T Consensus       211 ~a~~~RQtii~S~~~~pe~~slf~~~~~N~~G~v~~~~~~~~--------~g~i~~v~~~v~Q~F~r~~~~s~~~~~d~R  282 (442)
T PF06862_consen  211 QAKYYRQTIIFSSFQTPEINSLFNRHCQNYAGKVRLKPPYEA--------SGVISQVVVQVRQVFQRFDCSSPADDPDAR  282 (442)
T ss_pred             cchheeEeEEecCCCCHHHHHHHHhhCcCccceEEEeecccc--------ceeeeccccCCceEEEEecCCCcchhhhHH
Confidence                249999999999999999998777643 4444333210        1112356678888888765432       3


Q ss_pred             HHH----HHHHHh-cCCCCeEEEEecc
Q 028826          175 PSQ----LVDLLI-KNKSKKIIMYVQH  196 (203)
Q Consensus       175 ~~~----l~~ll~-~~~~~~~lIF~ns  196 (203)
                      ++.    ++..+. ....+.+|||++|
T Consensus       283 f~yF~~~iLP~l~~~~~~~~~LIfIPS  309 (442)
T PF06862_consen  283 FKYFTKKILPQLKRDSKMSGTLIFIPS  309 (442)
T ss_pred             HHHHHHHHHHHhhhccCCCcEEEEecc
Confidence            322    333334 5567799999987

; GO: 0005634 nucleus

>TIGR00603 rad25 DNA repair helicase rad25

Probab=99.11  E-value=3.2e-10  Score=100.33  Aligned_cols=106  Identities=12%  Similarity=0.121  Sum_probs=71.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHh-------CCCccC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMER-------MDVLDF   74 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~-------~~~~~l   74 (203)
                      +|||||+.+|+.|+.+++.+++.. +...+..+.|+....     . .....|+|+|...+.....+       ...+.-
T Consensus       301 tLILvps~~Lv~QW~~ef~~~~~l-~~~~I~~~tg~~k~~-----~-~~~~~VvVtTYq~l~~~~~r~~~~~~~l~~l~~  373 (732)
T TIGR00603       301 CLVLCTSAVSVEQWKQQFKMWSTI-DDSQICRFTSDAKER-----F-HGEAGVVVSTYSMVAHTGKRSYESEKVMEWLTN  373 (732)
T ss_pred             EEEEeCcHHHHHHHHHHHHHhcCC-CCceEEEEecCcccc-----c-ccCCcEEEEEHHHhhcccccchhhhHHHHHhcc
Confidence            699999999999999999998643 245666666653221     1 13468999999876432111       011223


Q ss_pred             CCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecCh
Q 028826           75 RNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (203)
Q Consensus        75 ~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  119 (203)
                      ....++|+||+|.+-...    .+.++..+ .....+++|||...
T Consensus       374 ~~~gLII~DEvH~lpA~~----fr~il~~l-~a~~RLGLTATP~R  413 (732)
T TIGR00603       374 REWGLILLDEVHVVPAAM----FRRVLTIV-QAHCKLGLTATLVR  413 (732)
T ss_pred             ccCCEEEEEccccccHHH----HHHHHHhc-CcCcEEEEeecCcc
Confidence            467799999999985543    44455555 35568999999864

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).

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

Probab=99.08  E-value=2.2e-10  Score=94.03  Aligned_cols=175  Identities=19%  Similarity=0.157  Sum_probs=114.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---Hh--CCCeEEEeccHHHHH-----HHHhCC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EE--EGANLLIGTPGRLYD-----IMERMD   70 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~--~~~~ilV~Tp~~l~~-----~~~~~~   70 (203)
                      +.||++|.-+|.....+.+.+|     ++++-.+.+-.+..+..+-+   ..  ....++.-||+.-..     +++  +
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            3689999777766554555554     78888888877766655533   22  346899999998532     222  2


Q ss_pred             CccCCCccEEEEcchhHhhhhc--hHHHHHHHH--HhCCCCCcEEEEeeecChhHHH--HHHhcCCCCeEEEeccCcccc
Q 028826           71 VLDFRNLVILVLDEADRLLDMG--FQKQISYII--SRLPKLRRTGLFSATQTEAVEE--LSKAGLRNPVRIEVRAESKSH  144 (203)
Q Consensus        71 ~~~l~~v~~lViDEad~l~~~~--~~~~~~~il--~~~~~~~q~i~~SAT~~~~v~~--~~~~~l~~~~~i~~~~~~~~~  144 (203)
                      ..+-+-++++|+||||+...||  |++++-.+-  +.--.....+.++||.+++|.+  +....+++|+-+..++.    
T Consensus       136 L~~r~~L~Y~vVDEAHCVSQWGHDFRPDYL~LG~LRS~~~~vpwvALTATA~~~VqEDi~~qL~L~~PVAiFkTP~----  211 (641)
T KOG0352|consen  136 LANRDVLRYIVVDEAHCVSQWGHDFRPDYLTLGSLRSVCPGVPWVALTATANAKVQEDIAFQLKLRNPVAIFKTPT----  211 (641)
T ss_pred             HhhhceeeeEEechhhhHhhhccccCcchhhhhhHHhhCCCCceEEeecccChhHHHHHHHHHhhcCcHHhccCcc----
Confidence            3345678999999999999998  888876653  2223577899999999999988  44566778886655443    


Q ss_pred             cccchhhhhccCCCCCceeEEEEEcC----CCCcHHHHHHHHhcC-------------CCCeEEEEeccCCcccC
Q 028826          145 HASASSQQLASSKTPLGLHLEYLECE----SDKKPSQLVDLLIKN-------------KSKKIIMYVQHGNFSED  202 (203)
Q Consensus       145 ~~~~~~~~~~~~~~~~~i~~~~~~~~----~~~k~~~l~~ll~~~-------------~~~~~lIF~ns~~~~e~  202 (203)
                                   -..|   .|+...    -++-+..|.++-...             ..+=.||||.||..||+
T Consensus       212 -------------FR~N---LFYD~~~K~~I~D~~~~LaDF~~~~LG~~~~~~~~~K~~~GCGIVYCRTR~~cEq  270 (641)
T KOG0352|consen  212 -------------FRDN---LFYDNHMKSFITDCLTVLADFSSSNLGKHEKASQNKKTFTGCGIVYCRTRNECEQ  270 (641)
T ss_pred             -------------hhhh---hhHHHHHHHHhhhHhHhHHHHHHHhcCChhhhhcCCCCcCcceEEEeccHHHHHH
Confidence                         1112   122211    134455555555321             12348999999999985

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

Probab=99.02  E-value=3.3e-09  Score=94.98  Aligned_cols=169  Identities=23%  Similarity=0.275  Sum_probs=110.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEE-EEcCcchHHHH---HHHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSML-LVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~-~~~g~~~~~~~---~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      ++|++||+-|+.|+++.+++++....+.++.. .+|.....+..   ..+.++..||+|+|..-|...+..   +.-.++
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 VYIIVPTTTLVRQVYERLKKFAEDAGSLDVLVVYHSALPTKEKEEALERIESGDFDILITTSQFLSKRFEE---LSKLKF  204 (1187)
T ss_pred             EEEEecCHHHHHHHHHHHHHHHhhcCCcceeeeeccccchHHHHHHHHHHhcCCccEEEEeHHHHHhhHHH---hcccCC
Confidence            68999999999999999999987653244444 55554444333   345567899999999999887765   222468


Q ss_pred             cEEEEcchhHhhhh-----------chHHH-H------HHHHHhC------------------------CCCCcEEEEee
Q 028826           78 VILVLDEADRLLDM-----------GFQKQ-I------SYIISRL------------------------PKLRRTGLFSA  115 (203)
Q Consensus        78 ~~lViDEad~l~~~-----------~~~~~-~------~~il~~~------------------------~~~~q~i~~SA  115 (203)
                      +++++|++|.++..           ||.+. +      ..+...+                        .+..+.++.||
T Consensus       205 dfifVDDVDA~LkaskNvDriL~LlGf~eE~i~~a~~~~~lr~~~~~~~~~~~~~e~~~~~e~~~~~~r~k~g~LvvsSA  284 (1187)
T COG1110         205 DFIFVDDVDAILKASKNVDRLLRLLGFSEEVIESAYELIKLRRKLYGEKRAERVREELREVEREREKKRRKLGILVVSSA  284 (1187)
T ss_pred             CEEEEccHHHHHhccccHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhccCCceEEEeec
Confidence            89999999998853           22221 1      1111111                        12358999999


Q ss_pred             ecChhHH-H-HHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEE
Q 028826          116 TQTEAVE-E-LSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMY  193 (203)
Q Consensus       116 T~~~~v~-~-~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF  193 (203)
                      |..+.-. . +.+..+.    +.++..               .....|+...|...   +-...+..+++..+.+ .|||
T Consensus       285 Tg~~rg~R~~LfReLlg----FevG~~---------------~~~LRNIvD~y~~~---~~~e~~~elvk~lG~G-gLIf  341 (1187)
T COG1110         285 TGKPRGSRLKLFRELLG----FEVGSG---------------GEGLRNIVDIYVES---ESLEKVVELVKKLGDG-GLIF  341 (1187)
T ss_pred             cCCCCCchHHHHHHHhC----CccCcc---------------chhhhheeeeeccC---ccHHHHHHHHHHhCCC-eEEE
Confidence            9866421 1 2222222    223333               45677888888665   5566667777766654 8999


Q ss_pred             ecc
Q 028826          194 VQH  196 (203)
Q Consensus       194 ~ns  196 (203)
                      ++.
T Consensus       342 V~~  344 (1187)
T COG1110         342 VPI  344 (1187)
T ss_pred             EEc
Confidence            998

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

Probab=98.97  E-value=5.1e-08  Score=84.59  Aligned_cols=112  Identities=21%  Similarity=0.398  Sum_probs=87.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHH---HHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKAD---VKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~---~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      ||..++||--||.|=+..+.++.+.+ ++++..++|.......   ...+.++..|++|||-.-+-      ....++++
T Consensus       313 Q~ALMAPTEILA~QH~~~~~~~l~~~-~i~V~lLtG~~kgk~r~~~l~~l~~G~~~ivVGTHALiQ------d~V~F~~L  385 (677)
T COG1200         313 QAALMAPTEILAEQHYESLRKWLEPL-GIRVALLTGSLKGKARKEILEQLASGEIDIVVGTHALIQ------DKVEFHNL  385 (677)
T ss_pred             eeEEeccHHHHHHHHHHHHHHHhhhc-CCeEEEeecccchhHHHHHHHHHhCCCCCEEEEcchhhh------cceeecce
Confidence            57889999999999999999999988 8999999997664443   33555677999999986554      57789999


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCC-CCcEEEEeeecChhHHHH
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPK-LRRTGLFSATQTEAVEEL  124 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~-~~q~i~~SAT~~~~v~~~  124 (203)
                      .++|+||-|++   |  -.=+..+..-.. .+..+++|||.-|....+
T Consensus       386 gLVIiDEQHRF---G--V~QR~~L~~KG~~~Ph~LvMTATPIPRTLAl  428 (677)
T COG1200         386 GLVIIDEQHRF---G--VHQRLALREKGEQNPHVLVMTATPIPRTLAL  428 (677)
T ss_pred             eEEEEeccccc---c--HHHHHHHHHhCCCCCcEEEEeCCCchHHHHH
Confidence            99999999986   2  222333444445 688999999987754444

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

Probab=98.96  E-value=2.6e-09  Score=90.75  Aligned_cols=102  Identities=19%  Similarity=0.231  Sum_probs=66.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCC-CeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEG-ANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~-~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +||||||++|+.|+.+.+.+....  +-.+. ..||....        .. ..|.|+|-..+...-.. .........++
T Consensus        83 ~Lvlv~~~~L~~Qw~~~~~~~~~~--~~~~g-~~~~~~~~--------~~~~~i~vat~qtl~~~~~l-~~~~~~~~~li  150 (442)
T COG1061          83 TLVLVPTKELLDQWAEALKKFLLL--NDEIG-IYGGGEKE--------LEPAKVTVATVQTLARRQLL-DEFLGNEFGLI  150 (442)
T ss_pred             EEEEECcHHHHHHHHHHHHHhcCC--ccccc-eecCceec--------cCCCcEEEEEhHHHhhhhhh-hhhcccccCEE
Confidence            699999999999998766665422  11233 34443321        12 46999999988764211 22334478899


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecCh
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  119 (203)
                      |+||+|++.+..+......+....+    .+++|||.+.
T Consensus       151 I~DE~Hh~~a~~~~~~~~~~~~~~~----~LGLTATp~R  185 (442)
T COG1061         151 IFDEVHHLPAPSYRRILELLSAAYP----RLGLTATPER  185 (442)
T ss_pred             EEEccccCCcHHHHHHHHhhhcccc----eeeeccCcee
Confidence            9999999977665554443333222    8999999763

>PRK13107 preprotein translocase subunit SecA; Reviewed

Probab=98.95  E-value=2.1e-09  Score=96.14  Aligned_cols=83  Identities=19%  Similarity=0.301  Sum_probs=71.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHH-HHHHHhCC-CccC-----
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMD-VLDF-----   74 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l-~~~~~~~~-~~~l-----   74 (203)
                      +.||+||++||.|..+++..+...+ |+++.++.+|.+..+..   ..-.+||++|||+++ .++++. + .++.     
T Consensus       126 VhIvT~ndyLA~RD~e~m~~l~~~l-Glsv~~i~~~~~~~~r~---~~Y~~dI~YgT~~e~gfDyLrd-nm~~~~~~~vq  200 (908)
T PRK13107        126 VHVITVNDYLARRDAENNRPLFEFL-GLTVGINVAGLGQQEKK---AAYNADITYGTNNEFGFDYLRD-NMAFSPQERVQ  200 (908)
T ss_pred             EEEEeCCHHHHHHHHHHHHHHHHhc-CCeEEEecCCCCHHHHH---hcCCCCeEEeCCCcccchhhhc-cCccchhhhhc
Confidence            6899999999999999999999998 99999999988764332   234799999999999 899987 4 4444     


Q ss_pred             CCccEEEEcchhHhh
Q 028826           75 RNLVILVLDEADRLL   89 (203)
Q Consensus        75 ~~v~~lViDEad~l~   89 (203)
                      ..+.+.||||||.++
T Consensus       201 r~~~~aIvDEvDsiL  215 (908)
T PRK13107        201 RPLHYALIDEVDSIL  215 (908)
T ss_pred             cccceeeecchhhhc
Confidence            789999999999987

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

Probab=98.85  E-value=1.5e-08  Score=89.00  Aligned_cols=120  Identities=14%  Similarity=0.202  Sum_probs=87.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCcc-CCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLD-FRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~-l~~v~~l   80 (203)
                      +|+++||+-|+.|....+..++.   +..+....||.........+ -..++|+|.||.-+...+.. +..+ ++++.++
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            68999999999888766666543   35666677774433333333 34689999999999988887 4444 6999999


Q ss_pred             EEcchhHhhhhc-hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHH
Q 028826           81 VLDEADRLLDMG-FQKQISYIISRLPKLRRTGLFSATQTEAVEELSK  126 (203)
Q Consensus        81 ViDEad~l~~~~-~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~  126 (203)
                      ||||||+-.... |..-++.++..-....|++++|||..+......+
T Consensus       184 v~DE~Hra~kn~~Y~~Vmr~~l~~k~~~~qILgLTASpG~~~~~v~~  230 (746)
T KOG0354|consen  184 VFDECHRTSKNHPYNNIMREYLDLKNQGNQILGLTASPGSKLEQVQN  230 (746)
T ss_pred             EEcccccccccccHHHHHHHHHHhhhccccEEEEecCCCccHHHHHH
Confidence            999999987654 5555556666665666999999999876555433

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

Probab=98.76  E-value=2e-07  Score=85.25  Aligned_cols=128  Identities=22%  Similarity=0.289  Sum_probs=103.3

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      |+.|||||--||.|=++.+++=.+++ ++++..+..=.+.+++..   .+.++..||||||-.-|.      +.+.++++
T Consensus       645 QVAvLVPTTlLA~QHy~tFkeRF~~f-PV~I~~LSRF~s~kE~~~il~~la~G~vDIvIGTHrLL~------kdv~FkdL  717 (1139)
T COG1197         645 QVAVLVPTTLLAQQHYETFKERFAGF-PVRIEVLSRFRSAKEQKEILKGLAEGKVDIVIGTHRLLS------KDVKFKDL  717 (1139)
T ss_pred             eEEEEcccHHhHHHHHHHHHHHhcCC-CeeEEEecccCCHHHHHHHHHHHhcCCccEEEechHhhC------CCcEEecC
Confidence            57899999999999999998877888 699888776666555544   455688999999974443      67889999


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccC
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAE  140 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~  140 (203)
                      .++||||=|++ .....+.    +..+..+.-++-+|||.-|...++.-..+++-..|...+.
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            99999999986 3335555    4445577889999999999999999999999888877766

>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=98.62  E-value=2.9e-07  Score=68.46  Aligned_cols=110  Identities=17%  Similarity=0.120  Sum_probs=69.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEE-----------EEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSML-----------LVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMD   70 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~-----------~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~   70 (203)
                      +++++|+..|+.|..+.+..+....  .....           ...................++++.|...+........
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            6899999999999999997775542  11111           0111111111222235678999999999998776411


Q ss_pred             ----------CccCCCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecC
Q 028826           71 ----------VLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (203)
Q Consensus        71 ----------~~~l~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  118 (203)
                                ........++|+||||.+....-   .+.++.  .+...++++|||.+
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                      12245678999999999865431   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 ....

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

Probab=98.48  E-value=3.1e-07  Score=82.05  Aligned_cols=88  Identities=14%  Similarity=0.129  Sum_probs=64.2

Q ss_pred             CceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhC-CCccCCCccEEEEcchhHhhhhchHHHHHHHHHhC--
Q 028826           28 DVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM-DVLDFRNLVILVLDEADRLLDMGFQKQISYIISRL--  104 (203)
Q Consensus        28 ~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~-~~~~l~~v~~lViDEad~l~~~~~~~~~~~il~~~--  104 (203)
                      |+++-...|+.......     +.-++-|+|-|+-..+++.. ..-++..+.++|+||.|.+.+.+....++.++..+  
T Consensus       297 G~~ve~y~g~~~p~~~~-----k~~sv~i~tiEkanslin~lie~g~~~~~g~vvVdElhmi~d~~rg~~lE~~l~k~~y  371 (1008)
T KOG0950|consen  297 GFPVEEYAGRFPPEKRR-----KRESVAIATIEKANSLINSLIEQGRLDFLGMVVVDELHMIGDKGRGAILELLLAKILY  371 (1008)
T ss_pred             CCcchhhcccCCCCCcc-----cceeeeeeehHhhHhHHHHHHhcCCccccCcEEEeeeeeeeccccchHHHHHHHHHHH
Confidence            66666666554443332     34589999999977666541 23357789999999999999988888888777665  


Q ss_pred             ---CCCCcEEEEeeecChh
Q 028826          105 ---PKLRRTGLFSATQTEA  120 (203)
Q Consensus       105 ---~~~~q~i~~SAT~~~~  120 (203)
                         ....|+|+.|||+|+.
T Consensus       372 ~~~~~~~~iIGMSATi~N~  390 (1008)
T KOG0950|consen  372 ENLETSVQIIGMSATIPNN  390 (1008)
T ss_pred             hccccceeEeeeecccCCh
Confidence               2345799999999973

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

Probab=98.47  E-value=3e-06  Score=75.43  Aligned_cols=168  Identities=15%  Similarity=0.274  Sum_probs=108.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      ++|||+|--.|..|+...++...    +.++..+++|.+..+...   .+..+...|+|||=..+.        ..++++
T Consensus       247 qvLvLVPEI~Ltpq~~~rf~~rF----g~~v~vlHS~Ls~~er~~~W~~~~~G~~~vVIGtRSAlF--------~Pf~~L  314 (730)
T COG1198         247 QVLVLVPEIALTPQLLARFKARF----GAKVAVLHSGLSPGERYRVWRRARRGEARVVIGTRSALF--------LPFKNL  314 (730)
T ss_pred             EEEEEeccccchHHHHHHHHHHh----CCChhhhcccCChHHHHHHHHHHhcCCceEEEEechhhc--------Cchhhc
Confidence            58999999999999988888765    578889999977554443   344588999999975543        346789


Q ss_pred             cEEEEcchhHh-hh--hc---hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhh
Q 028826           78 VILVLDEADRL-LD--MG---FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQ  151 (203)
Q Consensus        78 ~~lViDEad~l-~~--~~---~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~  151 (203)
                      .++||||=|-- +.  .+   +..++.-..++. .++++|+-|||-+-+  .+.+..-..+..+.+...           
T Consensus       315 GLIIvDEEHD~sYKq~~~prYhARdvA~~Ra~~-~~~pvvLgSATPSLE--S~~~~~~g~y~~~~L~~R-----------  380 (730)
T COG1198         315 GLIIVDEEHDSSYKQEDGPRYHARDVAVLRAKK-ENAPVVLGSATPSLE--SYANAESGKYKLLRLTNR-----------  380 (730)
T ss_pred             cEEEEeccccccccCCcCCCcCHHHHHHHHHHH-hCCCEEEecCCCCHH--HHHhhhcCceEEEEcccc-----------
Confidence            99999996643 21  12   344444444444 688999999997744  333333333455555544           


Q ss_pred             hhccCCCCCceeEEEEEcCCC-CcH-----HHHHHHHhc--CCCCeEEEEeccCC
Q 028826          152 QLASSKTPLGLHLEYLECESD-KKP-----SQLVDLLIK--NKSKKIIMYVQHGN  198 (203)
Q Consensus       152 ~~~~~~~~~~i~~~~~~~~~~-~k~-----~~l~~ll~~--~~~~~~lIF~ns~~  198 (203)
                          ..........++.+..+ .+.     ..|++.+++  ..++++|+|.|.|=
T Consensus       381 ----~~~a~~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~geQ~llflnRRG  431 (730)
T COG1198         381 ----AGRARLPRVEIIDMRKEPLETGRSLSPALLEAIRKTLERGEQVLLFLNRRG  431 (730)
T ss_pred             ----ccccCCCcceEEeccccccccCccCCHHHHHHHHHHHhcCCeEEEEEccCC
Confidence                22222223344444332 222     456666643  46779999999874

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

Probab=98.45  E-value=3.1e-06  Score=68.29  Aligned_cols=163  Identities=19%  Similarity=0.190  Sum_probs=99.0

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEE
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVL   82 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lVi   82 (203)
                      .|.+|--+-+..++..++.-   +++..+.+++|+++..        .+..++|+|.-.|+.+-..        +++++|
T Consensus       148 ciASPRvDVclEl~~Rlk~a---F~~~~I~~Lyg~S~~~--------fr~plvVaTtHQLlrFk~a--------FD~liI  208 (441)
T COG4098         148 CIASPRVDVCLELYPRLKQA---FSNCDIDLLYGDSDSY--------FRAPLVVATTHQLLRFKQA--------FDLLII  208 (441)
T ss_pred             EEecCcccchHHHHHHHHHh---hccCCeeeEecCCchh--------ccccEEEEehHHHHHHHhh--------ccEEEE
Confidence            45677777777776666654   3357888899987643        2367999999888877654        679999


Q ss_pred             cchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCce
Q 028826           83 DEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGL  162 (203)
Q Consensus        83 DEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i  162 (203)
                      ||+|.+-=..-...-..+-.......-+|++|||-++..+.-+...-  -..+.+...-              |..|-. 
T Consensus       209 DEVDAFP~~~d~~L~~Av~~ark~~g~~IylTATp~k~l~r~~~~g~--~~~~klp~Rf--------------H~~pLp-  271 (441)
T COG4098         209 DEVDAFPFSDDQSLQYAVKKARKKEGATIYLTATPTKKLERKILKGN--LRILKLPARF--------------HGKPLP-  271 (441)
T ss_pred             eccccccccCCHHHHHHHHHhhcccCceEEEecCChHHHHHHhhhCC--eeEeecchhh--------------cCCCCC-
Confidence            99998731111111122333344567889999999977665444332  2333343331              222222 


Q ss_pred             eEEEEEcCC-C-----CcH-HHHHHHHhcC--CCCeEEEEeccCCccc
Q 028826          163 HLEYLECES-D-----KKP-SQLVDLLIKN--KSKKIIMYVQHGNFSE  201 (203)
Q Consensus       163 ~~~~~~~~~-~-----~k~-~~l~~ll~~~--~~~~~lIF~ns~~~~e  201 (203)
                      .=.|.++.. .     .|+ ..|...|+..  .+.|++||+++-+..|
T Consensus       272 vPkf~w~~~~~k~l~r~kl~~kl~~~lekq~~~~~P~liF~p~I~~~e  319 (441)
T COG4098         272 VPKFVWIGNWNKKLQRNKLPLKLKRWLEKQRKTGRPVLIFFPEIETME  319 (441)
T ss_pred             CCceEEeccHHHHhhhccCCHHHHHHHHHHHhcCCcEEEEecchHHHH
Confidence            223333332 2     223 3677777644  4579999999876554

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

Probab=98.42  E-value=4.7e-07  Score=81.21  Aligned_cols=114  Identities=14%  Similarity=0.113  Sum_probs=79.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhC--CCccCCCccE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM--DVLDFRNLVI   79 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~--~~~~l~~v~~   79 (203)
                      +|+++||++|++|+...+..-.....-.+...+.|....+.+...   -+|+|+|+-|+.+-.++...  ..-...++++
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            589999999999997766554422212455556666655555432   26999999999998887651  2345789999


Q ss_pred             EEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChh
Q 028826           80 LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (203)
Q Consensus        80 lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~  120 (203)
                      +|+||+|++-...-.-....++-..  .+.++++|||+.+.
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            9999999985433222334444444  48899999999764

>PRK12906 secA preprotein translocase subunit SecA; Reviewed

Probab=98.41  E-value=1.4e-06  Score=77.98  Aligned_cols=85  Identities=15%  Similarity=0.123  Sum_probs=66.7

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHH-HHHHhC-----CCccC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-DIMERM-----DVLDF   74 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~-~~~~~~-----~~~~l   74 (203)
                      ++-|++||--||.|=++.+.++...+ |++++++.|+.+..+....   -.+||+.||...+. ++++..     ...-.
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            36789999999999999999999999 9999999888776655433   36899999998875 566541     11113


Q ss_pred             CCccEEEEcchhHhh
Q 028826           75 RNLVILVLDEADRLL   89 (203)
Q Consensus        75 ~~v~~lViDEad~l~   89 (203)
                      ....+.||||+|.++
T Consensus       199 r~~~~aIvDEvDSiL  213 (796)
T PRK12906        199 RPLNYAIVDEVDSIL  213 (796)
T ss_pred             cCcceeeeccchhee
Confidence            568899999999975

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

Probab=98.40  E-value=6.6e-07  Score=70.10  Aligned_cols=81  Identities=26%  Similarity=0.452  Sum_probs=65.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEc-CcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVG-GVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~-g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .|||+++---|..+.+.++.+...  +.+++-+++ ....+++...+.....+|.||||+|+..++.. +.+.+++++++
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            588888887788888888887422  345544444 35778899999778999999999999999988 99999999999


Q ss_pred             EEcch
Q 028826           81 VLDEA   85 (203)
Q Consensus        81 ViDEa   85 (203)
                      |+|--
T Consensus       206 vlD~s  210 (252)
T PF14617_consen  206 VLDWS  210 (252)
T ss_pred             EEcCC
Confidence            99973

>PRK14873 primosome assembly protein PriA; Provisional

Probab=98.29  E-value=4.1e-05  Score=68.19  Aligned_cols=114  Identities=10%  Similarity=0.177  Sum_probs=80.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      ++|||+|...|+.|+...+++..+   +-.+..++++.+..+..+   .+..+...|+|||-..+.        ..+.++
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            589999999999999998887642   256888999887665444   344567899999975542        357789


Q ss_pred             cEEEEcchh-Hhhhhc-----hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHH
Q 028826           78 VILVLDEAD-RLLDMG-----FQKQISYIISRLPKLRRTGLFSATQTEAVEELSK  126 (203)
Q Consensus        78 ~~lViDEad-~l~~~~-----~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~  126 (203)
                      .++|+||=| ..+...     ...++....... .+..+++-|||-+-+....+.
T Consensus       259 gLIIvdEEhd~sykq~~~p~yhaRdvA~~Ra~~-~~~~lvLgSaTPSles~~~~~  312 (665)
T PRK14873        259 GLVAIWDDGDDLLAEPRAPYPHAREVALLRAHQ-HGCALLIGGHARTAEAQALVE  312 (665)
T ss_pred             CEEEEEcCCchhhcCCCCCCccHHHHHHHHHHH-cCCcEEEECCCCCHHHHHHHh
Confidence            999999954 333222     223344444443 578899999998866655444

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=98.28  E-value=1.1e-05  Score=74.25  Aligned_cols=111  Identities=19%  Similarity=0.131  Sum_probs=61.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH--HHHhCCCeEEEeccHHHHHHHHhCCCccCCCccE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK--KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVI   79 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~--~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~   79 (203)
                      +|||||+ .|..|+..++.+..    ++....+.++........  .- -...+++|+|-+.+...-.....+.-...++
T Consensus       202 vLIVvP~-sL~~QW~~El~~kF----~l~~~i~~~~~~~~~~~~~~~p-f~~~~~vI~S~~~l~~~~~~~~~l~~~~wdl  275 (956)
T PRK04914        202 VLILVPE-TLQHQWLVEMLRRF----NLRFSLFDEERYAEAQHDADNP-FETEQLVICSLDFLRRNKQRLEQALAAEWDL  275 (956)
T ss_pred             EEEEcCH-HHHHHHHHHHHHHh----CCCeEEEcCcchhhhcccccCc-cccCcEEEEEHHHhhhCHHHHHHHhhcCCCE
Confidence            6999998 69999999986532    444444433321110000  00 0235799999887764111001122235779


Q ss_pred             EEEcchhHhhhh-chHHHHHHHHHhCC-CCCcEEEEeeecC
Q 028826           80 LVLDEADRLLDM-GFQKQISYIISRLP-KLRRTGLFSATQT  118 (203)
Q Consensus        80 lViDEad~l~~~-~~~~~~~~il~~~~-~~~q~i~~SAT~~  118 (203)
                      +|+||||++-.. +........+..+. +...++++|||..
T Consensus       276 vIvDEAH~lk~~~~~~s~~y~~v~~La~~~~~~LLLTATP~  316 (956)
T PRK04914        276 LVVDEAHHLVWSEEAPSREYQVVEQLAEVIPGVLLLTATPE  316 (956)
T ss_pred             EEEechhhhccCCCCcCHHHHHHHHHhhccCCEEEEEcCcc
Confidence            999999998411 11111123333332 3467899999964

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

Probab=98.21  E-value=1.1e-05  Score=72.27  Aligned_cols=106  Identities=17%  Similarity=0.164  Sum_probs=66.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhC-CCccCCCc-cE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM-DVLDFRNL-VI   79 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~-~~~~l~~v-~~   79 (203)
                      +|||+|..+|..|+.+.+.++....  .     .+..+...-...+.+....|+|+|..++...+... ......+- -+
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            5899999999999999999985321  1     11112222223343445789999999998654330 11111111 28


Q ss_pred             EEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecC
Q 028826           80 LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (203)
Q Consensus        80 lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  118 (203)
                      +|+||||+....++...+   ...+ ++...++||||.-
T Consensus       369 vIvDEaHrs~~~~~~~~l---~~~~-p~a~~lGfTaTP~  403 (667)
T TIGR00348       369 VIFDEAHRSQYGELAKNL---KKAL-KNASFFGFTGTPI  403 (667)
T ss_pred             EEEEcCccccchHHHHHH---HhhC-CCCcEEEEeCCCc
Confidence            999999986433333322   2344 4678999999974

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

>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=98.20  E-value=4.2e-06  Score=67.16  Aligned_cols=107  Identities=21%  Similarity=0.184  Sum_probs=67.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHH-----HHHHhCCCccCCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-----DIMERMDVLDFRN   76 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~-----~~~~~~~~~~l~~   76 (203)
                      +|||+|+ .+..|+..++.++.... ++++..+.|+.......... ....+++|+|.+.+.     ....   .+.--+
T Consensus        61 ~LIv~P~-~l~~~W~~E~~~~~~~~-~~~v~~~~~~~~~~~~~~~~-~~~~~vvi~ty~~~~~~~~~~~~~---~l~~~~  134 (299)
T PF00176_consen   61 TLIVVPS-SLLSQWKEEIEKWFDPD-SLRVIIYDGDSERRRLSKNQ-LPKYDVVITTYETLRKARKKKDKE---DLKQIK  134 (299)
T ss_dssp             EEEEE-T-TTHHHHHHHHHHHSGT--TS-EEEESSSCHHHHTTSSS-CCCSSEEEEEHHHHH--TSTHTTH---HHHTSE
T ss_pred             eeEeecc-chhhhhhhhhccccccc-cccccccccccccccccccc-cccceeeecccccccccccccccc---cccccc
Confidence            6999999 78899999999998543 57777766665122221111 256899999999998     1111   111234


Q ss_pred             ccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeec
Q 028826           77 LVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ  117 (203)
Q Consensus        77 v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  117 (203)
                      .+.+|+||+|.+=  +........+..+. ....+++|||.
T Consensus       135 ~~~vIvDEaH~~k--~~~s~~~~~l~~l~-~~~~~lLSgTP  172 (299)
T PF00176_consen  135 WDRVIVDEAHRLK--NKDSKRYKALRKLR-ARYRWLLSGTP  172 (299)
T ss_dssp             EEEEEETTGGGGT--TTTSHHHHHHHCCC-ECEEEEE-SS-
T ss_pred             ceeEEEecccccc--cccccccccccccc-cceEEeecccc
Confidence            8899999999982  22333344444464 67788899994

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.

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

Probab=98.16  E-value=7.1e-06  Score=76.79  Aligned_cols=113  Identities=12%  Similarity=0.045  Sum_probs=73.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhC----CCccCCCc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM----DVLDFRNL   77 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~----~~~~l~~v   77 (203)
                      +|+|+|+++|+.|+.+.+..+.... ......+++.....   .........|+|+|...+...+...    ....+.+.
T Consensus       466 VLfLvDR~~L~~Qa~~~F~~~~~~~-~~~~~~i~~i~~L~---~~~~~~~~~I~iaTiQtl~~~~~~~~~~~~~~~~~~f  541 (1123)
T PRK11448        466 ILFLVDRSALGEQAEDAFKDTKIEG-DQTFASIYDIKGLE---DKFPEDETKVHVATVQGMVKRILYSDDPMDKPPVDQY  541 (1123)
T ss_pred             EEEEecHHHHHHHHHHHHHhccccc-ccchhhhhchhhhh---hhcccCCCCEEEEEHHHHHHhhhccccccccCCCCcc
Confidence            6899999999999999998874321 11221222211111   1111345789999999987764320    12457788


Q ss_pred             cEEEEcchhHhhhh---------------chHHHHHHHHHhCCCCCcEEEEeeecChh
Q 028826           78 VILVLDEADRLLDM---------------GFQKQISYIISRLPKLRRTGLFSATQTEA  120 (203)
Q Consensus        78 ~~lViDEad~l~~~---------------~~~~~~~~il~~~~~~~q~i~~SAT~~~~  120 (203)
                      +++|+||||+-...               .+...++.++.++  +.-.++||||....
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            99999999995310               1245677888876  35779999998643

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

Probab=98.13  E-value=1.7e-05  Score=56.72  Aligned_cols=104  Identities=10%  Similarity=0.114  Sum_probs=60.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      .|||.|||.++..+++.++..     +++...-..+   .    . ..++.-|=|.|-+-+.+++.+  .....+.+++|
T Consensus        36 vLvL~PTRvva~em~~aL~~~-----~~~~~t~~~~---~----~-~~g~~~i~vMc~at~~~~~~~--p~~~~~yd~II  100 (148)
T PF07652_consen   36 VLVLAPTRVVAEEMYEALKGL-----PVRFHTNARM---R----T-HFGSSIIDVMCHATYGHFLLN--PCRLKNYDVII  100 (148)
T ss_dssp             EEEEESSHHHHHHHHHHTTTS-----SEEEESTTSS------------SSSSEEEEEHHHHHHHHHT--SSCTTS-SEEE
T ss_pred             EEEecccHHHHHHHHHHHhcC-----CcccCceeee---c----c-ccCCCcccccccHHHHHHhcC--cccccCccEEE
Confidence            699999999999887777654     2333211111   0    0 124456777888887777654  45578999999


Q ss_pred             EcchhHhhhhc--hHHHHHHHHHhCCCCCcEEEEeeecChhHH
Q 028826           82 LDEADRLLDMG--FQKQISYIISRLPKLRRTGLFSATQTEAVE  122 (203)
Q Consensus        82 iDEad~l~~~~--~~~~~~~il~~~~~~~q~i~~SAT~~~~v~  122 (203)
                      +||+|..-...  ++..+..... . ....+|+.|||-|....
T Consensus       101 ~DEcH~~Dp~sIA~rg~l~~~~~-~-g~~~~i~mTATPPG~~~  141 (148)
T PF07652_consen  101 MDECHFTDPTSIAARGYLRELAE-S-GEAKVIFMTATPPGSED  141 (148)
T ss_dssp             ECTTT--SHHHHHHHHHHHHHHH-T-TS-EEEEEESS-TT---
T ss_pred             EeccccCCHHHHhhheeHHHhhh-c-cCeeEEEEeCCCCCCCC
Confidence            99999863222  3333333322 2 34679999999987543

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 ....

>COG1203 CRISPR-associated helicase Cas3 [Defense mechanisms]

Probab=98.09  E-value=1.2e-05  Score=72.55  Aligned_cols=136  Identities=15%  Similarity=0.118  Sum_probs=79.6

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH-------------HHhCCCeEEEeccHHHHHHHHh
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK-------------IEEEGANLLIGTPGRLYDIMER   68 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~-------------l~~~~~~ilV~Tp~~l~~~~~~   68 (203)
                      .+++.|++.++.++++.++...... ++.....+|..........             ....-..+.++||..+......
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            5789999999999999999987654 3332213333322211110             0001234555555555442211


Q ss_pred             CCCcc---CCCccEEEEcchhHhhhhchHHHHHHHHHhCC-CCCcEEEEeeecChhHHHHHHhcCCCCeEEEec
Q 028826           69 MDVLD---FRNLVILVLDEADRLLDMGFQKQISYIISRLP-KLRRTGLFSATQTEAVEELSKAGLRNPVRIEVR  138 (203)
Q Consensus        69 ~~~~~---l~~v~~lViDEad~l~~~~~~~~~~~il~~~~-~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~  138 (203)
                      .....   .-.-+.+|+||+|.+-+......+..++..+. ....+++.|||+|+...+.+...+.....+...
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            01111   12356899999998866533333333333332 367899999999999999888877765554443

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

Probab=98.07  E-value=8.6e-05  Score=68.74  Aligned_cols=169  Identities=15%  Similarity=0.271  Sum_probs=107.5

Q ss_pred             EEEEcCcHHHHHHHHHHH-HHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVA-QPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~-~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      |++++|..+.+...++.+ +++... .|.+++.+.|..+..-...    ...+|+|+||+++..+ .     +.+.++++
T Consensus      1189 ~vyi~p~~~i~~~~~~~w~~~f~~~-~G~~~~~l~ge~s~~lkl~----~~~~vii~tpe~~d~l-q-----~iQ~v~l~ 1257 (1674)
T KOG0951|consen 1189 AVYIAPLEEIADEQYRDWEKKFSKL-LGLRIVKLTGETSLDLKLL----QKGQVIISTPEQWDLL-Q-----SIQQVDLF 1257 (1674)
T ss_pred             EEEecchHHHHHHHHHHHHHhhccc-cCceEEecCCccccchHHh----hhcceEEechhHHHHH-h-----hhhhcceE
Confidence            789999999986655544 555555 4888888888777654432    3478999999997654 2     56789999


Q ss_pred             EEcchhHhhhhc------hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhc
Q 028826           81 VLDEADRLLDMG------FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLA  154 (203)
Q Consensus        81 ViDEad~l~~~~------~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~  154 (203)
                      |.||+|.+-+..      ... ++.+.+.+.+...++.+|..+.+. ..+  .+......+....+              
T Consensus      1258 i~d~lh~igg~~g~v~evi~S-~r~ia~q~~k~ir~v~ls~~lana-~d~--ig~s~~~v~Nf~p~-------------- 1319 (1674)
T KOG0951|consen 1258 IVDELHLIGGVYGAVYEVICS-MRYIASQLEKKIRVVALSSSLANA-RDL--IGASSSGVFNFSPS-------------- 1319 (1674)
T ss_pred             eeehhhhhcccCCceEEEEee-HHHHHHHHHhheeEEEeehhhccc-hhh--ccccccceeecCcc--------------
Confidence            999999775321      122 667777777888899999888754 333  33344445555444              


Q ss_pred             cCCCCCceeEEEEEcCCCC---cHHH-----HHHHHh-cCCCCeEEEEeccCCccc
Q 028826          155 SSKTPLGLHLEYLECESDK---KPSQ-----LVDLLI-KNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       155 ~~~~~~~i~~~~~~~~~~~---k~~~-----l~~ll~-~~~~~~~lIF~ns~~~~e  201 (203)
                        ..+..+......++...   ....     +..+.+ ....++++||+.+++.|.
T Consensus      1320 --~R~~Pl~i~i~~~~~~~~~~~~~am~~~~~~ai~~~a~~~k~~~vf~p~rk~~~ 1373 (1674)
T KOG0951|consen 1320 --VRPVPLEIHIQSVDISHFESRMLAMTKPTYTAIVRHAGNRKPAIVFLPTRKHAR 1373 (1674)
T ss_pred             --cCCCceeEEEEEeccchhHHHHHHhhhhHHHHHHHHhcCCCCeEEEeccchhhh
Confidence              23333333333333322   1111     111112 236679999999998764

>KOG2340 consensus Uncharacterized conserved protein [Function unknown]

Probab=98.05  E-value=1.1e-05  Score=68.47  Aligned_cols=130  Identities=22%  Similarity=0.239  Sum_probs=86.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEE--------EEEcC--------cchHHHHH--------------------
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSM--------LLVGG--------VEVKADVK--------------------   45 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~--------~~~~g--------~~~~~~~~--------------------   45 (203)
                      +|||||+||-|..+.+.+..+..+...-+..        .-++|        .+..++.+                    
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            6999999999999999988884322110110        11111        01111111                    


Q ss_pred             --HHHh--CCCeEEEeccHHHHHHHHhC----CCc-cCCCccEEEEcchhHhhhhchHHHHHHHHHhCC---CC------
Q 028826           46 --KIEE--EGANLLIGTPGRLYDIMERM----DVL-DFRNLVILVLDEADRLLDMGFQKQISYIISRLP---KL------  107 (203)
Q Consensus        46 --~l~~--~~~~ilV~Tp~~l~~~~~~~----~~~-~l~~v~~lViDEad~l~~~~~~~~~~~il~~~~---~~------  107 (203)
                        .|..  ...||||++|--|.-.+.+.    +.. .++++.++|||-||.++-.+ .+.+..++.++.   ..      
T Consensus       376 tikLys~fy~SDIlVaSPLGLRmil~n~gdkkrd~dfLSSIEl~iIDQa~~~l~QN-wEhl~~ifdHLn~~P~k~h~~Df  454 (698)
T KOG2340|consen  376 TIKLYSKFYKSDILVASPLGLRMILGNTGDKKRDFDFLSSIELLIIDQADIMLMQN-WEHLLHIFDHLNLQPSKQHDVDF  454 (698)
T ss_pred             HHHHHhhhcccCeEEecchhhhhhhcCCCcccccchhhhhhhhhhhhhHHHHHHhh-HHHHHHHHHHhhcCcccccCCCh
Confidence              1111  35899999999988777631    122 27899999999999998654 566667776663   21      


Q ss_pred             ---------------CcEEEEeeecChhHHHHHHhcCCCC
Q 028826          108 ---------------RRTGLFSATQTEAVEELSKAGLRNP  132 (203)
Q Consensus       108 ---------------~q~i~~SAT~~~~v~~~~~~~l~~~  132 (203)
                                     +|+++||+-..+....+...++.+.
T Consensus       455 SRVR~wyL~~qsr~~rQtl~Fs~y~~~~~nS~fn~~c~N~  494 (698)
T KOG2340|consen  455 SRVRMWYLDGQSRYFRQTLLFSRYSHPLFNSLFNQYCQNM  494 (698)
T ss_pred             hheehheeccHHHHHHHHHHHHhhccHHHHHHHHHhhhhh
Confidence                           3999999999999888888877764

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

Probab=98.04  E-value=4.3e-05  Score=67.45  Aligned_cols=112  Identities=20%  Similarity=0.233  Sum_probs=74.3

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH--HHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK--KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~--~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ||++|-.-|.    .+++++....|+++++.++|+........  .+..++.||+|+|-+..+.=-   ..+.--+=+++
T Consensus       221 LVi~P~StL~----NW~~Ef~rf~P~l~~~~~~Gdk~eR~~~~r~~~~~~~fdV~iTsYEi~i~dk---~~lk~~~W~yl  293 (971)
T KOG0385|consen  221 LVIAPKSTLD----NWMNEFKRFTPSLNVVVYHGDKEERAALRRDIMLPGRFDVCITSYEIAIKDK---SFLKKFNWRYL  293 (971)
T ss_pred             EEEeeHhhHH----HHHHHHHHhCCCcceEEEeCCHHHHHHHHHHhhccCCCceEeehHHHHHhhH---HHHhcCCceEE
Confidence            7899977665    34444555567899999999875333222  223468999999999876421   22233456799


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHH
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEE  123 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~  123 (203)
                      ||||||++=.  -...+..+++.+......++.+..+-+++.+
T Consensus       294 vIDEaHRiKN--~~s~L~~~lr~f~~~nrLLlTGTPLQNNL~E  334 (971)
T KOG0385|consen  294 VIDEAHRIKN--EKSKLSKILREFKTDNRLLLTGTPLQNNLHE  334 (971)
T ss_pred             Eechhhhhcc--hhhHHHHHHHHhcccceeEeeCCcccccHHH
Confidence            9999999832  3555668888887666666666666655444

>PRK13103 secA preprotein translocase subunit SecA; Reviewed

Probab=97.96  E-value=3.1e-05  Score=70.07  Aligned_cols=83  Identities=17%  Similarity=0.223  Sum_probs=67.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHH-HHHHHhCCCcc------
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMDVLD------   73 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l-~~~~~~~~~~~------   73 (203)
                      .+-|++||--||.|=+.++..+...+ |+++.++.++.+..+.....   .+||++||..-+ -++++.  .+.      
T Consensus       125 ~VhvvT~ndyLA~RD~e~m~~l~~~l-Gl~v~~i~~~~~~~err~~Y---~~dI~YGT~~e~gFDYLrD--~~~~~~~~~  198 (913)
T PRK13103        125 GVHVVTVNDYLARRDANWMRPLYEFL-GLSVGIVTPFQPPEEKRAAY---AADITYGTNNEFGFDYLRD--NMAFSLDDK  198 (913)
T ss_pred             CEEEEeCCHHHHHHHHHHHHHHhccc-CCEEEEECCCCCHHHHHHHh---cCCEEEEcccccccchhhc--cceechhhh
Confidence            36789999999999999999999998 99999998887765554443   489999999887 345553  222      


Q ss_pred             -CCCccEEEEcchhHhh
Q 028826           74 -FRNLVILVLDEADRLL   89 (203)
Q Consensus        74 -l~~v~~lViDEad~l~   89 (203)
                       ...+.+.||||+|.++
T Consensus       199 vqr~l~~aIVDEvDsiL  215 (913)
T PRK13103        199 FQRELNFAVIDEVDSIL  215 (913)
T ss_pred             cccccceeEechhhhee
Confidence             3789999999999976

>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional

Probab=97.94  E-value=0.00013  Score=67.62  Aligned_cols=107  Identities=14%  Similarity=0.169  Sum_probs=70.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH--HHHhCCCeEEEeccHHHHHHHHhCCCccCCCccE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK--KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVI   79 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~--~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~   79 (203)
                      .|||||.. +..|+.+++.+++   |.+++..++|.........  .+.....+|+|+|.+.+......   +.--+..+
T Consensus       222 ~LIVvP~S-lL~nW~~Ei~kw~---p~l~v~~~~G~~~eR~~~~~~~~~~~~~dVvITSYe~l~~e~~~---L~k~~W~~  294 (1033)
T PLN03142        222 HMVVAPKS-TLGNWMNEIRRFC---PVLRAVKFHGNPEERAHQREELLVAGKFDVCVTSFEMAIKEKTA---LKRFSWRY  294 (1033)
T ss_pred             EEEEeChH-HHHHHHHHHHHHC---CCCceEEEeCCHHHHHHHHHHHhcccCCCcceecHHHHHHHHHH---hccCCCCE
Confidence            58999965 6678889988885   4577887777654322221  22235689999999988654322   22234679


Q ss_pred             EEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecC
Q 028826           80 LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (203)
Q Consensus        80 lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  118 (203)
                      +|+||||.+=.  ....+...+..+. ....+++|+|.-
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            99999999832  2344555666664 445577788853

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

Probab=97.90  E-value=9e-05  Score=66.07  Aligned_cols=101  Identities=17%  Similarity=0.180  Sum_probs=67.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhC----CCccCCCc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM----DVLDFRNL   77 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~----~~~~l~~v   77 (203)
                      .|+|+-.+.|..|.+..+..+.++.   ...-+..+...        ...++|.++|-..+..-....    ..+.....
T Consensus       218 VLFLaDR~~Lv~QA~~af~~~~P~~---~~~n~i~~~~~--------~~s~~i~lsTyqt~~~~~~~~~~~~~~f~~g~F  286 (875)
T COG4096         218 VLFLADRNALVDQAYGAFEDFLPFG---TKMNKIEDKKG--------DTSSEIYLSTYQTMTGRIEQKEDEYRRFGPGFF  286 (875)
T ss_pred             eeEEechHHHHHHHHHHHHHhCCCc---cceeeeecccC--------CcceeEEEeehHHHHhhhhccccccccCCCCce
Confidence            5899999999999999988886553   22222222221        124789999999998877651    24557779


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecCh
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  119 (203)
                      +++||||||+=    .....+.++.++....|.+  +||...
T Consensus       287 DlIvIDEaHRg----i~~~~~~I~dYFdA~~~gL--TATP~~  322 (875)
T COG4096         287 DLIVIDEAHRG----IYSEWSSILDYFDAATQGL--TATPKE  322 (875)
T ss_pred             eEEEechhhhh----HHhhhHHHHHHHHHHHHhh--ccCccc
Confidence            99999999984    3444446777774434333  666544

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

Probab=97.76  E-value=0.00031  Score=62.37  Aligned_cols=112  Identities=13%  Similarity=0.213  Sum_probs=73.4

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHh---CCCeEEEeccHHHH------HHHHhCCCcc
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEE---EGANLLIGTPGRLY------DIMERMDVLD   73 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~---~~~~ilV~Tp~~l~------~~~~~~~~~~   73 (203)
                      |||||+--|-    .++++|.+.+|.+++-..+|.....++.+....   .+.|||++|-....      .++++     
T Consensus       452 LVVvPsSTle----NWlrEf~kwCPsl~Ve~YyGSq~ER~~lR~~i~~~~~~ydVllTTY~la~~~kdDRsflk~-----  522 (941)
T KOG0389|consen  452 LVVVPSSTLE----NWLREFAKWCPSLKVEPYYGSQDERRELRERIKKNKDDYDVLLTTYNLAASSKDDRSFLKN-----  522 (941)
T ss_pred             EEEecchhHH----HHHHHHHHhCCceEEEeccCcHHHHHHHHHHHhccCCCccEEEEEeecccCChHHHHHHHh-----
Confidence            7999987654    567777777788999999998877666665433   36899999976553      23333     


Q ss_pred             CCCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHH
Q 028826           74 FRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSK  126 (203)
Q Consensus        74 l~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~  126 (203)
                       .++.++|+||.|.|=.. -.+.++++ ..++.+..+++.+..+-+++.+++.
T Consensus       523 -~~~n~viyDEgHmLKN~-~SeRy~~L-M~I~An~RlLLTGTPLQNNL~ELiS  572 (941)
T KOG0389|consen  523 -QKFNYVIYDEGHMLKNR-TSERYKHL-MSINANFRLLLTGTPLQNNLKELIS  572 (941)
T ss_pred             -ccccEEEecchhhhhcc-chHHHHHh-ccccccceEEeeCCcccccHHHHHH
Confidence             56779999999976333 23333443 3344444444444445666666554

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

Probab=97.68  E-value=0.0038  Score=56.98  Aligned_cols=127  Identities=17%  Similarity=0.211  Sum_probs=84.0

Q ss_pred             CCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHh-hhhc-hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHh
Q 028826           50 EGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRL-LDMG-FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (203)
Q Consensus        50 ~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l-~~~~-~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~  127 (203)
                      ..-.|-+.|.|.|+..+..  ...++.++++|+||||.= ++.+ ....+..++...+..-.+|+.|||+..  +.|.. 
T Consensus       138 ~~Trik~mTdGiLlrei~~--D~~Ls~ys~vIiDEaHERSl~tDilLgllk~~~~~rr~DLKiIimSATld~--~rfs~-  212 (845)
T COG1643         138 PRTRIKVMTDGILLREIQN--DPLLSGYSVVIIDEAHERSLNTDILLGLLKDLLARRRDDLKLIIMSATLDA--ERFSA-  212 (845)
T ss_pred             CCceeEEeccHHHHHHHhh--CcccccCCEEEEcchhhhhHHHHHHHHHHHHHHhhcCCCceEEEEecccCH--HHHHH-
Confidence            4578999999999999986  445899999999999962 3333 345566777777777899999999984  44444 


Q ss_pred             cCCCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCC-CC-cHHHHHHHHh---cCCCCeEEEEeccCCc
Q 028826          128 GLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECES-DK-KPSQLVDLLI---KNKSKKIIMYVQHGNF  199 (203)
Q Consensus       128 ~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~-~~-k~~~l~~ll~---~~~~~~~lIF~ns~~~  199 (203)
                      ++.+.-.+.+...                  ...+..+|..-.. +. -.+.+...+.   ....+.+|||.+-.+.
T Consensus       213 ~f~~apvi~i~GR------------------~fPVei~Y~~~~~~d~~l~~ai~~~v~~~~~~~~GdILvFLpG~~E  271 (845)
T COG1643         213 YFGNAPVIEIEGR------------------TYPVEIRYLPEAEADYILLDAIVAAVDIHLREGSGSILVFLPGQRE  271 (845)
T ss_pred             HcCCCCEEEecCC------------------ccceEEEecCCCCcchhHHHHHHHHHHHhccCCCCCEEEECCcHHH
Confidence            5555444444332                  2455666644333 23 2334444443   4457789999876543

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

Probab=97.66  E-value=0.0001  Score=63.41  Aligned_cols=181  Identities=10%  Similarity=-0.004  Sum_probs=110.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceE--EEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCC----ccCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKS--MLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDV----LDFR   75 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~--~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~----~~l~   75 (203)
                      .++..||+|+++.-.+-..-.....|..+.  +-.+.| ..+..++.+...+.++|.+.|+.+...+-- +.    ..+-
T Consensus       334 ~~~~~~~~~~~~~~~~~~~V~~~~I~~~K~A~V~~~D~-~sE~~~~A~~R~~~~~~~s~~~~~~s~~L~-~~~~~~~~~~  411 (1034)
T KOG4150|consen  334 SLLPSEMVEHLRNGSKGQVVHVEVIKARKSAYVEMSDK-LSETTKSALKRIGLNTLYSHQAEAISAALA-KSLCYNVPVF  411 (1034)
T ss_pred             eecchhHHHHhhccCCceEEEEEehhhhhcceeecccC-CCchhHHHHHhcCcceeecCHHHHHHHHhh-hccccccHHH
Confidence            356778888886443322222122222222  222333 334455666678999999999988654432 22    2355


Q ss_pred             CccEEEEcchhHhhhh-c--hHHHHHHHHHhC-----CCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCccccccc
Q 028826           76 NLVILVLDEADRLLDM-G--FQKQISYIISRL-----PKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHAS  147 (203)
Q Consensus        76 ~v~~lViDEad~l~~~-~--~~~~~~~il~~~-----~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~  147 (203)
                      ...+.++||.|..... +  -...++++++.+     +.+.|++-.|||+-+.++-+.+.+.-+.+.....++       
T Consensus       412 ~~~~~~~~~~~~Y~~~~~~~~~~~~R~L~~L~~~F~~~~~~~~~~~~~~~K~~~~~~~~~~~~~E~~Li~~DG-------  484 (1034)
T KOG4150|consen  412 EELCKDTNSCALYLFPTKALAQDQLRALSDLIKGFEASINMGVYDGDTPYKDRTRLRSELANLSELELVTIDG-------  484 (1034)
T ss_pred             HHHHhcccceeeeecchhhHHHHHHHHHHHHHHHHHhhcCcceEeCCCCcCCHHHHHHHhcCCcceEEEEecC-------
Confidence            7788999999976432 1  233344444444     357899999999999888877766555554444444       


Q ss_pred             chhhhhccCCCCCceeEEEEEcCC---------CCcHHHHHHHHhc--CCCCeEEEEeccCCccc
Q 028826          148 ASSQQLASSKTPLGLHLEYLECES---------DKKPSQLVDLLIK--NKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       148 ~~~~~~~~~~~~~~i~~~~~~~~~---------~~k~~~l~~ll~~--~~~~~~lIF~ns~~~~e  201 (203)
                                .|.+-+|++++-++         ++++....+++-+  ..+-++|.||.+|+-||
T Consensus       485 ----------SPs~~K~~V~WNP~~~P~~~~~~~~~i~E~s~~~~~~i~~~~R~IAFC~~R~~CE  539 (1034)
T KOG4150|consen  485 ----------SPSSEKLFVLWNPSAPPTSKSEKSSKVVEVSHLFAEMVQHGLRCIAFCPSRKLCE  539 (1034)
T ss_pred             ----------CCCccceEEEeCCCCCCcchhhhhhHHHHHHHHHHHHHHcCCcEEEeccHHHHHH
Confidence                      56777888887653         1233333334332  24458999999999886

>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=97.63  E-value=0.00066  Score=53.91  Aligned_cols=84  Identities=15%  Similarity=0.260  Sum_probs=64.1

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHH-HHHHhC---CCcc--CC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-DIMERM---DVLD--FR   75 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~-~~~~~~---~~~~--l~   75 (203)
                      +=|++.+..||..=++++..+...+ |+.+..+.++.+.++.....   .+||+.||...+. ++++..   +...  ..
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            3478899999999999999999999 99999999998865444333   4789999999986 566541   1111  46


Q ss_pred             CccEEEEcchhHhh
Q 028826           76 NLVILVLDEADRLL   89 (203)
Q Consensus        76 ~v~~lViDEad~l~   89 (203)
                      ...++||||+|.++
T Consensus       197 ~~~~~ivDEvDs~L  210 (266)
T PF07517_consen  197 GFDFAIVDEVDSIL  210 (266)
T ss_dssp             SSSEEEECTHHHHT
T ss_pred             CCCEEEEeccceEE
Confidence            88999999999986

SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner [,]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the IPR0011545 from INTERPRO.; GO: 0005524 ATP binding, 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 3DIN_B 3JUX_A 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 3BXZ_A ....

>PRK12326 preprotein translocase subunit SecA; Reviewed

Probab=97.57  E-value=0.00024  Score=63.23  Aligned_cols=84  Identities=14%  Similarity=0.145  Sum_probs=65.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHH-HHHHhC-----CCccCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-DIMERM-----DVLDFR   75 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~-~~~~~~-----~~~~l~   75 (203)
                      +-|++||-.||.|=++++.++...+ |++++++.++.+.++.....   .+||+.||...+- ++++..     ...-..
T Consensus       122 VhvvT~NdyLA~RDae~m~~ly~~L-GLsvg~i~~~~~~~err~aY---~~DItYgTn~e~gFDyLRDnm~~~~~~~v~R  197 (764)
T PRK12326        122 VHVITVNDYLARRDAEWMGPLYEAL-GLTVGWITEESTPEERRAAY---ACDVTYASVNEIGFDVLRDQLVTDVADLVSP  197 (764)
T ss_pred             eEEEcCCHHHHHHHHHHHHHHHHhc-CCEEEEECCCCCHHHHHHHH---cCCCEEcCCcccccccchhhhccChHhhcCC
Confidence            6789999999999999999999998 99999999887765444333   5899999998864 455431     111235


Q ss_pred             CccEEEEcchhHhh
Q 028826           76 NLVILVLDEADRLL   89 (203)
Q Consensus        76 ~v~~lViDEad~l~   89 (203)
                      .+.+.||||+|.++
T Consensus       198 ~~~faIVDEvDSiL  211 (764)
T PRK12326        198 NPDVAIIDEADSVL  211 (764)
T ss_pred             ccceeeecchhhhe
Confidence            68899999999986

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

Probab=97.57  E-value=0.00074  Score=59.83  Aligned_cols=40  Identities=20%  Similarity=0.095  Sum_probs=30.6

Q ss_pred             CCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHhhh
Q 028826           50 EGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLD   90 (203)
Q Consensus        50 ~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~~   90 (203)
                      ..+||||++..-|...++. +.--+-+...+||||||.+.+
T Consensus       181 ~~AdivItNHalL~~~~~~-~~~iLP~~~~lIiDEAH~L~d  220 (636)
T TIGR03117       181 RRCRILFCTHAMLGLAFRD-KWGLLPQPDILIVDEAHLFEQ  220 (636)
T ss_pred             ccCCEEEECHHHHHHHhhh-hcCCCCCCCEEEEeCCcchHH
Confidence            4579999999988876654 322345589999999999864

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.

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

Probab=97.40  E-value=0.0016  Score=59.75  Aligned_cols=37  Identities=19%  Similarity=0.218  Sum_probs=29.4

Q ss_pred             CEEEEcCcHHHHHHH-HHHHHHhhhcCCCceEEEEEcCc
Q 028826            1 MGMIISPTRELSAQI-YHVAQPFISTLPDVKSMLLVGGV   38 (203)
Q Consensus         1 ~alil~PtreLa~Qi-~~~~~~l~~~~~~i~~~~~~~g~   38 (203)
                      .+||++||++|+.|+ .+.+..+.+.+ ++++..+.||.
T Consensus       293 ~vvI~t~T~~Lq~Ql~~~~i~~l~~~~-~~~~~~~kg~~  330 (820)
T PRK07246        293 QIIVSVPTKILQDQIMAEEVKAIQEVF-HIDCHSLKGPQ  330 (820)
T ss_pred             cEEEEeCcHHHHHHHHHHHHHHHHHhc-CCcEEEEECCc
Confidence            379999999999999 57788887766 67777666643

>CHL00122 secA preprotein translocase subunit SecA; Validated

Probab=97.39  E-value=0.00045  Score=62.55  Aligned_cols=84  Identities=17%  Similarity=0.125  Sum_probs=66.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHH-HHHHhC-----CCccCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-DIMERM-----DVLDFR   75 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~-~~~~~~-----~~~~l~   75 (203)
                      +-|++++..||.+-.+++..+-..+ |+.++++.++.+..+....   -.+||+.||..-+- ++++..     ...-..
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            5689999999999999999999999 9999999888777655443   46899999998764 555541     011235


Q ss_pred             CccEEEEcchhHhh
Q 028826           76 NLVILVLDEADRLL   89 (203)
Q Consensus        76 ~v~~lViDEad~l~   89 (203)
                      .+.+.||||+|.++
T Consensus       196 ~~~faIVDEvDSiL  209 (870)
T CHL00122        196 PFNYCIIDEVDSIL  209 (870)
T ss_pred             ccceeeeecchhhe
Confidence            68899999999986

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

Probab=97.34  E-value=0.0011  Score=59.01  Aligned_cols=115  Identities=20%  Similarity=0.199  Sum_probs=71.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcch--------HHHHHH-H---HhCCCeEEEeccHHHHHHHHhC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEV--------KADVKK-I---EEEGANLLIGTPGRLYDIMERM   69 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~--------~~~~~~-l---~~~~~~ilV~Tp~~l~~~~~~~   69 (203)
                      ||||||.- +..|+.+++..+.   |.+++..++|..+.        ...... +   .....+|+|+|-+.+.-+=   
T Consensus       258 aLIVCP~T-ii~qW~~E~~~w~---p~~rv~ilh~t~s~~r~~~~~~~~~~~~~L~r~~~~~~~ilitty~~~r~~~---  330 (923)
T KOG0387|consen  258 ALIVCPAT-IIHQWMKEFQTWW---PPFRVFILHGTGSGARYDASHSSHKKDKLLIRKVATDGGILITTYDGFRIQG---  330 (923)
T ss_pred             eEEEccHH-HHHHHHHHHHHhC---cceEEEEEecCCcccccccchhhhhhhhhheeeecccCcEEEEehhhhcccC---
Confidence            79999976 6677878777774   46788888887662        111111 1   1235679999987765321   


Q ss_pred             CCccCCCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHH
Q 028826           70 DVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELS  125 (203)
Q Consensus        70 ~~~~l~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~  125 (203)
                      ..+.-..=.++|+||.|.+=..  -..+......++....+|+.++.+-+++.++-
T Consensus       331 d~l~~~~W~y~ILDEGH~IrNp--ns~islackki~T~~RiILSGTPiQNnL~ELw  384 (923)
T KOG0387|consen  331 DDLLGILWDYVILDEGHRIRNP--NSKISLACKKIRTVHRIILSGTPIQNNLTELW  384 (923)
T ss_pred             cccccccccEEEecCcccccCC--ccHHHHHHHhccccceEEeeCccccchHHHHH
Confidence            1122234469999999998433  33444455666545555555555666666654

>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]

Probab=97.28  E-value=0.0017  Score=55.40  Aligned_cols=101  Identities=15%  Similarity=0.189  Sum_probs=71.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHH-------------HHHHHh
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL-------------YDIMER   68 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l-------------~~~~~~   68 (203)
                      ||+|+.+---+.|+..++..++. ..+-.++.++++....      ...++.|+|+|-..+             .++++.
T Consensus       348 clvLcts~VSVeQWkqQfk~wst-i~d~~i~rFTsd~Ke~------~~~~~gvvvsTYsMva~t~kRS~eaek~m~~l~~  420 (776)
T KOG1123|consen  348 CLVLCTSAVSVEQWKQQFKQWST-IQDDQICRFTSDAKER------FPSGAGVVVTTYSMVAYTGKRSHEAEKIMDFLRG  420 (776)
T ss_pred             EEEEecCccCHHHHHHHHHhhcc-cCccceEEeecccccc------CCCCCcEEEEeeehhhhcccccHHHHHHHHHHhc
Confidence            78999998889999999988854 3355667776653321      246789999996544             444444


Q ss_pred             CCCccCCCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChh
Q 028826           69 MDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (203)
Q Consensus        69 ~~~~~l~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~  120 (203)
                            ..-.++++||+|.+-..-|+..+.-+-.+.     .+.++||+-.+
T Consensus       421 ------~EWGllllDEVHvvPA~MFRRVlsiv~aHc-----KLGLTATLvRE  461 (776)
T KOG1123|consen  421 ------REWGLLLLDEVHVVPAKMFRRVLSIVQAHC-----KLGLTATLVRE  461 (776)
T ss_pred             ------CeeeeEEeehhccchHHHHHHHHHHHHHHh-----hccceeEEeec
Confidence                  344599999999987777777666655444     48899998554

>PRK12902 secA preprotein translocase subunit SecA; Reviewed

Probab=97.28  E-value=0.00098  Score=60.58  Aligned_cols=84  Identities=15%  Similarity=0.142  Sum_probs=65.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHH-HHHHh-----CCCccCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-DIMER-----MDVLDFR   75 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~-~~~~~-----~~~~~l~   75 (203)
                      +-||+++..||.+=.+++..+-..+ |+.|+++.++.+..+...   .-.+||+.||+..+- ++++.     ....-..
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            5689999999999999999999999 999999988776554432   357999999999982 33332     1223356


Q ss_pred             CccEEEEcchhHhh
Q 028826           76 NLVILVLDEADRLL   89 (203)
Q Consensus        76 ~v~~lViDEad~l~   89 (203)
                      .+.+.||||+|.++
T Consensus       205 ~~~faIVDEvDSIL  218 (939)
T PRK12902        205 PFNYCVIDEVDSIL  218 (939)
T ss_pred             ccceEEEeccccee
Confidence            78899999999976

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

Probab=97.09  E-value=0.0004  Score=63.45  Aligned_cols=120  Identities=23%  Similarity=0.230  Sum_probs=76.5

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhC-CCccCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM-DVLDFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~-~~~~l~~v~~l   80 (203)
                      ++|++|-++|...-.+...+.. ..+|++++-+.|....+  ...+  ..++++|+||++.....+.- +.--+.+++.+
T Consensus       976 vvyIap~kalvker~~Dw~~r~-~~~g~k~ie~tgd~~pd--~~~v--~~~~~~ittpek~dgi~Rsw~~r~~v~~v~~i 1050 (1230)
T KOG0952|consen  976 VVYIAPDKALVKERSDDWSKRD-ELPGIKVIELTGDVTPD--VKAV--READIVITTPEKWDGISRSWQTRKYVQSVSLI 1050 (1230)
T ss_pred             EEEEcCCchhhcccccchhhhc-ccCCceeEeccCccCCC--hhhe--ecCceEEcccccccCccccccchhhhccccce
Confidence            6899999999876666555543 23489999888876654  2233  46899999999987766521 23347899999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhC-------CCCCcEEEEeeecChhHHHHHHhc
Q 028826           81 VLDEADRLLDMGFQKQISYIISRL-------PKLRRTGLFSATQTEAVEELSKAG  128 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~-------~~~~q~i~~SAT~~~~v~~~~~~~  128 (203)
                      |+||.|++- .++.+.++.+.+..       +...+.+.+| |...+...++++.
T Consensus      1051 v~de~hllg-~~rgPVle~ivsr~n~~s~~t~~~vr~~gls-ta~~na~dla~wl 1103 (1230)
T KOG0952|consen 1051 VLDEIHLLG-EDRGPVLEVIVSRMNYISSQTEEPVRYLGLS-TALANANDLADWL 1103 (1230)
T ss_pred             eeccccccc-CCCcceEEEEeeccccCccccCcchhhhhHh-hhhhccHHHHHHh
Confidence            999999874 34444444333332       2334555553 3333445555543

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

Probab=97.00  E-value=0.012  Score=51.67  Aligned_cols=127  Identities=14%  Similarity=0.169  Sum_probs=76.1

Q ss_pred             CCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHh-hhhc-hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhc
Q 028826           51 GANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRL-LDMG-FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAG  128 (203)
Q Consensus        51 ~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l-~~~~-~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~  128 (203)
                      .-.|.+.|-|.|+.-+-.  ...++.-+.+|+||||.= +..+ ....++.+++.- +.-.+|+.|||+..   +....|
T Consensus       140 ~TrikymTDG~LLRE~l~--Dp~LskYsvIIlDEAHERsl~TDiLlGlLKki~~~R-~~LklIimSATlda---~kfS~y  213 (674)
T KOG0922|consen  140 DTRIKYMTDGMLLREILK--DPLLSKYSVIILDEAHERSLHTDILLGLLKKILKKR-PDLKLIIMSATLDA---EKFSEY  213 (674)
T ss_pred             ceeEEEecchHHHHHHhc--CCccccccEEEEechhhhhhHHHHHHHHHHHHHhcC-CCceEEEEeeeecH---HHHHHH
Confidence            467999999999876653  457889999999999952 1111 222333443333 34689999999983   333445


Q ss_pred             CCCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHH----HHHHhcCCCCeEEEEeccCCccc
Q 028826          129 LRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQL----VDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       129 l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l----~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      +...-.+.+...                  .-.+...|..-+..+-++..    .++-...+.+-+|||-...++.|
T Consensus       214 F~~a~i~~i~GR------------------~fPVei~y~~~p~~dYv~a~~~tv~~Ih~~E~~GDILvFLtGqeEIe  272 (674)
T KOG0922|consen  214 FNNAPILTIPGR------------------TFPVEILYLKEPTADYVDAALITVIQIHLTEPPGDILVFLTGQEEIE  272 (674)
T ss_pred             hcCCceEeecCC------------------CCceeEEeccCCchhhHHHHHHHHHHHHccCCCCCEEEEeCCHHHHH
Confidence            555444444332                  23455556554444433332    22223456667899988765543

>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein

Probab=96.90  E-value=0.028  Score=50.93  Aligned_cols=117  Identities=12%  Similarity=0.101  Sum_probs=75.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +|+++--+.|+.++...++.-.  +.++....-.++.       .+...+.+-++...+.|..+-    .-.+++.++||
T Consensus        81 VLvVShRrSL~~sL~~rf~~~~--l~gFv~Y~d~~~~-------~i~~~~~~rLivqIdSL~R~~----~~~l~~yDvVI  147 (824)
T PF02399_consen   81 VLVVSHRRSLTKSLAERFKKAG--LSGFVNYLDSDDY-------IIDGRPYDRLIVQIDSLHRLD----GSLLDRYDVVI  147 (824)
T ss_pred             EEEEEhHHHHHHHHHHHHhhcC--CCcceeeeccccc-------cccccccCeEEEEehhhhhcc----cccccccCEEE
Confidence            5788888999998887776642  2133322211111       111224567777777775543    22466788999


Q ss_pred             EcchhHhhhhchHHHHH-------HHHHhCCCCCcEEEEeeecChhHHHHHHhcCCC
Q 028826           82 LDEADRLLDMGFQKQIS-------YIISRLPKLRRTGLFSATQTEAVEELSKAGLRN  131 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~-------~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~  131 (203)
                      +||+...+..-|.+.++       .+...+.+...+|++-|++....-+++...-++
T Consensus       148 IDEv~svL~qL~S~Tm~~~~~v~~~L~~lI~~ak~VI~~DA~ln~~tvdFl~~~Rp~  204 (824)
T PF02399_consen  148 IDEVMSVLNQLFSPTMRQREEVDNLLKELIRNAKTVIVMDADLNDQTVDFLASCRPD  204 (824)
T ss_pred             EehHHHHHHHHhHHHHhhHHHHHHHHHHHHHhCCeEEEecCCCCHHHHHHHHHhCCC
Confidence            99999987653333322       233444677899999999999999999876654

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

>KOG0390 consensus DNA repair protein, SNF2 family [Replication, recombination and repair]

Probab=96.77  E-value=0.011  Score=53.42  Aligned_cols=117  Identities=15%  Similarity=0.117  Sum_probs=76.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcch--HHHHHHHH----hCCCeEEEeccHHHHHHHHhCCCccCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEV--KADVKKIE----EEGANLLIGTPGRLYDIMERMDVLDFR   75 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~--~~~~~~l~----~~~~~ilV~Tp~~l~~~~~~~~~~~l~   75 (203)
                      +|||+|.- |..-+++++.+..... .+....+.|+.+.  ......+.    ...--|++-+-+.+.++.+.   +...
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            68999965 8888899998886643 5777777877663  11111110    12235677777777766654   5667


Q ss_pred             CccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeee-cChhHHHHHH
Q 028826           76 NLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT-QTEAVEELSK  126 (203)
Q Consensus        76 ~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT-~~~~v~~~~~  126 (203)
                      .+.++|.||.|.+  .+-...+...+..+.-.+ .|++|.| +-+++.++..
T Consensus       376 ~~glLVcDEGHrl--kN~~s~~~kaL~~l~t~r-RVLLSGTp~QNdl~EyFn  424 (776)
T KOG0390|consen  376 RPGLLVCDEGHRL--KNSDSLTLKALSSLKTPR-RVLLTGTPIQNDLKEYFN  424 (776)
T ss_pred             CCCeEEECCCCCc--cchhhHHHHHHHhcCCCc-eEEeeCCcccccHHHHHH
Confidence            8999999999997  223556667778885444 4555555 5556666554

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

Probab=96.64  E-value=0.018  Score=53.38  Aligned_cols=37  Identities=19%  Similarity=0.233  Sum_probs=26.7

Q ss_pred             EEEEcCcHHHHHHHHH-HHHHhhhcCC-CceEEEEEcCc
Q 028826            2 GMIISPTRELSAQIYH-VAQPFISTLP-DVKSMLLVGGV   38 (203)
Q Consensus         2 alil~PtreLa~Qi~~-~~~~l~~~~~-~i~~~~~~~g~   38 (203)
                      ++|.+||++|..|+.. .+..+.+.++ +++++.+.|+.
T Consensus       295 vvi~t~t~~Lq~Ql~~~~~~~l~~~~~~~~~~~~~kG~~  333 (850)
T TIGR01407       295 VVISTNTKVLQSQLLEKDIPLLNEILNFKINAALIKGKS  333 (850)
T ss_pred             EEEEeCcHHHHHHHHHHHHHHHHHHcCCCceEEEEEcch
Confidence            6899999999999855 6666655441 47777777644

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.

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

Probab=96.54  E-value=0.015  Score=54.54  Aligned_cols=111  Identities=18%  Similarity=0.246  Sum_probs=76.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHH---HHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLY---DIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~---~~~~~~~~~~l~~v~   78 (203)
                      +|||||+- |+-.+..++.++++.   +++...+|+.......+.- -++.+|+|++-+-+.   +.+.+ ..++     
T Consensus      1034 SLIVCPsT-LtGHW~~E~~kf~pf---L~v~~yvg~p~~r~~lR~q-~~~~~iiVtSYDv~RnD~d~l~~-~~wN----- 1102 (1549)
T KOG0392|consen 1034 SLIVCPST-LTGHWKSEVKKFFPF---LKVLQYVGPPAERRELRDQ-YKNANIIVTSYDVVRNDVDYLIK-IDWN----- 1102 (1549)
T ss_pred             eEEECCch-hhhHHHHHHHHhcch---hhhhhhcCChHHHHHHHhh-ccccceEEeeHHHHHHHHHHHHh-cccc-----
Confidence            68999975 888888888888655   6777777775544333321 145799999988875   23333 3444     


Q ss_pred             EEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHH
Q 028826           79 ILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELS  125 (203)
Q Consensus        79 ~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~  125 (203)
                      ++|+||=|.+ .. -...+....+++..+...|+.+..+-+++.++-
T Consensus      1103 YcVLDEGHVi-kN-~ktkl~kavkqL~a~hRLILSGTPIQNnvleLW 1147 (1549)
T KOG0392|consen 1103 YCVLDEGHVI-KN-SKTKLTKAVKQLRANHRLILSGTPIQNNVLELW 1147 (1549)
T ss_pred             eEEecCccee-cc-hHHHHHHHHHHHhhcceEEeeCCCcccCHHHHH
Confidence            9999999977 33 356667777777666666666666666666643

>PRK10689 transcription-repair coupling factor; Provisional

Probab=96.45  E-value=0.018  Score=54.76  Aligned_cols=78  Identities=14%  Similarity=0.201  Sum_probs=61.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      +++|++|+++-+..+.+.+.++   .|++++..++|+.+..+..+.   ..++..+|||+|.     .+.  .++|+.++
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            4789999998887777776665   457889999999887655443   3457899999996     333  58999999


Q ss_pred             cEEEEcchhHh
Q 028826           78 VILVLDEADRL   88 (203)
Q Consensus        78 ~~lViDEad~l   88 (203)
                      +++|++.+|.+
T Consensus       881 ~~VIi~~ad~f  891 (1147)
T PRK10689        881 NTIIIERADHF  891 (1147)
T ss_pred             CEEEEecCCCC
Confidence            99999999864

>TIGR00580 mfd transcription-repair coupling factor (mfd)

Probab=96.31  E-value=0.024  Score=52.79  Aligned_cols=78  Identities=14%  Similarity=0.235  Sum_probs=62.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      +++|++|+.+-+..+++.++++   .+++++..++|+.+..+....+   .++..+|||+|.     .+.  .++|+.++
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            4789999999888888777775   3478999999998876655533   357899999997     333  58999999


Q ss_pred             cEEEEcchhHh
Q 028826           78 VILVLDEADRL   88 (203)
Q Consensus        78 ~~lViDEad~l   88 (203)
                      .++|++.+|.+
T Consensus       732 ~~VIi~~a~~~  742 (926)
T TIGR00580       732 NTIIIERADKF  742 (926)
T ss_pred             CEEEEecCCCC
Confidence            99999999864

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.

>TIGR02562 cas3_yersinia CRISPR-associated helicase Cas3

Probab=96.31  E-value=0.0065  Score=56.35  Aligned_cols=71  Identities=23%  Similarity=0.061  Sum_probs=46.4

Q ss_pred             CeEEEeccHHHHHHHHhC--CCccCC----CccEEEEcchhHhhhhchHHHHHHHHHhCC-CCCcEEEEeeecChhHHH
Q 028826           52 ANLLIGTPGRLYDIMERM--DVLDFR----NLVILVLDEADRLLDMGFQKQISYIISRLP-KLRRTGLFSATQTEAVEE  123 (203)
Q Consensus        52 ~~ilV~Tp~~l~~~~~~~--~~~~l~----~v~~lViDEad~l~~~~~~~~~~~il~~~~-~~~q~i~~SAT~~~~v~~  123 (203)
                      ..++|||+..++......  +...+.    -=+.||+||+|.+ +......+.+++.... -...+++.|||+|+.+..
T Consensus       563 apv~V~TIDQlL~a~~~~r~~~~~l~ll~La~svlVlDEVHaY-D~~~~~~L~rlL~w~~~lG~~VlLmSATLP~~l~~  640 (1110)
T TIGR02562       563 APVLVCTIDHLIPATESHRGGHHIAPMLRLMSSDLILDEPDDY-EPEDLPALLRLVQLAGLLGSRVLLSSATLPPALVK  640 (1110)
T ss_pred             CCeEEecHHHHHHHhhhcccchhHHHHHHhcCCCEEEECCccC-CHHHHHHHHHHHHHHHHcCCCEEEEeCCCCHHHHH
Confidence            689999999998766210  111111    1358999999976 3333444555554332 257889999999998665

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.

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

Probab=96.30  E-value=0.013  Score=54.69  Aligned_cols=108  Identities=15%  Similarity=0.244  Sum_probs=65.6

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH--HHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK--KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~--~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ||||||--+.+ +.-++++++   |++++...+|.-.....++  |.+.+-.||+|++-..+.+=+   ..+.-.+-+++
T Consensus       669 LIVVpTsviLn-WEMElKRwc---PglKILTYyGs~kErkeKRqgW~kPnaFHVCItSYklv~qd~---~AFkrkrWqyL  741 (1958)
T KOG0391|consen  669 LIVVPTSVILN-WEMELKRWC---PGLKILTYYGSHKERKEKRQGWAKPNAFHVCITSYKLVFQDL---TAFKRKRWQYL  741 (1958)
T ss_pred             eEEeechhhhh-hhHHHhhhC---CcceEeeecCCHHHHHHHhhcccCCCeeEEeehhhHHHHhHH---HHHHhhcccee
Confidence            79999986553 556677775   5789998888754333332  444455799999887765422   12223455699


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeee-cChh
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT-QTEA  120 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT-~~~~  120 (203)
                      |+|||+.+=.+. ...+..++. +. ..+.++++.| +-+.
T Consensus       742 vLDEaqnIKnfk-sqrWQAlln-fn-sqrRLLLtgTPLqNs  779 (1958)
T KOG0391|consen  742 VLDEAQNIKNFK-SQRWQALLN-FN-SQRRLLLTGTPLQNS  779 (1958)
T ss_pred             ehhhhhhhcchh-HHHHHHHhc-cc-hhheeeecCCchhhH
Confidence            999999984332 333344443 32 3444555555 4433

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

Probab=96.23  E-value=0.0064  Score=53.77  Aligned_cols=113  Identities=18%  Similarity=0.175  Sum_probs=65.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHH----HHHhCC-CccCCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYD----IMERMD-VLDFRN   76 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~----~~~~~~-~~~l~~   76 (203)
                      .|||||-+ |..|++.++.+=...- .++|..++|....+...+.+  ...||+|+|-.-+..    =....+ .-.+.+
T Consensus       386 TLII~PaS-li~qW~~Ev~~rl~~n-~LsV~~~HG~n~r~i~~~~L--~~YDvViTTY~lva~~~~~e~~~~~~~spL~~  461 (901)
T KOG4439|consen  386 TLIICPAS-LIHQWEAEVARRLEQN-ALSVYLYHGPNKREISAKEL--RKYDVVITTYNLVANKPDDELEEGKNSSPLAR  461 (901)
T ss_pred             eEEeCcHH-HHHHHHHHHHHHHhhc-ceEEEEecCCccccCCHHHH--hhcceEEEeeeccccCCchhhhcccCccHHHH
Confidence            48999976 7778877775544433 68999999887655555555  468999999866544    111101 111333


Q ss_pred             c--cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChh
Q 028826           77 L--VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (203)
Q Consensus        77 v--~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~  120 (203)
                      +  ..+|+||||.+=..  ...-..-+..+......++.++.+-++
T Consensus       462 I~W~RVILDEAH~IrN~--~tq~S~AVC~L~a~~RWclTGTPiqNn  505 (901)
T KOG4439|consen  462 IAWSRVILDEAHNIRNS--NTQCSKAVCKLSAKSRWCLTGTPIQNN  505 (901)
T ss_pred             hhHHHhhhhhhhhhccc--chhHHHHHHHHhhcceeecccCccccc
Confidence            3  36999999987433  222223344443334444444444444

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

Probab=95.94  E-value=0.057  Score=50.60  Aligned_cols=108  Identities=15%  Similarity=0.157  Sum_probs=69.5

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccC-CCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDF-RNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l-~~v~~l   80 (203)
                      .++|+--++|-.|+.+.+.+++....  ...   ...+..+-.+.+....-.|+|+|-.++............ .+=-.+
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            57889999999999999999976542  111   334444444455434458999999999888866211112 223378


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  118 (203)
                      |+||||+--   +...-..+-..+ ++...++||.|.-
T Consensus       381 I~DEaHRSQ---~G~~~~~~~~~~-~~a~~~gFTGTPi  414 (962)
T COG0610         381 IIDEAHRSQ---YGELAKLLKKAL-KKAIFIGFTGTPI  414 (962)
T ss_pred             EEechhhcc---ccHHHHHHHHHh-ccceEEEeeCCcc
Confidence            899999852   222223333333 4588889988853

>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]

Probab=95.93  E-value=0.035  Score=47.55  Aligned_cols=107  Identities=17%  Similarity=0.250  Sum_probs=67.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHh-C------CCcc-
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMER-M------DVLD-   73 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~-~------~~~~-   73 (203)
                      .|||+|+-+|. |+.+++..+.++  ..++...+|. ......+.+  .+.|++.+|-.-+-.-.++ +      ++.+ 
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            58999999875 899999999874  6787766664 334445555  4689999999888766654 1      1122 


Q ss_pred             ----CCCcc--EEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeec
Q 028826           74 ----FRNLV--ILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ  117 (203)
Q Consensus        74 ----l~~v~--~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  117 (203)
                          +++++  .+|+||||.+=+..  ....+..-.+ .....+++|.|.
T Consensus       308 e~SlLHsi~~~RiIlDEAH~IK~R~--snTArAV~~L-~tt~rw~LSGTP  354 (791)
T KOG1002|consen  308 EKSLLHSIKFYRIILDEAHNIKDRQ--SNTARAVFAL-ETTYRWCLSGTP  354 (791)
T ss_pred             ccchhhhceeeeeehhhhccccccc--ccHHHHHHhh-HhhhhhhccCCc
Confidence                44554  58999999874432  2222222222 223346666664

>PRK04537 ATP-dependent RNA helicase RhlB; Provisional

Probab=95.90  E-value=0.062  Score=47.59  Aligned_cols=72  Identities=13%  Similarity=0.179  Sum_probs=56.8

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||+++|++.+.++++.+.+.     ++++..++|+.+..+....+   .++..+|||+|-     .+.  ..+|+.++
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            3799999999999998888764     68899999998876655533   346789999995     333  57999999


Q ss_pred             cEEEEcc
Q 028826           78 VILVLDE   84 (203)
Q Consensus        78 ~~lViDE   84 (203)
                      +++|.-+
T Consensus       327 ~~VInyd  333 (572)
T PRK04537        327 KYVYNYD  333 (572)
T ss_pred             CEEEEcC
Confidence            9998644

>PRK04837 ATP-dependent RNA helicase RhlB; Provisional

Probab=95.89  E-value=0.045  Score=46.51  Aligned_cols=71  Identities=15%  Similarity=0.224  Sum_probs=55.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.++|++-|..+.+.+...     ++++..++|+.+..++...+   .++..+|||+|-     .+.  .++|+.+++
T Consensus       258 ~lVF~~t~~~~~~l~~~L~~~-----g~~v~~lhg~~~~~~R~~~l~~F~~g~~~vLVaTd-----v~~--rGiDip~v~  325 (423)
T PRK04837        258 AIIFANTKHRCEEIWGHLAAD-----GHRVGLLTGDVAQKKRLRILEEFTRGDLDILVATD-----VAA--RGLHIPAVT  325 (423)
T ss_pred             EEEEECCHHHHHHHHHHHHhC-----CCcEEEecCCCChhHHHHHHHHHHcCCCcEEEEec-----hhh--cCCCccccC
Confidence            799999999998888777653     78899999998766555433   357899999995     333  589999999


Q ss_pred             EEEEcc
Q 028826           79 ILVLDE   84 (203)
Q Consensus        79 ~lViDE   84 (203)
                      ++|.-+
T Consensus       326 ~VI~~d  331 (423)
T PRK04837        326 HVFNYD  331 (423)
T ss_pred             EEEEeC
Confidence            887543

>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]

Probab=95.89  E-value=0.052  Score=50.95  Aligned_cols=114  Identities=15%  Similarity=0.192  Sum_probs=73.4

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhC-----CCeEEEeccHHHHHHHHhCCCccC
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEE-----GANLLIGTPGRLYDIMERMDVLDF   74 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~-----~~~ilV~Tp~~l~~~~~~~~~~~l   74 (203)
                      ||++|..-+. -+.+++...+    ++++++.+|.....+.++.   ....     .++++++|-+.++.=-   ..+.-
T Consensus       424 lvvvplst~~-~W~~ef~~w~----~mn~i~y~g~~~sr~~i~~ye~~~~~~~~~lkf~~lltTye~~LkDk---~~L~~  495 (1373)
T KOG0384|consen  424 LVVVPLSTIT-AWEREFETWT----DMNVIVYHGNLESRQLIRQYEFYHSSNTKKLKFNALLTTYEIVLKDK---AELSK  495 (1373)
T ss_pred             EEEeehhhhH-HHHHHHHHHh----hhceeeeecchhHHHHHHHHHheecCCccccccceeehhhHHHhccH---hhhcc
Confidence            7888966544 3445555554    6889999998766554443   2223     4899999999876311   11222


Q ss_pred             CCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHH
Q 028826           75 RNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSK  126 (203)
Q Consensus        75 ~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~  126 (203)
                      -+-+++++||||+|=.  -...+...+..+..+..+++.+..+-+.++++..
T Consensus       496 i~w~~~~vDeahrLkN--~~~~l~~~l~~f~~~~rllitgTPlQNsikEL~s  545 (1373)
T KOG0384|consen  496 IPWRYLLVDEAHRLKN--DESKLYESLNQFKMNHRLLITGTPLQNSLKELWS  545 (1373)
T ss_pred             CCcceeeecHHhhcCc--hHHHHHHHHHHhcccceeeecCCCccccHHHHHH
Confidence            2356899999999842  2344455577776666777776667777777654

>TIGR00631 uvrb excinuclease ABC, B subunit

Probab=95.85  E-value=0.19  Score=45.18  Aligned_cols=113  Identities=12%  Similarity=0.254  Sum_probs=74.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+++|+..+..+.+.+.+.     ++++..++|+.+..+...   .+..+..+|+|||-     .+.  .++++.+++
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-----GIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGIN-----LLR--EGLDLPEVS  512 (655)
T ss_pred             EEEEECCHHHHHHHHHHHhhh-----ccceeeeeCCCCHHHHHHHHHHHhcCCceEEEEcC-----hhc--CCeeeCCCc
Confidence            689999999999888888775     688888988876544433   33457789999983     333  589999999


Q ss_pred             EEEEcchhHhhhhchHHHHHHHHHhCCC--CCcEEEEeeecChhHHHHHH
Q 028826           79 ILVLDEADRLLDMGFQKQISYIISRLPK--LRRTGLFSATQTEAVEELSK  126 (203)
Q Consensus        79 ~lViDEad~l~~~~~~~~~~~il~~~~~--~~q~i~~SAT~~~~v~~~~~  126 (203)
                      ++|+-++|..--......+-+...+..+  ....+++-...+..+...+.
T Consensus       513 lVvi~DadifG~p~~~~~~iqriGRagR~~~G~vi~~~~~~~~~~~~ai~  562 (655)
T TIGR00631       513 LVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQKAIE  562 (655)
T ss_pred             EEEEeCcccccCCCCHHHHHHHhcCCCCCCCCEEEEEEcCCCHHHHHHHH
Confidence            9999888875221122333333333322  23456665566655444333

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

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

Probab=95.71  E-value=0.12  Score=48.70  Aligned_cols=104  Identities=13%  Similarity=0.194  Sum_probs=77.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      |+-||.|--|=..++...++.+   .|..+++..+|-+...+-++.+   .++..||+|||.     .+.  .++|..+.
T Consensus       805 QvfYv~NrV~~Ie~~~~~L~~L---VPEarI~vaHGQM~e~eLE~vM~~F~~g~~dVLv~TT-----IIE--tGIDIPnA  874 (1139)
T COG1197         805 QVFYVHNRVESIEKKAERLREL---VPEARIAVAHGQMRERELEEVMLDFYNGEYDVLVCTT-----IIE--TGIDIPNA  874 (1139)
T ss_pred             EEEEEecchhhHHHHHHHHHHh---CCceEEEEeecCCCHHHHHHHHHHHHcCCCCEEEEee-----eee--cCcCCCCC
Confidence            4667888777666666666666   5688999999988877666543   247899999997     343  68999999


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecC
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  118 (203)
                      ..+||+-||++   | ..++..+-.+..+..+.-..=-+.|
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            99999999987   4 4567777777776666554444444

>TIGR00596 rad1 DNA repair protein (rad1)

Probab=95.64  E-value=0.048  Score=50.02  Aligned_cols=67  Identities=15%  Similarity=0.155  Sum_probs=55.6

Q ss_pred             CCeEEEeccHHHH-HHHHhCCCccCCCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecCh
Q 028826           51 GANLLIGTPGRLY-DIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (203)
Q Consensus        51 ~~~ilV~Tp~~l~-~~~~~~~~~~l~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  119 (203)
                      ...|+++||..|. +++.  +.++++++..+||||||+..+..-..-+-++.+.-++..-+.+|||....
T Consensus         7 ~ggi~~~T~rIl~~DlL~--~ri~~~~itgiiv~~Ahr~~~~~~eaFI~rlyr~~n~~gfIkafSdsP~~   74 (814)
T TIGR00596         7 EGGIFSITSRILVVDLLT--GIIPPELITGILVLRADRIIESSQEAFILRLYRQKNKTGFIKAFSDNPEA   74 (814)
T ss_pred             cCCEEEEechhhHhHHhc--CCCCHHHccEEEEeecccccccccHHHHHHHHHHhCCCcceEEecCCCcc
Confidence            4579999998876 5665  68999999999999999998776677777777777778889999998653

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

>TIGR00643 recG ATP-dependent DNA helicase RecG

Probab=95.49  E-value=0.15  Score=45.69  Aligned_cols=81  Identities=20%  Similarity=0.343  Sum_probs=55.3

Q ss_pred             CEEEEcCcHHHH-----HHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCc
Q 028826            1 MGMIISPTRELS-----AQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVL   72 (203)
Q Consensus         1 ~alil~PtreLa-----~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~   72 (203)
                      +++|++|+.+-.     .......+.+...++++++..++|+.+..+....+   .++..+|||+|.     .+.  .++
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            478899976321     22223333333334588999999998866555433   346899999996     222  589


Q ss_pred             cCCCccEEEEcchhHh
Q 028826           73 DFRNLVILVLDEADRL   88 (203)
Q Consensus        73 ~l~~v~~lViDEad~l   88 (203)
                      |+.+++++|+..++.+
T Consensus       523 DiP~v~~VIi~~~~r~  538 (630)
T TIGR00643       523 DVPNATVMVIEDAERF  538 (630)
T ss_pred             ccCCCcEEEEeCCCcC
Confidence            9999999999888864

>PRK10917 ATP-dependent DNA helicase RecG; Provisional

Probab=95.35  E-value=0.17  Score=45.78  Aligned_cols=81  Identities=17%  Similarity=0.332  Sum_probs=55.7

Q ss_pred             CEEEEcCcHHH-----HHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCc
Q 028826            1 MGMIISPTREL-----SAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVL   72 (203)
Q Consensus         1 ~alil~PtreL-----a~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~   72 (203)
                      +++|++|+.+-     ........+.+...++++++..++|+.+..+....+   .++..+|||+|.     .+.  .++
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            47899996431     112233344444445568999999998766555533   346789999996     222  589


Q ss_pred             cCCCccEEEEcchhHh
Q 028826           73 DFRNLVILVLDEADRL   88 (203)
Q Consensus        73 ~l~~v~~lViDEad~l   88 (203)
                      |+.+++++|+..++.+
T Consensus       546 Dip~v~~VIi~~~~r~  561 (681)
T PRK10917        546 DVPNATVMVIENAERF  561 (681)
T ss_pred             ccCCCcEEEEeCCCCC
Confidence            9999999999988864

>PRK10590 ATP-dependent RNA helicase RhlE; Provisional

Probab=95.34  E-value=0.13  Score=44.21  Aligned_cols=69  Identities=16%  Similarity=0.208  Sum_probs=54.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.++|++-+..+.+.+.+.     ++++..++|+.+..+....+   .++..+|||+|-     .+.  ..+|+.+++
T Consensus       248 ~lVF~~t~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~R~~~l~~F~~g~~~iLVaTd-----v~~--rGiDip~v~  315 (456)
T PRK10590        248 VLVFTRTKHGANHLAEQLNKD-----GIRSAAIHGNKSQGARTRALADFKSGDIRVLVATD-----IAA--RGLDIEELP  315 (456)
T ss_pred             EEEEcCcHHHHHHHHHHHHHC-----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcc-----HHh--cCCCcccCC
Confidence            699999999999888877654     78899999998876555433   346789999995     333  579999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       316 ~VI~  319 (456)
T PRK10590        316 HVVN  319 (456)
T ss_pred             EEEE
Confidence            8875

>PRK11192 ATP-dependent RNA helicase SrmB; Provisional

Probab=95.34  E-value=0.088  Score=44.84  Aligned_cols=69  Identities=14%  Similarity=0.214  Sum_probs=55.1

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+++|++-+..+...+++.     ++++..++|+.+..+....+   .++..+|||+|-     .+.  ..+|+.++.
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            799999999999998888763     78999999998876665533   357899999994     333  578999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       316 ~VI~  319 (434)
T PRK11192        316 HVIN  319 (434)
T ss_pred             EEEE
Confidence            9884

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

Probab=95.33  E-value=0.037  Score=42.33  Aligned_cols=43  Identities=30%  Similarity=0.547  Sum_probs=36.1

Q ss_pred             HHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcc
Q 028826           41 KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDE   84 (203)
Q Consensus        41 ~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDE   84 (203)
                      +++...+.++..++-||||+|+-++++. +.+.++++.++|+|-
T Consensus       186 ~~~~k~~k~~~v~~gIgTp~Ri~~lv~~-~~f~~~~lk~iIlD~  228 (271)
T KOG3089|consen  186 QAQVKLLKKRVVHLGIGTPGRIKELVKQ-GGFNLSPLKFIILDW  228 (271)
T ss_pred             HHHHHHHhhcceeEeecCcHHHHHHHHh-cCCCCCcceeEEeec
Confidence            3455555567789999999999999999 779999999999874

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

Probab=95.31  E-value=0.12  Score=44.37  Aligned_cols=110  Identities=15%  Similarity=0.137  Sum_probs=68.4

Q ss_pred             CccCCCccEEEEcchhHh-hhhc-hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccc
Q 028826           71 VLDFRNLVILVLDEADRL-LDMG-FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASA  148 (203)
Q Consensus        71 ~~~l~~v~~lViDEad~l-~~~~-~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~  148 (203)
                      ...++.-+.+|+||||.= +..+ ....++.++..-| .-.+++.|||+.   ..-.+.|+.++-.+.+...        
T Consensus       154 ~p~l~~y~viiLDeahERtlATDiLmGllk~v~~~rp-dLk~vvmSatl~---a~Kfq~yf~n~Pll~vpg~--------  221 (699)
T KOG0925|consen  154 DPLLGRYGVIILDEAHERTLATDILMGLLKEVVRNRP-DLKLVVMSATLD---AEKFQRYFGNAPLLAVPGT--------  221 (699)
T ss_pred             CcccccccEEEechhhhhhHHHHHHHHHHHHHHhhCC-CceEEEeecccc---hHHHHHHhCCCCeeecCCC--------
Confidence            345788999999999962 2222 3444555555554 788999999987   3344557777766766543        


Q ss_pred             hhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHH----hcCCCCeEEEEeccCCcccCC
Q 028826          149 SSQQLASSKTPLGLHLEYLECESDKKPSQLVDLL----IKNKSKKIIMYVQHGNFSEDG  203 (203)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll----~~~~~~~~lIF~ns~~~~e~a  203 (203)
                                 ..+..+|..-.+.+..+..+..+    .....+-+++|....+.-|+|
T Consensus       222 -----------~PvEi~Yt~e~erDylEaairtV~qih~~ee~GDilvFLtgeeeIe~a  269 (699)
T KOG0925|consen  222 -----------HPVEIFYTPEPERDYLEAAIRTVLQIHMCEEPGDILVFLTGEEEIEDA  269 (699)
T ss_pred             -----------CceEEEecCCCChhHHHHHHHHHHHHHhccCCCCEEEEecCHHHHHHH
Confidence                       12334554444455555554444    234567899998877665543

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

Probab=95.19  E-value=0.29  Score=45.38  Aligned_cols=81  Identities=19%  Similarity=0.166  Sum_probs=55.9

Q ss_pred             CCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHhh-hhc-hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhc
Q 028826           51 GANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLL-DMG-FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAG  128 (203)
Q Consensus        51 ~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~-~~~-~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~  128 (203)
                      ...++++|.|-|+..+..  ...+.++.++|+||+|.=- +.+ +.-.++.++..- +.-++|+.|||+.   .+....|
T Consensus       264 ~t~L~fcTtGvLLr~L~~--~~~l~~vthiivDEVHER~i~~DflLi~lk~lL~~~-p~LkvILMSAT~d---ae~fs~Y  337 (924)
T KOG0920|consen  264 ETRLLFCTTGVLLRRLQS--DPTLSGVTHIIVDEVHERSINTDFLLILLKDLLPRN-PDLKVILMSATLD---AELFSDY  337 (924)
T ss_pred             ceeEEEecHHHHHHHhcc--CcccccCceeeeeeEEEccCCcccHHHHHHHHhhhC-CCceEEEeeeecc---hHHHHHH
Confidence            467999999999998864  5678999999999999632 233 334444555444 7889999999998   3333334


Q ss_pred             CCCCeEEEe
Q 028826          129 LRNPVRIEV  137 (203)
Q Consensus       129 l~~~~~i~~  137 (203)
                      ....-.+.+
T Consensus       338 F~~~pvi~i  346 (924)
T KOG0920|consen  338 FGGCPVITI  346 (924)
T ss_pred             hCCCceEee
Confidence            444333433

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

Probab=95.13  E-value=0.14  Score=44.68  Aligned_cols=70  Identities=13%  Similarity=0.167  Sum_probs=57.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||++.|+..+..+...+++.     |+++..++|+.+..+..+.+   .++..+|+|+|--.      . +.+|+.++
T Consensus       275 ~~IVF~~tk~~~~~l~~~l~~~-----g~~~~~lhG~l~q~~R~~~l~~F~~g~~~vLVaTDva------a-RGiDi~~v  342 (513)
T COG0513         275 RVIVFVRTKRLVEELAESLRKR-----GFKVAALHGDLPQEERDRALEKFKDGELRVLVATDVA------A-RGLDIPDV  342 (513)
T ss_pred             eEEEEeCcHHHHHHHHHHHHHC-----CCeEEEecCCCCHHHHHHHHHHHHcCCCCEEEEechh------h-ccCCcccc
Confidence            3899999999999988777765     79999999999987777655   35789999999633      2 68999999


Q ss_pred             cEEEE
Q 028826           78 VILVL   82 (203)
Q Consensus        78 ~~lVi   82 (203)
                      .++|=
T Consensus       343 ~~Vin  347 (513)
T COG0513         343 SHVIN  347 (513)
T ss_pred             ceeEE
Confidence            98864

>PRK11776 ATP-dependent RNA helicase DbpA; Provisional

Probab=95.12  E-value=0.11  Score=44.60  Aligned_cols=72  Identities=14%  Similarity=0.243  Sum_probs=56.1

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+|+|++-+..+++.+.+.     ++++..++|+.+..++...+   .++..+|+|+|-     .+.  .++|+.+++
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            799999999999888887664     78899999998876655533   346789999994     232  579999999


Q ss_pred             EEEEcch
Q 028826           79 ILVLDEA   85 (203)
Q Consensus        79 ~lViDEa   85 (203)
                      ++|.-+.
T Consensus       313 ~VI~~d~  319 (460)
T PRK11776        313 AVINYEL  319 (460)
T ss_pred             eEEEecC
Confidence            9886443

>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family

Probab=95.05  E-value=0.15  Score=43.97  Aligned_cols=72  Identities=15%  Similarity=0.252  Sum_probs=56.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.++|+.-+.++...+++.     ++++..++||.+..+....   ..++..+|||+|-.     +.  ..+|+.+++
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-----GIAAGAYHAGLEISARDDVHHKFQRDEIQVVVATVA-----FG--MGINKPDVR  296 (470)
T ss_pred             eEEEECcHHHHHHHHHHHHhc-----CCCeeEeeCCCCHHHHHHHHHHHHcCCCcEEEEech-----hh--ccCCcccce
Confidence            589999999999988887764     7889999999887655443   23578999999962     22  578999999


Q ss_pred             EEEEcch
Q 028826           79 ILVLDEA   85 (203)
Q Consensus        79 ~lViDEa   85 (203)
                      ++|.-..
T Consensus       297 ~VI~~~~  303 (470)
T TIGR00614       297 FVIHYSL  303 (470)
T ss_pred             EEEEeCC
Confidence            9986544

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

>PRK12903 secA preprotein translocase subunit SecA; Reviewed

Probab=95.04  E-value=0.065  Score=49.06  Aligned_cols=84  Identities=13%  Similarity=0.107  Sum_probs=63.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHH-HHHHhCCC-----ccCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-DIMERMDV-----LDFR   75 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~-~~~~~~~~-----~~l~   75 (203)
                      +=|++.+--||..=..++..+-..+ |+.|+++..+.+..+....   -.+||..||..-+. ++++..=.     .-..
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            3467788889988888888888888 9999999888776544433   46999999998874 56664111     1146


Q ss_pred             CccEEEEcchhHhh
Q 028826           76 NLVILVLDEADRLL   89 (203)
Q Consensus        76 ~v~~lViDEad~l~   89 (203)
                      .+.+.||||+|.++
T Consensus       198 ~~~faIVDEVDSIL  211 (925)
T PRK12903        198 GLNFCLIDEVDSIL  211 (925)
T ss_pred             ccceeeeccchhee
Confidence            78899999999976

>PRK11634 ATP-dependent RNA helicase DeaD; Provisional

Probab=94.85  E-value=0.18  Score=45.20  Aligned_cols=70  Identities=16%  Similarity=0.260  Sum_probs=52.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||+|+|+.-+.++.+.+.+.     ++.+..++|+.+..+...   ...++..+|||+|-     .+.  ..+|+.++
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            4799999999999888877664     688899999887665544   33457899999994     333  46777777


Q ss_pred             cEEEE
Q 028826           78 VILVL   82 (203)
Q Consensus        78 ~~lVi   82 (203)
                      .++|.
T Consensus       315 ~~VI~  319 (629)
T PRK11634        315 SLVVN  319 (629)
T ss_pred             CEEEE
Confidence            77764

>PTZ00110 helicase; Provisional

Probab=94.84  E-value=0.18  Score=44.40  Aligned_cols=69  Identities=10%  Similarity=0.108  Sum_probs=53.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.|+|++-|..+.+.++..     ++.+..++|+.+..++...   ..++...|||+|-     .+.  ..+|+.+++
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            799999999999888877643     6788999999887665543   3346789999995     232  589999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       448 ~VI~  451 (545)
T PTZ00110        448 YVIN  451 (545)
T ss_pred             EEEE
Confidence            9886

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

Probab=94.84  E-value=0.42  Score=42.65  Aligned_cols=120  Identities=15%  Similarity=0.160  Sum_probs=69.1

Q ss_pred             CeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHh-hhhc-hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcC
Q 028826           52 ANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRL-LDMG-FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGL  129 (203)
Q Consensus        52 ~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l-~~~~-~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l  129 (203)
                      .-+=+.|-|.|+.=+-  ...+|.+-+.+||||||.= +..+ ....+..|. .+.+.-..++.|||+..  +.|-. |+
T Consensus       356 TvlKYMTDGmLlREfL--~epdLasYSViiiDEAHERTL~TDILfgLvKDIa-r~RpdLKllIsSAT~DA--ekFS~-fF  429 (902)
T KOG0923|consen  356 TVLKYMTDGMLLREFL--SEPDLASYSVIIVDEAHERTLHTDILFGLVKDIA-RFRPDLKLLISSATMDA--EKFSA-FF  429 (902)
T ss_pred             eeeeeecchhHHHHHh--ccccccceeEEEeehhhhhhhhhhHHHHHHHHHH-hhCCcceEEeeccccCH--HHHHH-hc
Confidence            4566889998876443  4678999999999999952 2211 222233333 33467789999999984  33333 44


Q ss_pred             CCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHh----cCCCCeEEEEec
Q 028826          130 RNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLI----KNKSKKIIMYVQ  195 (203)
Q Consensus       130 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~----~~~~~~~lIF~n  195 (203)
                      .+.-++.+...                  ...+..+|...++-+-+++-+..+.    ..+.+-+|||-.
T Consensus       430 DdapIF~iPGR------------------RyPVdi~Yt~~PEAdYldAai~tVlqIH~tqp~GDILVFlt  481 (902)
T KOG0923|consen  430 DDAPIFRIPGR------------------RYPVDIFYTKAPEADYLDAAIVTVLQIHLTQPLGDILVFLT  481 (902)
T ss_pred             cCCcEEeccCc------------------ccceeeecccCCchhHHHHHHhhheeeEeccCCccEEEEec
Confidence            54444444332                  3445556665665555544443332    123345666643

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

Probab=94.79  E-value=0.16  Score=43.91  Aligned_cols=68  Identities=16%  Similarity=0.233  Sum_probs=55.5

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHH---hCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIE---EEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~---~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      .+|++.++.-|.-+.+.+.+.     +++++.++||.+.++....|.   .+..+|+|+|--.      . +.+|..+|+
T Consensus       520 iIIFvN~kk~~d~lAk~LeK~-----g~~~~tlHg~k~qeQRe~aL~~fr~~t~dIlVaTDvA------g-RGIDIpnVS  587 (673)
T KOG0333|consen  520 IIIFVNTKKGADALAKILEKA-----GYKVTTLHGGKSQEQRENALADFREGTGDILVATDVA------G-RGIDIPNVS  587 (673)
T ss_pred             EEEEEechhhHHHHHHHHhhc-----cceEEEeeCCccHHHHHHHHHHHHhcCCCEEEEeccc------c-cCCCCCccc
Confidence            589999999888777777776     799999999999887777553   3678999999632      2 689999999


Q ss_pred             EEE
Q 028826           79 ILV   81 (203)
Q Consensus        79 ~lV   81 (203)
                      ++|
T Consensus       588 lVi  590 (673)
T KOG0333|consen  588 LVI  590 (673)
T ss_pred             eee
Confidence            887

>PF13872 AAA_34: P-loop containing NTP hydrolase pore-1

Probab=94.78  E-value=0.094  Score=42.34  Aligned_cols=112  Identities=17%  Similarity=0.139  Sum_probs=67.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHH--------------H
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIM--------------E   67 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~--------------~   67 (203)
                      +|.++.+-+|-....+.++.++..  .+.+..+..-...  ...   .-+-.||.+|-..|..--              .
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--DII---RLKEGVLFSTYSTLISESQSGGKYRSRLDQLVD  166 (303)
T ss_pred             eEEEECChhhhhHHHHHHHHhCCC--cccceechhhccC--cCC---CCCCCccchhHHHHHhHHhccCCccchHHHHHH
Confidence            678888999999999999998765  3444333321100  000   123358888866654432              2


Q ss_pred             hCCCccCCCccEEEEcchhHhhhhc--------hHHHHHHHHHhCCCCCcEEEEeeecChhHHHH
Q 028826           68 RMDVLDFRNLVILVLDEADRLLDMG--------FQKQISYIISRLPKLRRTGLFSATQTEAVEEL  124 (203)
Q Consensus        68 ~~~~~~l~~v~~lViDEad~l~~~~--------~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~  124 (203)
                      .++ -+++  ..+|+||+|..=...        ....+..+...+| +..++.+|||--.+.+++
T Consensus       167 W~g-~dfd--gvivfDEcH~akn~~~~~~~~sk~g~avl~LQ~~LP-~ARvvY~SATgasep~Nm  227 (303)
T PF13872_consen  167 WCG-EDFD--GVIVFDECHKAKNLSSGSKKPSKTGIAVLELQNRLP-NARVVYASATGASEPRNM  227 (303)
T ss_pred             HHh-cCCC--ceEEeccchhcCCCCccCccccHHHHHHHHHHHhCC-CCcEEEecccccCCCcee
Confidence            211 1222  389999999984321        2234556677786 445999999986665554

>PRK01297 ATP-dependent RNA helicase RhlB; Provisional

Probab=94.42  E-value=0.25  Score=42.70  Aligned_cols=71  Identities=13%  Similarity=0.148  Sum_probs=54.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||++++++-+..+++.+.+.     ++++..++|+...+++...   ..++...|||+|.     .+.  .++|+.++
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            3799999999998888777654     6788889998877665443   3356789999994     333  58999999


Q ss_pred             cEEEEc
Q 028826           78 VILVLD   83 (203)
Q Consensus        78 ~~lViD   83 (203)
                      +++|.-
T Consensus       405 ~~VI~~  410 (475)
T PRK01297        405 SHVINF  410 (475)
T ss_pred             CEEEEe
Confidence            999864

>PRK11057 ATP-dependent DNA helicase RecQ; Provisional

Probab=94.39  E-value=0.25  Score=44.18  Aligned_cols=69  Identities=12%  Similarity=0.161  Sum_probs=51.1

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.++|++-+.++...+++.     ++++..++||.+..+....+   ..+..+|||+|..     +.  .++|+.+++
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-----GISAAAYHAGLDNDVRADVQEAFQRDDLQIVVATVA-----FG--MGINKPNVR  306 (607)
T ss_pred             EEEEECcHHHHHHHHHHHHhC-----CCCEEEecCCCCHHHHHHHHHHHHCCCCCEEEEech-----hh--ccCCCCCcC
Confidence            689999999999888877764     78899999998876555433   2467899999963     11  456666666


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       307 ~VI~  310 (607)
T PRK11057        307 FVVH  310 (607)
T ss_pred             EEEE
Confidence            6664

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

Probab=94.37  E-value=0.64  Score=40.53  Aligned_cols=110  Identities=14%  Similarity=0.306  Sum_probs=78.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.+-|+-+|..+-+-+...     |+++.+++++.+.-+...   .|..+..||+||     ..+++.  ++|+-.|+
T Consensus       449 vLVTtLTKkmAEdLT~Yl~e~-----gikv~YlHSdidTlER~eIirdLR~G~~DvLVG-----INLLRE--GLDiPEVs  516 (663)
T COG0556         449 VLVTTLTKKMAEDLTEYLKEL-----GIKVRYLHSDIDTLERVEIIRDLRLGEFDVLVG-----INLLRE--GLDLPEVS  516 (663)
T ss_pred             EEEEeehHHHHHHHHHHHHhc-----CceEEeeeccchHHHHHHHHHHHhcCCccEEEe-----ehhhhc--cCCCccee
Confidence            466677776665555544443     899999999988665554   455588999999     457775  79999999


Q ss_pred             EEEEcchhHhhhhchHHHHHHHHHhCC-----CCCcEEEEeeecChhHHHHHH
Q 028826           79 ILVLDEADRLLDMGFQKQISYIISRLP-----KLRRTGLFSATQTEAVEELSK  126 (203)
Q Consensus        79 ~lViDEad~l~~~~~~~~~~~il~~~~-----~~~q~i~~SAT~~~~v~~~~~  126 (203)
                      ++.|=+||.   .||...-+.++.-+.     .+-.+|+..-.+++.+...+.
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            999999996   466555555554443     245788888888877665544

>TIGR01054 rgy reverse gyrase

Probab=94.35  E-value=0.21  Score=47.90  Aligned_cols=73  Identities=21%  Similarity=0.278  Sum_probs=53.9

Q ss_pred             CEEEEcCcH---HHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCC-
Q 028826            1 MGMIISPTR---ELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRN-   76 (203)
Q Consensus         1 ~alil~Ptr---eLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~-   76 (203)
                      .+||.+||+   +-|.++...+++.     |+++..++|+... ...+...++..+|||||... .+.+.  +++|+.+ 
T Consensus       328 ~~IVFv~t~~~~~~a~~l~~~L~~~-----g~~a~~lhg~~~~-~~l~~Fr~G~~~vLVata~~-tdv~a--RGIDip~~  398 (1171)
T TIGR01054       328 GGIVYVSIDYGKEKAEEIAEFLENH-----GVKAVAYHATKPK-EDYEKFAEGEIDVLIGVASY-YGTLV--RGLDLPER  398 (1171)
T ss_pred             CEEEEEeccccHHHHHHHHHHHHhC-----CceEEEEeCCCCH-HHHHHHHcCCCCEEEEeccc-cCccc--ccCCCCcc
Confidence            379999999   8888887777664     7899999999753 34455557889999998411 11122  5789888 


Q ss_pred             ccEEEE
Q 028826           77 LVILVL   82 (203)
Q Consensus        77 v~~lVi   82 (203)
                      ++++|+
T Consensus       399 V~~vI~  404 (1171)
T TIGR01054       399 VRYAVF  404 (1171)
T ss_pred             ccEEEE
Confidence            799888

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.

>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]

Probab=94.26  E-value=0.11  Score=46.83  Aligned_cols=110  Identities=19%  Similarity=0.194  Sum_probs=63.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHH-HHHhCCCccCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYD-IMERMDVLDFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~-~~~~~~~~~l~~v~~l   80 (203)
                      .||++|+- +..|...++.+..+.. .+.+...+|   ...+...+  .++||+++|++.+.. -+.      --.--.+
T Consensus       192 tLivcp~s-~~~qW~~elek~~~~~-~l~v~v~~g---r~kd~~el--~~~dVVltTy~il~~~~l~------~i~w~Ri  258 (674)
T KOG1001|consen  192 TLIVCPTS-LLTQWKTELEKVTEED-KLSIYVYHG---RTKDKSEL--NSYDVVLTTYDILKNSPLV------KIKWLRI  258 (674)
T ss_pred             eeEecchH-HHHHHHHHHhccCCcc-ceEEEEecc---cccccchh--cCCceEEeeHHHhhccccc------ceeEEEE
Confidence            47888876 5567777776665543 677777776   22233333  468899999988763 111      1223478


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHH
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSK  126 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~  126 (203)
                      |+||||.+-...  .........+....+.++.+...-..+.++..
T Consensus       259 ildea~~ikn~~--tq~~~a~~~L~a~~RWcLtgtPiqn~~~~lys  302 (674)
T KOG1001|consen  259 VLDEAHTIKNKD--TQIFKAVCQLDAKYRWCLTGTPIQNNLDELYS  302 (674)
T ss_pred             EeccccccCCcc--hHhhhhheeeccceeeeecCChhhhhHHHHHH
Confidence            999999875443  22333344443344444444444444555443

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

Probab=94.26  E-value=0.33  Score=42.54  Aligned_cols=71  Identities=8%  Similarity=0.141  Sum_probs=54.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.++|+.-+..+.+.+...   . ++++..++|+.+..++...+   .++..+|||+|.     .+.  .++|+.+++
T Consensus       370 ~iVFv~s~~~a~~l~~~L~~~---~-g~~~~~~Hg~~~~~eR~~il~~Fr~G~~~ILVaTd-----vl~--rGiDip~v~  438 (518)
T PLN00206        370 AVVFVSSRLGADLLANAITVV---T-GLKALSIHGEKSMKERREVMKSFLVGEVPVIVATG-----VLG--RGVDLLRVR  438 (518)
T ss_pred             EEEEcCCchhHHHHHHHHhhc---c-CcceEEeeCCCCHHHHHHHHHHHHCCCCCEEEEec-----Hhh--ccCCcccCC
Confidence            689999999888777766543   2 78899999998876655543   347789999997     232  589999999


Q ss_pred             EEEEc
Q 028826           79 ILVLD   83 (203)
Q Consensus        79 ~lViD   83 (203)
                      ++|.=
T Consensus       439 ~VI~~  443 (518)
T PLN00206        439 QVIIF  443 (518)
T ss_pred             EEEEe
Confidence            99863

>KOG1000 consensus Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics]

Probab=94.25  E-value=0.25  Score=42.60  Aligned_cols=104  Identities=16%  Similarity=0.205  Sum_probs=62.3

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEE
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVL   82 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lVi   82 (203)
                      ||+||.. +-.-+.+.++++.+..  ..+..+.++.+.-...    ...+.|.|.+-+.+..+-+   .+.-..-+.+|+
T Consensus       245 liVcPAs-vrftWa~al~r~lps~--~pi~vv~~~~D~~~~~----~t~~~v~ivSye~ls~l~~---~l~~~~~~vvI~  314 (689)
T KOG1000|consen  245 LIVCPAS-VRFTWAKALNRFLPSI--HPIFVVDKSSDPLPDV----CTSNTVAIVSYEQLSLLHD---ILKKEKYRVVIF  314 (689)
T ss_pred             EEEecHH-HhHHHHHHHHHhcccc--cceEEEecccCCcccc----ccCCeEEEEEHHHHHHHHH---HHhcccceEEEE
Confidence            7888965 3344556666665543  2244555554432221    2236788888877665443   233445789999


Q ss_pred             cchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeec
Q 028826           83 DEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ  117 (203)
Q Consensus        83 DEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  117 (203)
                      ||.|.|=+. .....+.++..+.....+|++|.|.
T Consensus       315 DEsH~Lk~s-ktkr~Ka~~dllk~akhvILLSGTP  348 (689)
T KOG1000|consen  315 DESHMLKDS-KTKRTKAATDLLKVAKHVILLSGTP  348 (689)
T ss_pred             echhhhhcc-chhhhhhhhhHHHHhhheEEecCCc
Confidence            999977433 3334555555555566778888874

>PTZ00424 helicase 45; Provisional

Probab=94.05  E-value=0.29  Score=41.07  Aligned_cols=70  Identities=14%  Similarity=0.185  Sum_probs=53.5

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.++|++-+..+.+.+...     ++++..++|+.+..++...   ..++..+|||+|-     .+.  .++|+.+++
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            689999999888777766553     6889999999876655443   3346799999995     232  579999999


Q ss_pred             EEEEc
Q 028826           79 ILVLD   83 (203)
Q Consensus        79 ~lViD   83 (203)
                      ++|.-
T Consensus       338 ~VI~~  342 (401)
T PTZ00424        338 LVINY  342 (401)
T ss_pred             EEEEE
Confidence            99863

>TIGR01389 recQ ATP-dependent DNA helicase RecQ

Probab=93.94  E-value=0.39  Score=42.74  Aligned_cols=69  Identities=12%  Similarity=0.197  Sum_probs=50.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.++|+..+.++.+.+...     ++++..++||.+.++....+   ..+.++|||+|-.-     .  .++|+.+++
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-----GISALAYHAGLSNKVRAENQEDFLYDDVKVMVATNAF-----G--MGIDKPNVR  294 (591)
T ss_pred             EEEEECcHHHHHHHHHHHHhC-----CCCEEEEECCCCHHHHHHHHHHHHcCCCcEEEEechh-----h--ccCcCCCCC
Confidence            689999999999888877653     78899999998876555433   24678999999522     2  356666777


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       295 ~VI~  298 (591)
T TIGR01389       295 FVIH  298 (591)
T ss_pred             EEEE
Confidence            6664

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.

>PRK09401 reverse gyrase; Reviewed

Probab=93.94  E-value=0.15  Score=48.76  Aligned_cols=72  Identities=17%  Similarity=0.403  Sum_probs=51.8

Q ss_pred             CEEEEcCcHHH---HHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCC-
Q 028826            1 MGMIISPTREL---SAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRN-   76 (203)
Q Consensus         1 ~alil~PtreL---a~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~-   76 (203)
                      .+||.|||++-   |..+.+.+++.     |+++..++|+.  ........++..+|||||..- .+.+.  +++|+.+ 
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            47999999554   77777666664     79999999998  334456667889999998522 11111  5788887 


Q ss_pred             ccEEEE
Q 028826           77 LVILVL   82 (203)
Q Consensus        77 v~~lVi   82 (203)
                      ++++|.
T Consensus       400 IryVI~  405 (1176)
T PRK09401        400 IRYAIF  405 (1176)
T ss_pred             eeEEEE
Confidence            888887

>KOG0388 consensus SNF2 family DNA-dependent ATPase [Replication, recombination and repair]

Probab=93.77  E-value=0.37  Score=43.36  Aligned_cols=104  Identities=16%  Similarity=0.242  Sum_probs=67.2

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH--------HhCCCeEEEeccHHHH---HHHHhCCC
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI--------EEEGANLLIGTPGRLY---DIMERMDV   71 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l--------~~~~~~ilV~Tp~~l~---~~~~~~~~   71 (203)
                      |||+|..-    ++.+..+++.++|+++++-.-|+.......+..        ...+.||+|+|-..+.   .++..   
T Consensus       621 LVVtpaSt----L~NWaqEisrFlP~~k~lpywGs~~eRkiLrKfw~rKnmY~rna~fhVviTSYQlvVtDeky~qk---  693 (1185)
T KOG0388|consen  621 LVVTPAST----LHNWAQEISRFLPSFKVLPYWGSPSERKILRKFWNRKNMYRRNAPFHVVITSYQLVVTDEKYLQK---  693 (1185)
T ss_pred             EEeehHHH----HhHHHHHHHHhCccceeecCcCChhhhHHHHHhcchhhhhccCCCceEEEEeeeeeechHHHHHh---
Confidence            67888554    456777788888899999888887654444321        2367899999876653   23333   


Q ss_pred             ccCCCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecCh
Q 028826           72 LDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (203)
Q Consensus        72 ~~l~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  119 (203)
                         -.-++.|+|||-.+=+ .....++.+++.-.  +-.++++.|.-+
T Consensus       694 ---vKWQYMILDEAQAIKS-SsS~RWKtLLsF~c--RNRLLLTGTPIQ  735 (1185)
T KOG0388|consen  694 ---VKWQYMILDEAQAIKS-SSSSRWKTLLSFKC--RNRLLLTGTPIQ  735 (1185)
T ss_pred             ---hhhhheehhHHHHhhh-hhhhHHHHHhhhhc--cceeeecCCccc
Confidence               1235899999987743 34555666666543  334666677544

>PRK11664 ATP-dependent RNA helicase HrpB; Provisional

Probab=93.74  E-value=0.41  Score=44.25  Aligned_cols=71  Identities=15%  Similarity=0.201  Sum_probs=55.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHh---CCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEE---EGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~---~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||++|+++-+.++.+.+++...  .++.+..++|+.+..++...+..   +...|||+|.     .. . .++++.+++
T Consensus       215 iLVFlpg~~ei~~l~~~L~~~~~--~~~~v~~Lhg~l~~~eq~~~~~~~~~G~rkVlvATn-----IA-E-rsLtIp~V~  285 (812)
T PRK11664        215 LLLFLPGVGEIQRVQEQLASRVA--SDVLLCPLYGALSLAEQQKAILPAPAGRRKVVLATN-----IA-E-TSLTIEGIR  285 (812)
T ss_pred             EEEEcCCHHHHHHHHHHHHHhcc--CCceEEEeeCCCCHHHHHHHhccccCCCeEEEEecc-----hH-H-hcccccCce
Confidence            69999999999988888876322  26889999999998877776642   3468999998     22 3 689999999


Q ss_pred             EEE
Q 028826           79 ILV   81 (203)
Q Consensus        79 ~lV   81 (203)
                      +||
T Consensus       286 ~VI  288 (812)
T PRK11664        286 LVV  288 (812)
T ss_pred             EEE
Confidence            776

>PRK05580 primosome assembly protein PriA; Validated

Probab=93.71  E-value=1.3  Score=40.21  Aligned_cols=71  Identities=17%  Similarity=0.210  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHHHhhhcCCCceEEEEEcCcch-----HHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcc
Q 028826           10 ELSAQIYHVAQPFISTLPDVKSMLLVGGVEV-----KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDE   84 (203)
Q Consensus        10 eLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~-----~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDE   84 (203)
                      .-+.++.++++++   +|+.++..+.++...     ++......++.++|+|||..     +.  +.+|+.++.++++-.
T Consensus       437 ~G~e~~~e~l~~~---fp~~~v~~~~~d~~~~~~~~~~~l~~f~~g~~~ILVgT~~-----ia--kG~d~p~v~lV~il~  506 (679)
T PRK05580        437 PGTERLEEELAEL---FPEARILRIDRDTTRRKGALEQLLAQFARGEADILIGTQM-----LA--KGHDFPNVTLVGVLD  506 (679)
T ss_pred             ccHHHHHHHHHHh---CCCCcEEEEeccccccchhHHHHHHHHhcCCCCEEEEChh-----hc--cCCCCCCcCEEEEEc
Confidence            3445556666555   557888888877542     23344555678999999994     32  579999999999999


Q ss_pred             hhHhhh
Q 028826           85 ADRLLD   90 (203)
Q Consensus        85 ad~l~~   90 (203)
                      +|..+.
T Consensus       507 aD~~l~  512 (679)
T PRK05580        507 ADLGLF  512 (679)
T ss_pred             Cchhcc
Confidence            998764

>PRK05298 excinuclease ABC subunit B; Provisional

Probab=93.67  E-value=2.4  Score=38.32  Aligned_cols=75  Identities=13%  Similarity=0.313  Sum_probs=57.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      ++|+++|+.-+..+.+.+.+.     ++++..++|+.+..+...   ....++.+|+|||-     .+.  .++++.+++
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            789999999998888877664     788999988877554443   33346789999984     333  589999999


Q ss_pred             EEEEcchhHh
Q 028826           79 ILVLDEADRL   88 (203)
Q Consensus        79 ~lViDEad~l   88 (203)
                      ++|+=|++..
T Consensus       517 lVii~d~eif  526 (652)
T PRK05298        517 LVAILDADKE  526 (652)
T ss_pred             EEEEeCCccc
Confidence            9998777753

>PRK13767 ATP-dependent helicase; Provisional

Probab=93.58  E-value=0.57  Score=43.76  Aligned_cols=75  Identities=11%  Similarity=0.142  Sum_probs=54.5

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhc-CCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            2 GMIISPTRELSAQIYHVAQPFIST-LPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~-~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      +||+|+||..|..+...+++.... ..+..+...+|+.+.++...   .+.++...+||+|..     +.  .++|+.++
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 TLIFTNTRSGAERVLYNLRKRFPEEYDEDNIGAHHSSLSREVRLEVEEKLKRGELKVVVSSTS-----LE--LGIDIGYI  359 (876)
T ss_pred             EEEEeCCHHHHHHHHHHHHHhchhhccccceeeeeCCCCHHHHHHHHHHHHcCCCeEEEECCh-----HH--hcCCCCCC
Confidence            799999999999998888775331 12467888999988665443   445577899999973     22  46777778


Q ss_pred             cEEEEc
Q 028826           78 VILVLD   83 (203)
Q Consensus        78 ~~lViD   83 (203)
                      +++|.-
T Consensus       360 d~VI~~  365 (876)
T PRK13767        360 DLVVLL  365 (876)
T ss_pred             cEEEEe
Confidence            877753

>COG4889 Predicted helicase [General function prediction only]

Probab=93.48  E-value=0.4  Score=44.24  Aligned_cols=85  Identities=18%  Similarity=0.226  Sum_probs=59.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH------------------------HHHhCCCeEEEe
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK------------------------KIEEEGANLLIG   57 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~------------------------~l~~~~~~ilV~   57 (203)
                      .|+|+|+-.|..|..++...=. .+ .++...++++....+..+                        .-...+--|+++
T Consensus       209 iL~LvPSIsLLsQTlrew~~~~-~l-~~~a~aVcSD~kvsrs~eDik~sdl~~p~sT~~~~il~~~~~~~k~~~~~vvFs  286 (1518)
T COG4889         209 ILFLVPSISLLSQTLREWTAQK-EL-DFRASAVCSDDKVSRSAEDIKASDLPIPVSTDLEDILSEMEHRQKANGLTVVFS  286 (1518)
T ss_pred             eEeecchHHHHHHHHHHHhhcc-Cc-cceeEEEecCccccccccccccccCCCCCcccHHHHHHHHHHhhccCCcEEEEE
Confidence            5899999999999988887642 33 677777777543321111                        111245678888


Q ss_pred             ccHHHHHHHHhCCCccCCCccEEEEcchhHhh
Q 028826           58 TPGRLYDIMERMDVLDFRNLVILVLDEADRLL   89 (203)
Q Consensus        58 Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~   89 (203)
                      |-..+...-.. ...-+..++++|-||||+..
T Consensus       287 TYQSl~~i~eA-Qe~G~~~fDliicDEAHRTt  317 (1518)
T COG4889         287 TYQSLPRIKEA-QEAGLDEFDLIICDEAHRTT  317 (1518)
T ss_pred             cccchHHHHHH-HHcCCCCccEEEecchhccc
Confidence            88887765554 55567889999999999974

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=93.31  E-value=0.15  Score=47.38  Aligned_cols=83  Identities=12%  Similarity=0.194  Sum_probs=61.4

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHH-HHHHhC-----CCccCCC
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-DIMERM-----DVLDFRN   76 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~-~~~~~~-----~~~~l~~   76 (203)
                      =||+.+--||..=.+++..+..++ |+.|+++..+.+..+...   .-.+||..||..-+- ++++.+     ...-...
T Consensus       183 HvVTvNDYLA~RDaewm~p~y~fl-GLtVg~i~~~~~~~~Rr~---aY~~DItYgTn~EfGFDYLRDnma~~~~~~vqR~  258 (1025)
T PRK12900        183 HVVTVNDYLAQRDKEWMNPVFEFH-GLSVGVILNTMRPEERRE---QYLCDITYGTNNEFGFDYLRDNMAGTPEEMVQRD  258 (1025)
T ss_pred             EEEeechHhhhhhHHHHHHHHHHh-CCeeeeeCCCCCHHHHHH---hCCCcceecCCCccccccchhccccchhhhhccC
Confidence            366777788888888888888888 999999977766554443   357999999998874 555541     0111357


Q ss_pred             ccEEEEcchhHhh
Q 028826           77 LVILVLDEADRLL   89 (203)
Q Consensus        77 v~~lViDEad~l~   89 (203)
                      ..+.||||+|.++
T Consensus       259 ~~faIVDEvDSvL  271 (1025)
T PRK12900        259 FYFAIVDEVDSVL  271 (1025)
T ss_pred             CceEEEechhhhh
Confidence            8899999999975

>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB

Probab=93.28  E-value=0.54  Score=43.50  Aligned_cols=72  Identities=14%  Similarity=0.206  Sum_probs=55.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHh---CCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEE---EGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~---~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||++|+++-+.++++.+++...  +++.+..++|+.+..++.+.+..   +...|||+|.     .. . .++++.+|+
T Consensus       212 iLVFlpg~~eI~~l~~~L~~~~~--~~~~v~pLHg~L~~~eq~~~~~~~~~G~rkVlVATn-----IA-E-rgItIp~V~  282 (819)
T TIGR01970       212 ILVFLPGQAEIRRVQEQLAERLD--SDVLICPLYGELSLAAQDRAIKPDPQGRRKVVLATN-----IA-E-TSLTIEGIR  282 (819)
T ss_pred             EEEEECCHHHHHHHHHHHHhhcC--CCcEEEEecCCCCHHHHHHHHhhcccCCeEEEEecc-----hH-h-hcccccCce
Confidence            69999999999888888876322  27899999999998887776643   3468999997     22 3 688999998


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|=
T Consensus       283 ~VID  286 (819)
T TIGR01970       283 VVID  286 (819)
T ss_pred             EEEE
Confidence            7763

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.

>PRK05642 DNA replication initiation factor; Validated

Probab=93.17  E-value=1.1  Score=35.04  Aligned_cols=89  Identities=16%  Similarity=0.192  Sum_probs=52.6

Q ss_pred             eEEEEEcCc--chHHHHHHH----HhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHhhh-hchHHHHHHHHH
Q 028826           30 KSMLLVGGV--EVKADVKKI----EEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIIS  102 (203)
Q Consensus        30 ~~~~~~~g~--~~~~~~~~l----~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~~-~~~~~~~~~il~  102 (203)
                      +...++|..  ...+-...+    ...+..+++.+.+.+...... -.-.+.+.+++++|++|.+-. ....+.+.+++.
T Consensus        46 ~~l~l~G~~G~GKTHLl~a~~~~~~~~~~~v~y~~~~~~~~~~~~-~~~~~~~~d~LiiDDi~~~~~~~~~~~~Lf~l~n  124 (234)
T PRK05642         46 SLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLPLAELLDRGPE-LLDNLEQYELVCLDDLDVIAGKADWEEALFHLFN  124 (234)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEeeHHHHHhhhHH-HHHhhhhCCEEEEechhhhcCChHHHHHHHHHHH
Confidence            456677643  344443332    234678899888887643221 011255678999999997743 234566778887


Q ss_pred             hCCCCCcEEEEeeecCh
Q 028826          103 RLPKLRRTGLFSATQTE  119 (203)
Q Consensus       103 ~~~~~~q~i~~SAT~~~  119 (203)
                      .+..+...++++++.++
T Consensus       125 ~~~~~g~~ilits~~~p  141 (234)
T PRK05642        125 RLRDSGRRLLLAASKSP  141 (234)
T ss_pred             HHHhcCCEEEEeCCCCH
Confidence            76544344555555544

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

Probab=93.12  E-value=0.49  Score=41.13  Aligned_cols=69  Identities=12%  Similarity=0.109  Sum_probs=55.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHH---hCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIE---EEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~---~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.|-|+.-|.++.+.++..     +.++.+++|+.+..+....|.   ++.+.|||+|--.      . +.+|+.+|+
T Consensus       344 vIIFc~tkr~~~~l~~~l~~~-----~~~a~~iHGd~sQ~eR~~~L~~FreG~~~vLVATdVA------a-RGLDi~dV~  411 (519)
T KOG0331|consen  344 VIIFCETKRTCDELARNLRRK-----GWPAVAIHGDKSQSERDWVLKGFREGKSPVLVATDVA------A-RGLDVPDVD  411 (519)
T ss_pred             EEEEecchhhHHHHHHHHHhc-----CcceeeecccccHHHHHHHHHhcccCCcceEEEcccc------c-ccCCCcccc
Confidence            789999999888887777664     578999999999887777664   4678999999622      2 689999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|-
T Consensus       412 lVIn  415 (519)
T KOG0331|consen  412 LVIN  415 (519)
T ss_pred             EEEe
Confidence            9984

>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=92.84  E-value=1.3  Score=30.21  Aligned_cols=73  Identities=14%  Similarity=0.231  Sum_probs=52.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      .||++++++-+.++.+.+.+.     +..+..++|+.+..+...   ...++...|+++|..     +.  .++++..++
T Consensus        31 ~lvf~~~~~~~~~~~~~l~~~-----~~~~~~~~~~~~~~~~~~~~~~f~~~~~~ili~t~~-----~~--~G~d~~~~~   98 (131)
T cd00079          31 VLIFCPSKKMLDELAELLRKP-----GIKVAALHGDGSQEEREEVLKDFREGEIVVLVATDV-----IA--RGIDLPNVS   98 (131)
T ss_pred             EEEEeCcHHHHHHHHHHHHhc-----CCcEEEEECCCCHHHHHHHHHHHHcCCCcEEEEcCh-----hh--cCcChhhCC
Confidence            589999999998888888772     677888998876444333   233456689999863     22  578888888


Q ss_pred             EEEEcchh
Q 028826           79 ILVLDEAD   86 (203)
Q Consensus        79 ~lViDEad   86 (203)
                      .+|+.+.+
T Consensus        99 ~vi~~~~~  106 (131)
T cd00079          99 VVINYDLP  106 (131)
T ss_pred             EEEEeCCC
Confidence            88876663

>PF09848 DUF2075: Uncharacterized conserved protein (DUF2075); InterPro: IPR018647 This domain, found in putative ATP/GTP binding proteins, has no known function

Probab=92.74  E-value=0.54  Score=38.97  Aligned_cols=100  Identities=18%  Similarity=0.189  Sum_probs=52.6

Q ss_pred             CceEEEEEcCcchHHHHHHHHhCCC-----eEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHhhhhc-------hHH
Q 028826           28 DVKSMLLVGGVEVKADVKKIEEEGA-----NLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMG-------FQK   95 (203)
Q Consensus        28 ~i~~~~~~~g~~~~~~~~~l~~~~~-----~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~~~~-------~~~   95 (203)
                      +-++..++++...............     ...+..|..+...... ......+.+++||||||+|.+.+       ...
T Consensus        31 ~~~~~~l~~n~~l~~~l~~~l~~~~~~~~~~~~~~~~~~~i~~~~~-~~~~~~~~DviivDEAqrl~~~~~~~~~~~~~~  109 (352)
T PF09848_consen   31 GKKVLYLCGNHPLRNKLREQLAKKYNPKLKKSDFRKPTSFINNYSE-SDKEKNKYDVIIVDEAQRLRTKGDQYNNFSEPN  109 (352)
T ss_pred             CCceEEEEecchHHHHHHHHHhhhcccchhhhhhhhhHHHHhhccc-ccccCCcCCEEEEehhHhhhhccccccccccHH
Confidence            4566666666665544433222221     3344445444433331 22446788999999999998732       235


Q ss_pred             HHHHHHHhCC------CCCcEEEEeeecChh-HHHHHHhc
Q 028826           96 QISYIISRLP------KLRRTGLFSATQTEA-VEELSKAG  128 (203)
Q Consensus        96 ~~~~il~~~~------~~~q~i~~SAT~~~~-v~~~~~~~  128 (203)
                      .+..++..-.      ...|.+-.+.....+ +..++..+
T Consensus       110 ~L~~i~~~~kv~v~f~D~~Q~i~~~e~~~~~~l~~~~~~~  149 (352)
T PF09848_consen  110 QLDEIIKRAKVVVFFYDENQSIRPSEIGTLENLEEIAENL  149 (352)
T ss_pred             HHHHHHhcCCEEEEEEccccEeecccCCCHHHHHHHHHhc
Confidence            5666666521      133555555544433 44444433

It is found in some proteins described as Schlafen family members, which may have a role in hematopoeitic cell differentiation [].

>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]

Probab=92.72  E-value=0.57  Score=43.23  Aligned_cols=115  Identities=17%  Similarity=0.175  Sum_probs=66.5

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCce-EEEEEcCcch----HHHHHHHHhCC----CeEEEeccHHHHHHHHhCCCc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVK-SMLLVGGVEV----KADVKKIEEEG----ANLLIGTPGRLYDIMERMDVL   72 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~-~~~~~~g~~~----~~~~~~l~~~~----~~ilV~Tp~~l~~~~~~~~~~   72 (203)
                      ++|++|+. +..++.+++.++.+.   ++ +....|....    .+....+....    .+++++|-+.+.........+
T Consensus       393 ~liv~p~s-~~~nw~~e~~k~~~~---~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~v~itty~~l~~~~~~~~~l  468 (866)
T COG0553         393 ALIVVPAS-LLSNWKREFEKFAPD---LRLVLVYHGEKSELDKKREALRDLLKLHLVIIFDVVITTYELLRRFLVDHGGL  468 (866)
T ss_pred             eEEEecHH-HHHHHHHHHhhhCcc---ccceeeeeCCcccccHHHHHHHHHhhhcccceeeEEechHHHHHHhhhhHHHH
Confidence            57888876 566777777777554   44 6666665541    33333333322    799999999988732111334


Q ss_pred             cCCCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeec-ChhHHH
Q 028826           73 DFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ-TEAVEE  123 (203)
Q Consensus        73 ~l~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~-~~~v~~  123 (203)
                      .-.....+|+||+|.+-.. -......+. .+..... +++|.|. .+.+.+
T Consensus       469 ~~~~~~~~v~DEa~~ikn~-~s~~~~~l~-~~~~~~~-~~LtgTPlen~l~e  517 (866)
T COG0553         469 KKIEWDRVVLDEAHRIKND-QSSEGKALQ-FLKALNR-LDLTGTPLENRLGE  517 (866)
T ss_pred             hhceeeeeehhhHHHHhhh-hhHHHHHHH-HHhhcce-eeCCCChHhhhHHH
Confidence            5566789999999996332 222222333 4433334 4455554 444444

>PHA02653 RNA helicase NPH-II; Provisional

Probab=92.71  E-value=0.54  Score=42.52  Aligned_cols=70  Identities=14%  Similarity=0.297  Sum_probs=52.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHH-HHHH-HhCCCeEEEeccHHHHHHHHhCCCccCCCccE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKAD-VKKI-EEEGANLLIGTPGRLYDIMERMDVLDFRNLVI   79 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~-~~~l-~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~   79 (203)
                      +||.+|+++-+..+.+.+++..   +++++..++|+.+..++ .+.. .++...|||+|.     .. . +++++.++.+
T Consensus       398 iLVFlpg~~ei~~l~~~L~~~~---~~~~v~~LHG~Lsq~eq~l~~ff~~gk~kILVATd-----IA-E-RGIDIp~V~~  467 (675)
T PHA02653        398 GIVFVASVSQCEEYKKYLEKRL---PIYDFYIIHGKVPNIDEILEKVYSSKNPSIIISTP-----YL-E-SSVTIRNATH  467 (675)
T ss_pred             EEEEECcHHHHHHHHHHHHhhc---CCceEEeccCCcCHHHHHHHHHhccCceeEEeccC-----hh-h-ccccccCeeE
Confidence            6999999998877777666542   36889999999876533 2444 245689999998     22 3 6899999988


Q ss_pred             EE
Q 028826           80 LV   81 (203)
Q Consensus        80 lV   81 (203)
                      +|
T Consensus       468 VI  469 (675)
T PHA02653        468 VY  469 (675)
T ss_pred             EE
Confidence            76

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

Probab=92.30  E-value=0.87  Score=36.61  Aligned_cols=69  Identities=14%  Similarity=0.171  Sum_probs=52.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      ||+|+|.||.-+.-+.+.++.-     +..+.+.+|+...++....+   ..+...|+|+|--+      . +.+|...+
T Consensus       268 QavIFcnTk~kVdwLtekm~~~-----nftVssmHGDm~qkERd~im~dFRsg~SrvLitTDVw------a-RGiDv~qV  335 (400)
T KOG0328|consen  268 QAVIFCNTKRKVDWLTEKMREA-----NFTVSSMHGDMEQKERDKIMNDFRSGKSRVLITTDVW------A-RGIDVQQV  335 (400)
T ss_pred             eEEEEecccchhhHHHHHHHhh-----CceeeeccCCcchhHHHHHHHHhhcCCceEEEEechh------h-ccCCccee
Confidence            6899999998776555555543     78899999998877766644   24678999998632      2 67899999


Q ss_pred             cEEE
Q 028826           78 VILV   81 (203)
Q Consensus        78 ~~lV   81 (203)
                      +++|
T Consensus       336 slvi  339 (400)
T KOG0328|consen  336 SLVI  339 (400)
T ss_pred             EEEE
Confidence            9887

>PRK12422 chromosomal replication initiation protein; Provisional

Probab=92.19  E-value=2.6  Score=36.27  Aligned_cols=121  Identities=12%  Similarity=0.170  Sum_probs=65.6

Q ss_pred             EEcCcHHHHHHHHHHHHH-hhhcC-CCceEEEEEcCcc--hHHHHHHH----HhCCCeEEEeccHHHHHHHHh---CCCc
Q 028826            4 IISPTRELSAQIYHVAQP-FISTL-PDVKSMLLVGGVE--VKADVKKI----EEEGANLLIGTPGRLYDIMER---MDVL   72 (203)
Q Consensus         4 il~PtreLa~Qi~~~~~~-l~~~~-~~i~~~~~~~g~~--~~~~~~~l----~~~~~~ilV~Tp~~l~~~~~~---~~~~   72 (203)
                      |+.|.-++|......+.+ ..... ...+...++|+..  ..+-...+    ...+..++..+.+.+...+..   .+..
T Consensus       114 v~g~~N~~a~~~a~~~a~~~~~~~~~~~npl~L~G~~G~GKTHLl~Ai~~~l~~~~~~v~yi~~~~f~~~~~~~l~~~~~  193 (445)
T PRK12422        114 LVTPENDLPHRILQEFTKVSEQGKGFPFNPIYLFGPEGSGKTHLMQAAVHALRESGGKILYVRSELFTEHLVSAIRSGEM  193 (445)
T ss_pred             eeCCcHHHHHHHHHHHHhccccccCCCCceEEEEcCCCCCHHHHHHHHHHHHHHcCCCEEEeeHHHHHHHHHHHHhcchH
Confidence            345666666444333322 21110 1245677887543  33333322    234688999998876543321   0111


Q ss_pred             -----cCCCccEEEEcchhHhhhhc-hHHHHHHHHHhC-CCCCcEEEEeeecChhHHHH
Q 028826           73 -----DFRNLVILVLDEADRLLDMG-FQKQISYIISRL-PKLRRTGLFSATQTEAVEEL  124 (203)
Q Consensus        73 -----~l~~v~~lViDEad~l~~~~-~~~~~~~il~~~-~~~~q~i~~SAT~~~~v~~~  124 (203)
                           ...+.+++++||+|.+-... ..+.+..++..+ ....|+++.|.+.|..+..+
T Consensus       194 ~~f~~~~~~~dvLiIDDiq~l~~k~~~qeelf~l~N~l~~~~k~IIlts~~~p~~l~~l  252 (445)
T PRK12422        194 QRFRQFYRNVDALFIEDIEVFSGKGATQEEFFHTFNSLHTEGKLIVISSTCAPQDLKAM  252 (445)
T ss_pred             HHHHHHcccCCEEEEcchhhhcCChhhHHHHHHHHHHHHHCCCcEEEecCCCHHHHhhh
Confidence                 14678899999999875432 344555555443 24567777766666655443

>TIGR00595 priA primosomal protein N'

Probab=91.92  E-value=3.1  Score=36.46  Aligned_cols=68  Identities=19%  Similarity=0.256  Sum_probs=49.1

Q ss_pred             HHHHHHHHHhhhcCCCceEEEEEcCcch-----HHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhH
Q 028826           13 AQIYHVAQPFISTLPDVKSMLLVGGVEV-----KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADR   87 (203)
Q Consensus        13 ~Qi~~~~~~l~~~~~~i~~~~~~~g~~~-----~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~   87 (203)
                      .++.+++.++   +|+.++..+.++...     ++....+.++.++|+|||+.     +.  +.+++.++.++++=.+|.
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 EQVEEELAKL---FPGARIARIDSDTTSRKGAHEALLNQFANGKADILIGTQM-----IA--KGHHFPNVTLVGVLDADS  341 (505)
T ss_pred             HHHHHHHHhh---CCCCcEEEEecccccCccHHHHHHHHHhcCCCCEEEeCcc-----cc--cCCCCCcccEEEEEcCcc
Confidence            4555555554   567888888887643     23344555678999999994     32  578999999999999998


Q ss_pred             hhh
Q 028826           88 LLD   90 (203)
Q Consensus        88 l~~   90 (203)
                      .+.
T Consensus       342 ~l~  344 (505)
T TIGR00595       342 GLH  344 (505)
T ss_pred             ccc
Confidence            663

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).

>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=91.90  E-value=0.23  Score=38.12  Aligned_cols=41  Identities=24%  Similarity=0.320  Sum_probs=33.6

Q ss_pred             CCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEee
Q 028826           75 RNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSA  115 (203)
Q Consensus        75 ~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SA  115 (203)
                      ...-++++||+|.=+|......+..++..+++..|+++.|.
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            45679999999999999999999999999988999998864

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 ....

>KOG0386 consensus Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics; Transcription]

Probab=91.78  E-value=0.22  Score=46.18  Aligned_cols=106  Identities=17%  Similarity=0.249  Sum_probs=59.8

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHH-HHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADV-KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~-~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ||+||+--|.+ +..++.+.   .|.+..+...|........ .++..+..+|+++|-+.+..  .. ..+.--+-.++|
T Consensus       448 LvivPlstL~N-W~~Ef~kW---aPSv~~i~YkGtp~~R~~l~~qir~gKFnVLlTtyEyiik--dk-~lLsKI~W~yMI  520 (1157)
T KOG0386|consen  448 LIIVPLSTLVN-WSSEFPKW---APSVQKIQYKGTPQQRSGLTKQQRHGKFNVLLTTYEYIIK--DK-ALLSKISWKYMI  520 (1157)
T ss_pred             EEeccccccCC-chhhcccc---ccceeeeeeeCCHHHHhhHHHHHhcccceeeeeeHHHhcC--CH-HHHhccCCccee
Confidence            78999888774 23444444   3467766666654432222 23445789999999988764  11 112222345899


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeec
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ  117 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  117 (203)
                      |||-|+|=  .....+...+.-.......++++.|-
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            99999982  23334444444222333345555553

>PF00308 Bac_DnaA: Bacterial dnaA protein; InterPro: IPR013317 This entry represents the central domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication

Probab=91.68  E-value=1.9  Score=33.28  Aligned_cols=116  Identities=13%  Similarity=0.140  Sum_probs=66.3

Q ss_pred             EEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcc--hHHHHHHHH------hCCCeEEEeccHHHHHHHHh---CCCc
Q 028826            4 IISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVE--VKADVKKIE------EEGANLLIGTPGRLYDIMER---MDVL   72 (203)
Q Consensus         4 il~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~--~~~~~~~l~------~~~~~ilV~Tp~~l~~~~~~---~~~~   72 (203)
                      |..+..++|....+.+..-. .. ......++|+..  ..+-...+.      ..+..|+..+.+.+...+..   .+.+
T Consensus        11 v~g~~N~~a~~~~~~ia~~~-~~-~~~~l~l~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~y~~~~~f~~~~~~~~~~~~~   88 (219)
T PF00308_consen   11 VVGESNELAYAAAKAIAENP-GE-RYNPLFLYGPSGLGKTHLLQAIANEAQKQHPGKRVVYLSAEEFIREFADALRDGEI   88 (219)
T ss_dssp             --TTTTHHHHHHHHHHHHST-TT-SSSEEEEEESTTSSHHHHHHHHHHHHHHHCTTS-EEEEEHHHHHHHHHHHHHTTSH
T ss_pred             CcCCcHHHHHHHHHHHHhcC-CC-CCCceEEECCCCCCHHHHHHHHHHHHHhccccccceeecHHHHHHHHHHHHHcccc
Confidence            34555666665544443321 11 345677887653  444333321      13678999998887654321   0222


Q ss_pred             -----cCCCccEEEEcchhHhhhh-chHHHHHHHHHhCC-CCCcEEEEeeecChhH
Q 028826           73 -----DFRNLVILVLDEADRLLDM-GFQKQISYIISRLP-KLRRTGLFSATQTEAV  121 (203)
Q Consensus        73 -----~l~~v~~lViDEad~l~~~-~~~~~~~~il~~~~-~~~q~i~~SAT~~~~v  121 (203)
                           .+.+.+++++|++|.+-.. ...+.+.+++..+. ...|+++.|...|.++
T Consensus        89 ~~~~~~~~~~DlL~iDDi~~l~~~~~~q~~lf~l~n~~~~~~k~li~ts~~~P~~l  144 (219)
T PF00308_consen   89 EEFKDRLRSADLLIIDDIQFLAGKQRTQEELFHLFNRLIESGKQLILTSDRPPSEL  144 (219)
T ss_dssp             HHHHHHHCTSSEEEEETGGGGTTHHHHHHHHHHHHHHHHHTTSEEEEEESS-TTTT
T ss_pred             hhhhhhhhcCCEEEEecchhhcCchHHHHHHHHHHHHHHhhCCeEEEEeCCCCccc
Confidence                 2678999999999998643 24566666666663 4567777776776654

DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; PDB: 2KJQ_A 2Z4S_A 2Z4R_C 2HCB_B 3R8F_C 1L8Q_A 3SC3_B 3BOS_A.

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

Probab=91.67  E-value=0.97  Score=43.08  Aligned_cols=69  Identities=13%  Similarity=0.179  Sum_probs=51.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.|.||.-+.++...+.+.     ++++..++||.+..+....+   ..+..+|||+|-.     +.  .++|..+|+
T Consensus       683 gIIYC~SRke~E~LAe~L~~~-----Gika~~YHAGLs~eeR~~vqe~F~~Gei~VLVATdA-----FG--MGIDkPDVR  750 (1195)
T PLN03137        683 GIIYCLSRMDCEKVAERLQEF-----GHKAAFYHGSMDPAQRAFVQKQWSKDEINIICATVA-----FG--MGINKPDVR  750 (1195)
T ss_pred             ceeEeCchhHHHHHHHHHHHC-----CCCeeeeeCCCCHHHHHHHHHHHhcCCCcEEEEech-----hh--cCCCccCCc
Confidence            589999999888887777654     78999999998876655433   2467899999952     22  467777777


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|-
T Consensus       751 ~VIH  754 (1195)
T PLN03137        751 FVIH  754 (1195)
T ss_pred             EEEE
Confidence            7763

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

Probab=91.59  E-value=1.1  Score=41.01  Aligned_cols=77  Identities=10%  Similarity=0.085  Sum_probs=55.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcC---CCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTL---PDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDF   74 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~---~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l   74 (203)
                      .+||.++||..+..+...+++.....   .+.++..++||...++..+   .+.++..++||+|..     +.  ..+|+
T Consensus       273 ~~IVF~~sr~~ae~l~~~l~~~l~~~~~~l~~~v~~~hgg~~~~eR~~ie~~f~~G~i~vLVaTd~-----le--rGIDI  345 (742)
T TIGR03817       273 RTLTFVRSRRGAELVAAIARRLLGEVDPDLAERVAAYRAGYLPEDRRELERALRDGELLGVATTNA-----LE--LGVDI  345 (742)
T ss_pred             CEEEEcCCHHHHHHHHHHHHHHHHhhccccccchhheecCCCHHHHHHHHHHHHcCCceEEEECch-----Hh--ccCCc
Confidence            47999999999999998887753221   1467888899988665544   344577899999962     22  46788


Q ss_pred             CCccEEEEcc
Q 028826           75 RNLVILVLDE   84 (203)
Q Consensus        75 ~~v~~lViDE   84 (203)
                      .+++.+|.-+
T Consensus       346 ~~vd~VI~~~  355 (742)
T TIGR03817       346 SGLDAVVIAG  355 (742)
T ss_pred             ccccEEEEeC
Confidence            8888777654

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.

>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional

Probab=91.42  E-value=1.2  Score=41.72  Aligned_cols=114  Identities=18%  Similarity=0.203  Sum_probs=61.6

Q ss_pred             EEEEcCcHHHHHHHHHHHH-----Hhhh-cCCC--ceEEEEEcCc-------chHHHHHHHHh-C-----CCeEEEeccH
Q 028826            2 GMIISPTRELSAQIYHVAQ-----PFIS-TLPD--VKSMLLVGGV-------EVKADVKKIEE-E-----GANLLIGTPG   60 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~-----~l~~-~~~~--i~~~~~~~g~-------~~~~~~~~l~~-~-----~~~ilV~Tp~   60 (203)
                      .||+||+.+.-..+...+.     .... .+.+  ++...+.++.       ......+.-.. .     ..+|+|.|-+
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            5899999888777766554     1111 1222  4444444432       11333332222 2     5899999999


Q ss_pred             HHHHH-H-HhC-------CC-cc---CCCcc-EEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecCh
Q 028826           61 RLYDI-M-ERM-------DV-LD---FRNLV-ILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (203)
Q Consensus        61 ~l~~~-~-~~~-------~~-~~---l~~v~-~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  119 (203)
                      .+..- . ...       +. ..   +...+ ++|+||.|++-..+  .....| ..+.+.. ++.||||.+.
T Consensus       172 a~n~~~~~~~~~D~~l~~g~~~p~~~i~~~~PivIiDEPh~~~~~~--k~~~~i-~~lnpl~-~lrysAT~~~  240 (986)
T PRK15483        172 MLNSASMTRDDYDQTLLGGFTSPVDALAATRPVVIIDEPHRFPRDN--KFYQAI-EALKPQM-IIRFGATFPD  240 (986)
T ss_pred             HhcccccccchhhhhhccCCCChHHHHHhCCCEEEEECCCCCCcch--HHHHHH-HhcCccc-EEEEeeecCC
Confidence            88641 1 110       01 11   22222 78999999984422  122333 4443222 4669999987

>PRK09694 helicase Cas3; Provisional

Probab=91.25  E-value=1.4  Score=41.16  Aligned_cols=74  Identities=15%  Similarity=0.258  Sum_probs=50.1

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHH---HH----H-HhCC---CeEEEeccHHHHHHHHhCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADV---KK----I-EEEG---ANLLIGTPGRLYDIMERMD   70 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~---~~----l-~~~~---~~ilV~Tp~~l~~~~~~~~   70 (203)
                      +||+++|.+-|.++++.+++....  +.++..++|.....+..   +.    . .++.   ..|||+|.     .+.  .
T Consensus       563 vLVf~NTV~~Aq~ly~~L~~~~~~--~~~v~llHsrf~~~dR~~~E~~vl~~fgk~g~r~~~~ILVaTQ-----ViE--~  633 (878)
T PRK09694        563 VCLICNLVDDAQKLYQRLKELNNT--QVDIDLFHARFTLNDRREKEQRVIENFGKNGKRNQGRILVATQ-----VVE--Q  633 (878)
T ss_pred             EEEEECCHHHHHHHHHHHHhhCCC--CceEEEEeCCCCHHHHHHHHHHHHHHHHhcCCcCCCeEEEECc-----chh--h
Confidence            689999999999999999875322  46889999986644331   11    1 1122   37999994     232  4


Q ss_pred             CccCCCccEEEEcch
Q 028826           71 VLDFRNLVILVLDEA   85 (203)
Q Consensus        71 ~~~l~~v~~lViDEa   85 (203)
                      ++|+ +++++|.|-+
T Consensus       634 GLDI-d~DvlItdla  647 (878)
T PRK09694        634 SLDL-DFDWLITQLC  647 (878)
T ss_pred             eeec-CCCeEEECCC
Confidence            6776 4778887753

>TIGR03158 cas3_cyano CRISPR-associated helicase, Cyano-type

Probab=91.20  E-value=1.7  Score=36.13  Aligned_cols=68  Identities=19%  Similarity=0.202  Sum_probs=49.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||+++|+.-+..++..+++..  . ++.+..++|.....++.+.   ...+|+|+|.     .+.  .++|+..+ .+|
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 4677778887776655433   3689999998     222  57888776 566


Q ss_pred             Ec
Q 028826           82 LD   83 (203)
Q Consensus        82 iD   83 (203)
                      +|
T Consensus       341 ~~  342 (357)
T TIGR03158       341 FS  342 (357)
T ss_pred             EC
Confidence            64

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.

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

Probab=91.00  E-value=3.5  Score=36.26  Aligned_cols=74  Identities=14%  Similarity=0.214  Sum_probs=58.1

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      .||.+-+.|-|.|++.++..    ++++++..++|..+..+..+.   ...+...++|+|-     ++.  +++|++++.
T Consensus       390 ~lIfVQs~eRak~L~~~L~~----~~~i~v~vIh~e~~~~qrde~~~~FR~g~IwvLicTd-----ll~--RGiDf~gvn  458 (593)
T KOG0344|consen  390 VLIFVQSKERAKQLFEELEI----YDNINVDVIHGERSQKQRDETMERFRIGKIWVLICTD-----LLA--RGIDFKGVN  458 (593)
T ss_pred             eEEEEecHHHHHHHHHHhhh----ccCcceeeEecccchhHHHHHHHHHhccCeeEEEehh-----hhh--ccccccCcc
Confidence            57888999999999998872    348999999999765554443   3447789999985     454  469999999


Q ss_pred             EEEEcchh
Q 028826           79 ILVLDEAD   86 (203)
Q Consensus        79 ~lViDEad   86 (203)
                      ++|-++.-
T Consensus       459 ~VInyD~p  466 (593)
T KOG0344|consen  459 LVINYDFP  466 (593)
T ss_pred             eEEecCCC
Confidence            99997754

>PHA02544 44 clamp loader, small subunit; Provisional

Probab=90.84  E-value=5.6  Score=32.19  Aligned_cols=41  Identities=17%  Similarity=0.136  Sum_probs=29.5

Q ss_pred             CCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEee
Q 028826           75 RNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSA  115 (203)
Q Consensus        75 ~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SA  115 (203)
                      ..-+++|+||+|.+-.......+..+++..+...++++.+.
T Consensus        99 ~~~~vliiDe~d~l~~~~~~~~L~~~le~~~~~~~~Ilt~n  139 (316)
T PHA02544         99 GGGKVIIIDEFDRLGLADAQRHLRSFMEAYSKNCSFIITAN  139 (316)
T ss_pred             CCCeEEEEECcccccCHHHHHHHHHHHHhcCCCceEEEEcC
Confidence            45789999999988333345667777888777777766554

>PF13401 AAA_22: AAA domain; PDB: 2QBY_B 1FNN_B 1W5T_A 1W5S_B

Probab=90.84  E-value=0.25  Score=34.29  Aligned_cols=36  Identities=31%  Similarity=0.477  Sum_probs=20.3

Q ss_pred             ccEEEEcchhHhhhhchHHHHHHHHHhC-CCCCcEEEEee
Q 028826           77 LVILVLDEADRLLDMGFQKQISYIISRL-PKLRRTGLFSA  115 (203)
Q Consensus        77 v~~lViDEad~l~~~~~~~~~~~il~~~-~~~~q~i~~SA  115 (203)
                      ..++|+||+|.+.+   .+.+..+.... ....++++++.
T Consensus        88 ~~~lviDe~~~l~~---~~~l~~l~~l~~~~~~~vvl~G~  124 (131)
T PF13401_consen   88 VVLLVIDEADHLFS---DEFLEFLRSLLNESNIKVVLVGT  124 (131)
T ss_dssp             EEEEEEETTHHHHT---HHHHHHHHHHTCSCBEEEEEEES
T ss_pred             CeEEEEeChHhcCC---HHHHHHHHHHHhCCCCeEEEEEC
Confidence            37999999999642   33333443333 23344555443

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

Probab=90.83  E-value=1.7  Score=36.36  Aligned_cols=116  Identities=14%  Similarity=0.140  Sum_probs=72.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      +++|+|-||.-|.-++..+..-     |-.|.+++|.....+....+   ..+...|+|+|.-.-       +++|...+
T Consensus       332 qsiIFc~tk~ta~~l~~~m~~~-----Gh~V~~l~G~l~~~~R~~ii~~Fr~g~~kVLitTnV~A-------RGiDv~qV  399 (477)
T KOG0332|consen  332 QSIIFCHTKATAMWLYEEMRAE-----GHQVSLLHGDLTVEQRAAIIDRFREGKEKVLITTNVCA-------RGIDVAQV  399 (477)
T ss_pred             heEEEEeehhhHHHHHHHHHhc-----CceeEEeeccchhHHHHHHHHHHhcCcceEEEEechhh-------cccccceE
Confidence            5899999999999888888775     67788889887766554433   346789999997332       68999999


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCC----CCcEEEEe---eecChhHHHHHHhcCC
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPK----LRRTGLFS---ATQTEAVEELSKAGLR  130 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~----~~q~i~~S---AT~~~~v~~~~~~~l~  130 (203)
                      .++|=  -|.-.+.+-.++....+.++.+    .+.-+.++   .-.+.++.+.+.+|+.
T Consensus       400 s~VvN--ydlP~~~~~~pD~etYlHRiGRtGRFGkkG~a~n~v~~~~s~~~mn~iq~~F~  457 (477)
T KOG0332|consen  400 SVVVN--YDLPVKYTGEPDYETYLHRIGRTGRFGKKGLAINLVDDKDSMNIMNKIQKHFN  457 (477)
T ss_pred             EEEEe--cCCccccCCCCCHHHHHHHhcccccccccceEEEeecccCcHHHHHHHHHHHh
Confidence            98884  2222222223444444555532    22233333   2233445555555554

>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda

Probab=90.66  E-value=4.2  Score=31.02  Aligned_cols=103  Identities=10%  Similarity=0.110  Sum_probs=50.1

Q ss_pred             HHHHHHHHhhhcCCCceEEEEEcCc--chHHHHHHHH----hCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhH
Q 028826           14 QIYHVAQPFISTLPDVKSMLLVGGV--EVKADVKKIE----EEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADR   87 (203)
Q Consensus        14 Qi~~~~~~l~~~~~~i~~~~~~~g~--~~~~~~~~l~----~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~   87 (203)
                      +....++++...- .-+...++|..  ....-...+.    ..+..++..+-..+...... -.-.+.+.+++++||+|.
T Consensus        24 ~~~~~l~~~~~~~-~~~~lll~G~~G~GKT~la~~~~~~~~~~~~~~~~i~~~~~~~~~~~-~~~~~~~~~lLvIDdi~~  101 (226)
T TIGR03420        24 ELLAALRQLAAGK-GDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLPLAELAQADPE-VLEGLEQADLVCLDDVEA  101 (226)
T ss_pred             HHHHHHHHHHhcC-CCCeEEEECCCCCCHHHHHHHHHHHHHhcCCcEEEEeHHHHHHhHHH-HHhhcccCCEEEEeChhh
Confidence            4444555543222 34556666643  3333333322    23456666655554332111 001134567999999998


Q ss_pred             hhhh-chHHHHHHHHHhCCCCCcEEEEeeecC
Q 028826           88 LLDM-GFQKQISYIISRLPKLRRTGLFSATQT  118 (203)
Q Consensus        88 l~~~-~~~~~~~~il~~~~~~~q~i~~SAT~~  118 (203)
                      +-.. .....+..++.........+++|++.+
T Consensus       102 l~~~~~~~~~L~~~l~~~~~~~~~iIits~~~  133 (226)
T TIGR03420       102 IAGQPEWQEALFHLYNRVREAGGRLLIAGRAA  133 (226)
T ss_pred             hcCChHHHHHHHHHHHHHHHcCCeEEEECCCC
Confidence            7532 225556666655432222455555544

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.

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

Probab=90.46  E-value=0.75  Score=41.09  Aligned_cols=81  Identities=21%  Similarity=0.328  Sum_probs=58.7

Q ss_pred             CEEEEcCcHHHH-----HHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCc
Q 028826            1 MGMIISPTRELS-----AQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVL   72 (203)
Q Consensus         1 ~alil~PtreLa-----~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~   72 (203)
                      ||.+|||--|-.     .-....+..+...+++.++..++|-.+..+....+   .++..||+|+|.-     + + =.+
T Consensus       475 QaY~VcPLIeESE~l~l~~a~~~~~~L~~~~~~~~vgL~HGrm~~~eKd~vM~~Fk~~e~~ILVaTTV-----I-E-VGV  547 (677)
T COG1200         475 QAYVVCPLIEESEKLELQAAEELYEELKSFLPELKVGLVHGRMKPAEKDAVMEAFKEGEIDILVATTV-----I-E-VGV  547 (677)
T ss_pred             EEEEEeccccccccchhhhHHHHHHHHHHHcccceeEEEecCCChHHHHHHHHHHHcCCCcEEEEeeE-----E-E-ecc
Confidence            577888874433     23345555565667789999999988766554433   3468999999972     2 2 468


Q ss_pred             cCCCccEEEEcchhHh
Q 028826           73 DFRNLVILVLDEADRL   88 (203)
Q Consensus        73 ~l~~v~~lViDEad~l   88 (203)
                      |+-+-.+.||..|+++
T Consensus       548 dVPnATvMVIe~AERF  563 (677)
T COG1200         548 DVPNATVMVIENAERF  563 (677)
T ss_pred             cCCCCeEEEEechhhh
Confidence            8999999999999987

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

Probab=90.41  E-value=6.3  Score=35.79  Aligned_cols=77  Identities=17%  Similarity=0.179  Sum_probs=47.6

Q ss_pred             CCeEEEeccHHHHH-HHHhCCCccCCCccEEEEcchhHhh-hhc-hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHh
Q 028826           51 GANLLIGTPGRLYD-IMERMDVLDFRNLVILVLDEADRLL-DMG-FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (203)
Q Consensus        51 ~~~ilV~Tp~~l~~-~~~~~~~~~l~~v~~lViDEad~l~-~~~-~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~  127 (203)
                      ...|=..|-+.|+. .+..   -+|.+-+.+|+||||.=. ..+ ....++.+++.- .+..+|+.|||+..  ..|.+.
T Consensus       445 ~T~IkymTDGiLLrEsL~d---~~L~kYSviImDEAHERslNtDilfGllk~~larR-rdlKliVtSATm~a--~kf~nf  518 (1042)
T KOG0924|consen  445 DTKIKYMTDGILLRESLKD---RDLDKYSVIIMDEAHERSLNTDILFGLLKKVLARR-RDLKLIVTSATMDA--QKFSNF  518 (1042)
T ss_pred             ceeEEEeccchHHHHHhhh---hhhhheeEEEechhhhcccchHHHHHHHHHHHHhh-ccceEEEeeccccH--HHHHHH
Confidence            34577889988875 3332   356788899999999631 111 122233333332 47789999999974  566665


Q ss_pred             cCCCCe
Q 028826          128 GLRNPV  133 (203)
Q Consensus       128 ~l~~~~  133 (203)
                      |.+-|.
T Consensus       519 Fgn~p~  524 (1042)
T KOG0924|consen  519 FGNCPQ  524 (1042)
T ss_pred             hCCCce
Confidence            544443

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

Probab=90.34  E-value=4.2  Score=37.20  Aligned_cols=98  Identities=15%  Similarity=0.251  Sum_probs=63.5

Q ss_pred             HHHHHHHHHHhhhcCCCceEEEEEcCcchHH-----HHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchh
Q 028826           12 SAQIYHVAQPFISTLPDVKSMLLVGGVEVKA-----DVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEAD   86 (203)
Q Consensus        12 a~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~-----~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad   86 (203)
                      ..++.+++.++   +|+.++..+.++.....     ......++..||||||+     |+.  +++++.++.++++=.||
T Consensus       493 terieeeL~~~---FP~~rv~r~d~Dtt~~k~~~~~~l~~~~~ge~dILiGTQ-----mia--KG~~fp~vtLVgvl~aD  562 (730)
T COG1198         493 TERIEEELKRL---FPGARIIRIDSDTTRRKGALEDLLDQFANGEADILIGTQ-----MIA--KGHDFPNVTLVGVLDAD  562 (730)
T ss_pred             HHHHHHHHHHH---CCCCcEEEEccccccchhhHHHHHHHHhCCCCCeeecch-----hhh--cCCCcccceEEEEEech
Confidence            34566666666   56788888888765432     23345568899999998     443  57999999999999999


Q ss_pred             Hhhhh-chH--HHHHHHHHhC----C---CCCcEEEEeeecCh
Q 028826           87 RLLDM-GFQ--KQISYIISRL----P---KLRRTGLFSATQTE  119 (203)
Q Consensus        87 ~l~~~-~~~--~~~~~il~~~----~---~~~q~i~~SAT~~~  119 (203)
                      .++.. +|+  +....++.+.    .   ...++++=|+....
T Consensus       563 ~~L~~~DfRA~Er~fqll~QvaGRAgR~~~~G~VvIQT~~P~h  605 (730)
T COG1198         563 TGLGSPDFRASERTFQLLMQVAGRAGRAGKPGEVVIQTYNPDH  605 (730)
T ss_pred             hhhcCCCcchHHHHHHHHHHHHhhhccCCCCCeEEEEeCCCCc
Confidence            98743 233  2333333333    2   23366666666543

>PRK14701 reverse gyrase; Provisional

Probab=90.32  E-value=0.73  Score=45.75  Aligned_cols=69  Identities=26%  Similarity=0.313  Sum_probs=47.9

Q ss_pred             CEEEEcCcHHHH---HHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEecc---HHHHHHHHhCCCccC
Q 028826            1 MGMIISPTRELS---AQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTP---GRLYDIMERMDVLDF   74 (203)
Q Consensus         1 ~alil~PtreLa---~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp---~~l~~~~~~~~~~~l   74 (203)
                      .+||.|||++-+   .++.+.+.+   .  |+++..++|+.  ....+...++..+|+|||.   +-+.      +++|+
T Consensus       332 ~gIVF~~t~~~~e~ae~la~~L~~---~--Gi~a~~~h~~R--~~~l~~F~~G~~~VLVaT~s~~gvaa------RGIDi  398 (1638)
T PRK14701        332 GGLIFVPIDEGAEKAEEIEKYLLE---D--GFKIELVSAKN--KKGFDLFEEGEIDYLIGVATYYGTLV------RGLDL  398 (1638)
T ss_pred             CeEEEEeccccchHHHHHHHHHHH---C--CCeEEEecchH--HHHHHHHHcCCCCEEEEecCCCCeeE------ecCcc
Confidence            368999998754   455554444   2  89999999872  3334455578899999995   2222      57887


Q ss_pred             CC-ccEEEE
Q 028826           75 RN-LVILVL   82 (203)
Q Consensus        75 ~~-v~~lVi   82 (203)
                      .+ |+++|+
T Consensus       399 P~~Vryvi~  407 (1638)
T PRK14701        399 PERIRFAVF  407 (1638)
T ss_pred             CCccCEEEE
Confidence            76 888887

>TIGR01587 cas3_core CRISPR-associated helicase Cas3

Probab=90.13  E-value=1.7  Score=35.87  Aligned_cols=72  Identities=18%  Similarity=0.272  Sum_probs=50.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH-------HHHhCCCeEEEeccHHHHHHHHhCCCccC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK-------KIEEEGANLLIGTPGRLYDIMERMDVLDF   74 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~-------~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l   74 (203)
                      +||+++|++-|..+++.+++...   +.++..++|+....+..+       ...++...|||+|.     .+.  .++|+
T Consensus       225 ~lVf~~t~~~~~~~~~~L~~~~~---~~~~~~~h~~~~~~~r~~~~~~~~~~f~~~~~~ilvaT~-----~~~--~GiDi  294 (358)
T TIGR01587       225 IAIIVNTVDRAQEFYQQLKENAP---EEEIMLLHSRFTEKDRAKKEAELLEEMKKNEKFVIVATQ-----VIE--ASLDI  294 (358)
T ss_pred             EEEEECCHHHHHHHHHHHHhhcC---CCeEEEEECCCCHHHHHHHHHHHHHHhcCCCCeEEEECc-----chh--ceecc
Confidence            79999999999988888876532   457889999976554432       23346788999997     222  46777


Q ss_pred             CCccEEEEcc
Q 028826           75 RNLVILVLDE   84 (203)
Q Consensus        75 ~~v~~lViDE   84 (203)
                       ++.++|.+.
T Consensus       295 -~~~~vi~~~  303 (358)
T TIGR01587       295 -SADVMITEL  303 (358)
T ss_pred             -CCCEEEEcC
Confidence             466766543

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.

>PRK12901 secA preprotein translocase subunit SecA; Reviewed

Probab=90.12  E-value=0.54  Score=44.14  Aligned_cols=83  Identities=17%  Similarity=0.148  Sum_probs=59.0

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcC-cchHHHHHHHHhCCCeEEEeccHHHH-HHHHhC-----CCccCC
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGG-VEVKADVKKIEEEGANLLIGTPGRLY-DIMERM-----DVLDFR   75 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g-~~~~~~~~~l~~~~~~ilV~Tp~~l~-~~~~~~-----~~~~l~   75 (203)
                      -||+.+--||..=.+++..+-.++ |+.++++... .+..+.. .  .-.+||..||..-+- ++++.+     ...-..
T Consensus       214 HvVTVNDYLA~RDaewmgply~fL-GLsvg~i~~~~~~~~~rr-~--aY~~DItYgTn~EfGFDYLRDnm~~~~~~~vqR  289 (1112)
T PRK12901        214 HVVTVNDYLAKRDSEWMGPLYEFH-GLSVDCIDKHQPNSEARR-K--AYNADITYGTNNEFGFDYLRDNMAHSPEDLVQR  289 (1112)
T ss_pred             EEEEechhhhhccHHHHHHHHHHh-CCceeecCCCCCCHHHHH-H--hCCCcceecCCCccccccchhccccchHhhhCc
Confidence            467777788887788888888888 9999988763 3433333 2  357999999998873 555541     111235


Q ss_pred             CccEEEEcchhHhh
Q 028826           76 NLVILVLDEADRLL   89 (203)
Q Consensus        76 ~v~~lViDEad~l~   89 (203)
                      ...+.||||+|.++
T Consensus       290 ~~~fAIVDEvDSIL  303 (1112)
T PRK12901        290 KHNYAIVDEVDSVL  303 (1112)
T ss_pred             CCceeEeechhhhh
Confidence            68899999999976

>PRK14087 dnaA chromosomal replication initiation protein; Provisional

Probab=90.00  E-value=3  Score=35.97  Aligned_cols=115  Identities=10%  Similarity=0.035  Sum_probs=62.1

Q ss_pred             EEcCcHHHHHHHHHHHHHhhhcC-CCceEEEEEcCcc--hHHHHHHHH------hCCCeEEEeccHHHHHHHHh---C--
Q 028826            4 IISPTRELSAQIYHVAQPFISTL-PDVKSMLLVGGVE--VKADVKKIE------EEGANLLIGTPGRLYDIMER---M--   69 (203)
Q Consensus         4 il~PtreLa~Qi~~~~~~l~~~~-~~i~~~~~~~g~~--~~~~~~~l~------~~~~~ilV~Tp~~l~~~~~~---~--   69 (203)
                      |+.|+.++|...   ++.++... ...+...++|+..  ..+-...+.      ..+..++..|++.+...+..   .  
T Consensus       118 v~g~~n~~A~~a---a~~~a~~~~~~~npl~i~G~~G~GKTHLl~Ai~~~l~~~~~~~~v~yv~~~~f~~~~~~~l~~~~  194 (450)
T PRK14087        118 VIGSSNEQAFIA---VQTVSKNPGISYNPLFIYGESGMGKTHLLKAAKNYIESNFSDLKVSYMSGDEFARKAVDILQKTH  194 (450)
T ss_pred             cCCCcHHHHHHH---HHHHHhCcCcccCceEEECCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHHHhh
Confidence            344555555433   33333321 1235567777543  333333321      23578889998887654432   0  


Q ss_pred             CCc-----cCCCccEEEEcchhHhhh-hchHHHHHHHHHhCC-CCCcEEEEeeecChhH
Q 028826           70 DVL-----DFRNLVILVLDEADRLLD-MGFQKQISYIISRLP-KLRRTGLFSATQTEAV  121 (203)
Q Consensus        70 ~~~-----~l~~v~~lViDEad~l~~-~~~~~~~~~il~~~~-~~~q~i~~SAT~~~~v  121 (203)
                      +.+     ...++++|++||+|.+-. ....+.+..++..+. ...|+++.|-..|...
T Consensus       195 ~~~~~~~~~~~~~dvLiIDDiq~l~~k~~~~e~lf~l~N~~~~~~k~iIltsd~~P~~l  253 (450)
T PRK14087        195 KEIEQFKNEICQNDVLIIDDVQFLSYKEKTNEIFFTIFNNFIENDKQLFFSSDKSPELL  253 (450)
T ss_pred             hHHHHHHHHhccCCEEEEeccccccCCHHHHHHHHHHHHHHHHcCCcEEEECCCCHHHH
Confidence            011     146788999999997743 224556666666653 3446666655544433

>PRK08903 DnaA regulatory inactivator Hda; Validated

Probab=89.67  E-value=7.7  Score=29.77  Aligned_cols=85  Identities=13%  Similarity=0.083  Sum_probs=48.9

Q ss_pred             ceEEEEEcCc--chHHHHHHH----HhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHhhhhchHHHHHHHHH
Q 028826           29 VKSMLLVGGV--EVKADVKKI----EEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIIS  102 (203)
Q Consensus        29 i~~~~~~~g~--~~~~~~~~l----~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~~~~~~~~~~~il~  102 (203)
                      -+...++|..  .+..-...+    ...+..+++.+...+...+..     ..+.+++++||+|.+-. .....+..++.
T Consensus        42 ~~~~~l~G~~G~GKT~La~ai~~~~~~~~~~~~~i~~~~~~~~~~~-----~~~~~~liiDdi~~l~~-~~~~~L~~~~~  115 (227)
T PRK08903         42 DRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDAASPLLAFDF-----DPEAELYAVDDVERLDD-AQQIALFNLFN  115 (227)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHhCCCcEEEEehHHhHHHHhh-----cccCCEEEEeChhhcCc-hHHHHHHHHHH
Confidence            4556677643  333333322    234567788777766543321     23567899999998743 33455666665


Q ss_pred             hCCCCCc-EEEEeeecCh
Q 028826          103 RLPKLRR-TGLFSATQTE  119 (203)
Q Consensus       103 ~~~~~~q-~i~~SAT~~~  119 (203)
                      ....... +++++++.++
T Consensus       116 ~~~~~~~~~vl~~~~~~~  133 (227)
T PRK08903        116 RVRAHGQGALLVAGPAAP  133 (227)
T ss_pred             HHHHcCCcEEEEeCCCCH
Confidence            5543443 4677777654

>PRK14088 dnaA chromosomal replication initiation protein; Provisional

Probab=89.27  E-value=7.3  Score=33.49  Aligned_cols=120  Identities=13%  Similarity=0.267  Sum_probs=62.3

Q ss_pred             EEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcc--hHHHHHHHH----h--CCCeEEEeccHHHHHHHHh-C--CCc
Q 028826            4 IISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVE--VKADVKKIE----E--EGANLLIGTPGRLYDIMER-M--DVL   72 (203)
Q Consensus         4 il~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~--~~~~~~~l~----~--~~~~ilV~Tp~~l~~~~~~-~--~~~   72 (203)
                      |+.|..++|...   +.+++......+...++|+..  ..+-...+.    .  .+..+++.|.+.+..-+.. .  +..
T Consensus       108 v~g~~n~~a~~~---~~~~~~~~~~~n~l~lyG~~G~GKTHLl~ai~~~l~~~~~~~~v~yi~~~~f~~~~~~~~~~~~~  184 (440)
T PRK14088        108 VVGPGNSFAYHA---ALEVAKNPGRYNPLFIYGGVGLGKTHLLQSIGNYVVQNEPDLRVMYITSEKFLNDLVDSMKEGKL  184 (440)
T ss_pred             ccCCchHHHHHH---HHHHHhCcCCCCeEEEEcCCCCcHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHhcccH
Confidence            345666665433   333333221245677887543  333333221    1  2457898888876543321 0  111


Q ss_pred             -c----C-CCccEEEEcchhHhhhhc-hHHHHHHHHHhCC-CCCcEEEEeeecChhHHHHHH
Q 028826           73 -D----F-RNLVILVLDEADRLLDMG-FQKQISYIISRLP-KLRRTGLFSATQTEAVEELSK  126 (203)
Q Consensus        73 -~----l-~~v~~lViDEad~l~~~~-~~~~~~~il~~~~-~~~q~i~~SAT~~~~v~~~~~  126 (203)
                       .    . .+.+++++||+|.+.+.. ....+..++..+. ...|+++.|..-|..+..+..
T Consensus       185 ~~f~~~~~~~~dvLlIDDi~~l~~~~~~q~elf~~~n~l~~~~k~iIitsd~~p~~l~~l~~  246 (440)
T PRK14088        185 NEFREKYRKKVDVLLIDDVQFLIGKTGVQTELFHTFNELHDSGKQIVICSDREPQKLSEFQD  246 (440)
T ss_pred             HHHHHHHHhcCCEEEEechhhhcCcHHHHHHHHHHHHHHHHcCCeEEEECCCCHHHHHHHHH
Confidence             0    1 257899999999886432 3345555555443 345666655555555444433

>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=88.91  E-value=0.28  Score=36.26  Aligned_cols=41  Identities=29%  Similarity=0.400  Sum_probs=25.7

Q ss_pred             CCCeEEEeccHHHHHHHHh--CCCccCCCccEEEEcchhHhhhh
Q 028826           50 EGANLLIGTPGRLYDIMER--MDVLDFRNLVILVLDEADRLLDM   91 (203)
Q Consensus        50 ~~~~ilV~Tp~~l~~~~~~--~~~~~l~~v~~lViDEad~l~~~   91 (203)
                      ..+||||++-.-|.+-...  ...+++. -.++||||||.+.+.
T Consensus       118 ~~adivi~~y~yl~~~~~~~~~~~~~~~-~~ivI~DEAHNL~~~  160 (174)
T PF06733_consen  118 KNADIVICNYNYLFDPSIRKSLFGIDLK-DNIVIFDEAHNLEDA  160 (174)
T ss_dssp             GG-SEEEEETHHHHSHHHHHHHCT--CC-CEEEEETTGGGCGGG
T ss_pred             ccCCEEEeCHHHHhhHHHHhhhcccccc-CcEEEEecccchHHH
Confidence            4589999998877653322  0113333 369999999998653

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.

>PF05621 TniB: Bacterial TniB protein; InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins

Probab=88.85  E-value=0.58  Score=37.90  Aligned_cols=40  Identities=18%  Similarity=0.161  Sum_probs=28.3

Q ss_pred             CCCccEEEEcchhHhhhhc--hHHHHHHHHHhCCCCCcEEEE
Q 028826           74 FRNLVILVLDEADRLLDMG--FQKQISYIISRLPKLRRTGLF  113 (203)
Q Consensus        74 l~~v~~lViDEad~l~~~~--~~~~~~~il~~~~~~~q~i~~  113 (203)
                      --+++++||||+|.++...  -.......++.+.+.-++-++
T Consensus       143 ~~~vrmLIIDE~H~lLaGs~~~qr~~Ln~LK~L~NeL~ipiV  184 (302)
T PF05621_consen  143 RLGVRMLIIDEFHNLLAGSYRKQREFLNALKFLGNELQIPIV  184 (302)
T ss_pred             HcCCcEEEeechHHHhcccHHHHHHHHHHHHHHhhccCCCeE
Confidence            3579999999999998665  344555667777766665333

TniB is a probable ATP-binding protein [] which is involved in Tn5053 mercury resistance transposition [].

>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]

Probab=88.78  E-value=1.2  Score=36.14  Aligned_cols=55  Identities=15%  Similarity=0.142  Sum_probs=38.6

Q ss_pred             CCCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecC---hhHHHHHHhcC
Q 028826           74 FRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT---EAVEELSKAGL  129 (203)
Q Consensus        74 l~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~---~~v~~~~~~~l  129 (203)
                      ....+.+|+||+|.|.+. -...+++.++..++...+++...-++   ..+.....+|.
T Consensus       127 ~~~fKiiIlDEcdsmtsd-aq~aLrr~mE~~s~~trFiLIcnylsrii~pi~SRC~Kfr  184 (346)
T KOG0989|consen  127 CPPFKIIILDECDSMTSD-AQAALRRTMEDFSRTTRFILICNYLSRIIRPLVSRCQKFR  184 (346)
T ss_pred             CCcceEEEEechhhhhHH-HHHHHHHHHhccccceEEEEEcCChhhCChHHHhhHHHhc
Confidence            455699999999999654 46778888888888888888766643   33443444443

>KOG0926 consensus DEAH-box RNA helicase [RNA processing and modification; Translation, ribosomal structure and biogenesis]

Probab=88.75  E-value=1.1  Score=41.16  Aligned_cols=129  Identities=19%  Similarity=0.249  Sum_probs=70.8

Q ss_pred             CCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHhh-h----hchHHHHHHHHHhCCC------CCcEEEEeeecC
Q 028826           50 EGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLL-D----MGFQKQISYIISRLPK------LRRTGLFSATQT  118 (203)
Q Consensus        50 ~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~-~----~~~~~~~~~il~~~~~------~~q~i~~SAT~~  118 (203)
                      ....|-++|-|-|+.=+.+  .+-+..-+.+|+||||.=. .    -|....+-.+.....+      .-..|+.|||+-
T Consensus       348 e~T~IkFMTDGVLLrEi~~--DflL~kYSvIIlDEAHERSvnTDILiGmLSRiV~LR~k~~ke~~~~kpLKLIIMSATLR  425 (1172)
T KOG0926|consen  348 EDTSIKFMTDGVLLREIEN--DFLLTKYSVIILDEAHERSVNTDILIGMLSRIVPLRQKYYKEQCQIKPLKLIIMSATLR  425 (1172)
T ss_pred             CCceeEEecchHHHHHHHH--hHhhhhceeEEechhhhccchHHHHHHHHHHHHHHHHHHhhhhcccCceeEEEEeeeEE
Confidence            3467999999999887764  5667888999999999621 0    1222222222233322      345899999984


Q ss_pred             hhHHHHHH-h-cCC-CCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCC----CcHHHHHHHHhcCCCCeEE
Q 028826          119 EAVEELSK-A-GLR-NPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESD----KKPSQLVDLLIKNKSKKII  191 (203)
Q Consensus       119 ~~v~~~~~-~-~l~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~----~k~~~l~~ll~~~~~~~~l  191 (203)
                        +.+|.+ + .++ -|-.+.++..                +-|  +...|-.-...    +-+.....+=+..+.+-+|
T Consensus       426 --VsDFtenk~LFpi~pPlikVdAR----------------QfP--VsIHF~krT~~DYi~eAfrKtc~IH~kLP~G~IL  485 (1172)
T KOG0926|consen  426 --VSDFTENKRLFPIPPPLIKVDAR----------------QFP--VSIHFNKRTPDDYIAEAFRKTCKIHKKLPPGGIL  485 (1172)
T ss_pred             --ecccccCceecCCCCceeeeecc----------------cCc--eEEEeccCCCchHHHHHHHHHHHHhhcCCCCcEE
Confidence              344442 1 222 2225555443                122  22233222221    1223333333466788899


Q ss_pred             EEeccCCcc
Q 028826          192 MYVQHGNFS  200 (203)
Q Consensus       192 IF~ns~~~~  200 (203)
                      ||+.-.+.+
T Consensus       486 VFvTGQqEV  494 (1172)
T KOG0926|consen  486 VFVTGQQEV  494 (1172)
T ss_pred             EEEeChHHH
Confidence            999765443

>PRK04914 ATP-dependent helicase HepA; Validated

Probab=88.26  E-value=3.2  Score=39.23  Aligned_cols=70  Identities=14%  Similarity=0.210  Sum_probs=53.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHh-----CCCeEEEeccHHHHHHHHhCCCccCCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEE-----EGANLLIGTPGRLYDIMERMDVLDFRN   76 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~-----~~~~ilV~Tp~~l~~~~~~~~~~~l~~   76 (203)
                      +||++.+++-+..+.+.++..   . |+++..++||.+..+..+.+..     +++.|+|+|- .     -. .++++..
T Consensus       496 vLVF~~~~~t~~~L~~~L~~~---~-Gi~~~~ihG~~s~~eR~~~~~~F~~~~~~~~VLIsTd-v-----gs-eGlNlq~  564 (956)
T PRK04914        496 VLVICAKAATALQLEQALRER---E-GIRAAVFHEGMSIIERDRAAAYFADEEDGAQVLLCSE-I-----GS-EGRNFQF  564 (956)
T ss_pred             EEEEeCcHHHHHHHHHHHhhc---c-CeeEEEEECCCCHHHHHHHHHHHhcCCCCccEEEech-h-----hc-cCCCccc
Confidence            689999999999998888543   2 7899999999987766665421     2589999983 2     12 5788888


Q ss_pred             ccEEEE
Q 028826           77 LVILVL   82 (203)
Q Consensus        77 v~~lVi   82 (203)
                      ++++|.
T Consensus       565 a~~VIn  570 (956)
T PRK04914        565 ASHLVL  570 (956)
T ss_pred             ccEEEE
Confidence            888876

>PHA02558 uvsW UvsW helicase; Provisional

Probab=88.14  E-value=2.8  Score=36.56  Aligned_cols=71  Identities=13%  Similarity=0.202  Sum_probs=51.1

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      .+|++...+=+..+.+.+++.     +.++..++|+.+.++....+   .++...+||+|-+.+.      .++|+.+++
T Consensus       347 ~lV~~~~~~h~~~L~~~L~~~-----g~~v~~i~G~~~~~eR~~i~~~~~~~~~~vLvaT~~~l~------eG~Dip~ld  415 (501)
T PHA02558        347 TFVMFKYVEHGKPLYEMLKKV-----YDKVYYVSGEVDTEDRNEMKKIAEGGKGIIIVASYGVFS------TGISIKNLH  415 (501)
T ss_pred             EEEEEEEHHHHHHHHHHHHHc-----CCCEEEEeCCCCHHHHHHHHHHHhCCCCeEEEEEcceec------ccccccccc
Confidence            477888877777666666663     67899999998766554422   2244578999876654      578999999


Q ss_pred             EEEEc
Q 028826           79 ILVLD   83 (203)
Q Consensus        79 ~lViD   83 (203)
                      .+|+.
T Consensus       416 ~vIl~  420 (501)
T PHA02558        416 HVIFA  420 (501)
T ss_pred             EEEEe
Confidence            99974

>TIGR00362 DnaA chromosomal replication initiator protein DnaA

Probab=88.08  E-value=4.4  Score=34.23  Aligned_cols=115  Identities=13%  Similarity=0.188  Sum_probs=58.4

Q ss_pred             EcCcHHHHHHHHHHHHHhhhcC-CCceEEEEEcCcc--hHHHHHHH----HhC--CCeEEEeccHHHHHHHHh---CCCc
Q 028826            5 ISPTRELSAQIYHVAQPFISTL-PDVKSMLLVGGVE--VKADVKKI----EEE--GANLLIGTPGRLYDIMER---MDVL   72 (203)
Q Consensus         5 l~PtreLa~Qi~~~~~~l~~~~-~~i~~~~~~~g~~--~~~~~~~l----~~~--~~~ilV~Tp~~l~~~~~~---~~~~   72 (203)
                      +.+...+|......   ++... ...+...++|+..  ...-...+    ...  +..++..|.+.+...+..   .+..
T Consensus       114 ~g~~n~~a~~~~~~---~~~~~~~~~n~l~l~G~~G~GKThL~~ai~~~l~~~~~~~~v~yi~~~~~~~~~~~~~~~~~~  190 (405)
T TIGR00362       114 VGKSNRLAHAAALA---VAENPGKAYNPLFIYGGVGLGKTHLLHAIGNEILENNPNAKVVYVSSEKFTNDFVNALRNNKM  190 (405)
T ss_pred             cCCcHHHHHHHHHH---HHhCcCccCCeEEEECCCCCcHHHHHHHHHHHHHHhCCCCcEEEEEHHHHHHHHHHHHHcCCH
Confidence            34555555544333   33321 1235567777543  33333322    122  567888888775532211   0111


Q ss_pred             -----cCCCccEEEEcchhHhhhhc-hHHHHHHHHHhC-CCCCcEEEEeeecChhHH
Q 028826           73 -----DFRNLVILVLDEADRLLDMG-FQKQISYIISRL-PKLRRTGLFSATQTEAVE  122 (203)
Q Consensus        73 -----~l~~v~~lViDEad~l~~~~-~~~~~~~il~~~-~~~~q~i~~SAT~~~~v~  122 (203)
                           .+.+.++|++||+|.+.... ..+.+..++..+ ....|+++.|...|..+.
T Consensus       191 ~~~~~~~~~~dlLiiDDi~~l~~~~~~~~~l~~~~n~~~~~~~~iiits~~~p~~l~  247 (405)
T TIGR00362       191 EEFKEKYRSVDLLLIDDIQFLAGKERTQEEFFHTFNALHENGKQIVLTSDRPPKELP  247 (405)
T ss_pred             HHHHHHHHhCCEEEEehhhhhcCCHHHHHHHHHHHHHHHHCCCCEEEecCCCHHHHh
Confidence                 14567899999999875432 234455555444 244666655444444443

DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).

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

Probab=87.94  E-value=4.8  Score=33.44  Aligned_cols=107  Identities=21%  Similarity=0.269  Sum_probs=72.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCc-chHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGV-EVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~-~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+|.+|+-+-+.|....+++-   ++..++.++++.. ...++..+..++..+++|+|.     .+.  ++.-+.+++.+
T Consensus       308 ~liF~p~I~~~eq~a~~lk~~---~~~~~i~~Vhs~d~~R~EkV~~fR~G~~~lLiTTT-----ILE--RGVTfp~vdV~  377 (441)
T COG4098         308 VLIFFPEIETMEQVAAALKKK---LPKETIASVHSEDQHRKEKVEAFRDGKITLLITTT-----ILE--RGVTFPNVDVF  377 (441)
T ss_pred             EEEEecchHHHHHHHHHHHhh---CCccceeeeeccCccHHHHHHHHHcCceEEEEEee-----hhh--cccccccceEE
Confidence            589999999999998888553   3355666666643 466777788888999999997     333  57888999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCC-----CCcEEEEeeecChhH
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPK-----LRRTGLFSATQTEAV  121 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~-----~~q~i~~SAT~~~~v  121 (203)
                      |++-=|.++..   ..+-.|..+..+     .--+++|---.+.++
T Consensus       378 Vlgaeh~vfTe---saLVQIaGRvGRs~~~PtGdv~FFH~G~skaM  420 (441)
T COG4098         378 VLGAEHRVFTE---SALVQIAGRVGRSLERPTGDVLFFHYGKSKAM  420 (441)
T ss_pred             EecCCcccccH---HHHHHHhhhccCCCcCCCCcEEEEeccchHHH
Confidence            99988877543   233344444322     224555544444443

>PRK05986 cob(I)alamin adenolsyltransferase/cobinamide ATP-dependent adenolsyltransferase; Validated

Probab=87.81  E-value=9.6  Score=28.86  Aligned_cols=54  Identities=15%  Similarity=0.220  Sum_probs=45.6

Q ss_pred             CCCccEEEEcchhHhhhhch--HHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHh
Q 028826           74 FRNLVILVLDEADRLLDMGF--QKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (203)
Q Consensus        74 l~~v~~lViDEad~l~~~~~--~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~  127 (203)
                      -...+++|+||+-..++.|+  .+++..++..-|...-+|+..-..|+++.++++.
T Consensus       113 ~~~ydlvVLDEi~~Al~~gli~~eevi~~L~~rp~~~evVlTGR~~p~~Lie~ADl  168 (191)
T PRK05986        113 DESYDLVVLDELTYALKYGYLDVEEVLEALNARPGMQHVVITGRGAPRELIEAADL  168 (191)
T ss_pred             CCCCCEEEEehhhHHHHCCCccHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCch
Confidence            35788999999998888884  6778888888888889999999999988887774

>PRK06893 DNA replication initiation factor; Validated

Probab=87.78  E-value=1.4  Score=34.26  Aligned_cols=90  Identities=11%  Similarity=0.094  Sum_probs=50.2

Q ss_pred             eEEEEEcCc--chHHHHHHHH----hCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHhhh-hchHHHHHHHHH
Q 028826           30 KSMLLVGGV--EVKADVKKIE----EEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIIS  102 (203)
Q Consensus        30 ~~~~~~~g~--~~~~~~~~l~----~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~~-~~~~~~~~~il~  102 (203)
                      ...+++|..  .+.+-...+.    ..+..+.+.+.......... -.-.+.+.+++++||+|.+.. ......+..++.
T Consensus        40 ~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~y~~~~~~~~~~~~-~~~~~~~~dlLilDDi~~~~~~~~~~~~l~~l~n  118 (229)
T PRK06893         40 PFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLSKSQYFSPA-VLENLEQQDLVCLDDLQAVIGNEEWELAIFDLFN  118 (229)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCCeEEeeHHHhhhhhHH-HHhhcccCCEEEEeChhhhcCChHHHHHHHHHHH
Confidence            445677643  3444333332    24567777776543322211 111356788999999998753 223445666666


Q ss_pred             hCCC-CCcEEEEeeecChh
Q 028826          103 RLPK-LRRTGLFSATQTEA  120 (203)
Q Consensus       103 ~~~~-~~q~i~~SAT~~~~  120 (203)
                      .... ..+++++|++.++.
T Consensus       119 ~~~~~~~~illits~~~p~  137 (229)
T PRK06893        119 RIKEQGKTLLLISADCSPH  137 (229)
T ss_pred             HHHHcCCcEEEEeCCCChH
Confidence            5543 44667777777554

>KOG2170 consensus ATPase of the AAA+ superfamily [General function prediction only]

Probab=87.70  E-value=0.73  Score=37.35  Aligned_cols=57  Identities=14%  Similarity=0.242  Sum_probs=41.2

Q ss_pred             cCCCccEEEEcchhHhhhhchHHHHHHHHHhCC-------CCCcEEEEeeecChhHHHHHHhcCC
Q 028826           73 DFRNLVILVLDEADRLLDMGFQKQISYIISRLP-------KLRRTGLFSATQTEAVEELSKAGLR  130 (203)
Q Consensus        73 ~l~~v~~lViDEad~l~~~~~~~~~~~il~~~~-------~~~q~i~~SAT~~~~v~~~~~~~l~  130 (203)
                      ....=+++|+||+|.| ..|..+.+.-.+.+.|       +..-+|++|.+-..++.+.+-.+++
T Consensus       175 ~~C~rslFIFDE~DKm-p~gLld~lkpfLdyyp~v~gv~frkaIFIfLSN~gg~eI~~~aL~~~~  238 (344)
T KOG2170|consen  175 QACQRSLFIFDEVDKL-PPGLLDVLKPFLDYYPQVSGVDFRKAIFIFLSNAGGSEIARIALENAR  238 (344)
T ss_pred             HhcCCceEEechhhhc-CHhHHHHHhhhhccccccccccccceEEEEEcCCcchHHHHHHHHHHH
Confidence            3455679999999998 4556777777777654       4567899998888777765554443

>PRK00149 dnaA chromosomal replication initiation protein; Reviewed

Probab=87.70  E-value=4.1  Score=35.04  Aligned_cols=94  Identities=16%  Similarity=0.255  Sum_probs=50.3

Q ss_pred             ceEEEEEcCcc--hHHHHHHHH----hC--CCeEEEeccHHHHHHHHh-C--CCc-----cCCCccEEEEcchhHhhhhc
Q 028826           29 VKSMLLVGGVE--VKADVKKIE----EE--GANLLIGTPGRLYDIMER-M--DVL-----DFRNLVILVLDEADRLLDMG   92 (203)
Q Consensus        29 i~~~~~~~g~~--~~~~~~~l~----~~--~~~ilV~Tp~~l~~~~~~-~--~~~-----~l~~v~~lViDEad~l~~~~   92 (203)
                      .+...++|+..  ...-...+.    ..  +..++..|.+.+..-+.. .  +..     .+.++++|++||+|.+....
T Consensus       148 ~~~l~l~G~~G~GKThL~~ai~~~~~~~~~~~~v~yi~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlLiiDDi~~l~~~~  227 (450)
T PRK00149        148 YNPLFIYGGVGLGKTHLLHAIGNYILEKNPNAKVVYVTSEKFTNDFVNALRNNTMEEFKEKYRSVDVLLIDDIQFLAGKE  227 (450)
T ss_pred             CCeEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEEEHHHHHHHHHHHHHcCcHHHHHHHHhcCCEEEEehhhhhcCCH
Confidence            45567777543  333333321    22  567888888776543221 0  111     24568899999999875432


Q ss_pred             -hHHHHHHHHHhCC-CCCcEEEEeeecChhHH
Q 028826           93 -FQKQISYIISRLP-KLRRTGLFSATQTEAVE  122 (203)
Q Consensus        93 -~~~~~~~il~~~~-~~~q~i~~SAT~~~~v~  122 (203)
                       ..+.+..++..+. ...|+++.|...|..+.
T Consensus       228 ~~~~~l~~~~n~l~~~~~~iiits~~~p~~l~  259 (450)
T PRK00149        228 RTQEEFFHTFNALHEAGKQIVLTSDRPPKELP  259 (450)
T ss_pred             HHHHHHHHHHHHHHHCCCcEEEECCCCHHHHH
Confidence             2344555554442 34566555544444433

>TIGR00708 cobA cob(I)alamin adenosyltransferase

Probab=87.51  E-value=1.5  Score=32.58  Aligned_cols=54  Identities=17%  Similarity=0.164  Sum_probs=45.5

Q ss_pred             CCCccEEEEcchhHhhhhc--hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHh
Q 028826           74 FRNLVILVLDEADRLLDMG--FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (203)
Q Consensus        74 l~~v~~lViDEad~l~~~~--~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~  127 (203)
                      -.+.+++|+||+-..++.|  -.+++..+++.-|...-+|+.+-..|+.+.++++.
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            3578899999998888887  46677888888888889999999999988888773

Alternate name: corrinoid adenosyltransferase.

>cd00561 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP

Probab=87.41  E-value=1.6  Score=32.04  Aligned_cols=55  Identities=15%  Similarity=0.157  Sum_probs=45.7

Q ss_pred             cCCCccEEEEcchhHhhhhc--hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHh
Q 028826           73 DFRNLVILVLDEADRLLDMG--FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (203)
Q Consensus        73 ~l~~v~~lViDEad~l~~~~--~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~  127 (203)
                      .....+++|+||+-..++.+  -.+++..+++.-|...-+|+.+-..|+++.++++.
T Consensus        92 ~~~~~dLlVLDEi~~a~~~gli~~~~v~~ll~~rp~~~evIlTGr~~p~~l~e~AD~  148 (159)
T cd00561          92 ASGEYDLVILDEINYALGYGLLDVEEVVDLLKAKPEDLELVLTGRNAPKELIEAADL  148 (159)
T ss_pred             hcCCCCEEEEechHhHhhCCCCCHHHHHHHHHcCCCCCEEEEECCCCCHHHHHhCce
Confidence            34678999999998887777  46778888888888889999999999988887763

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.

>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]

Probab=87.05  E-value=8.4  Score=32.75  Aligned_cols=117  Identities=14%  Similarity=0.217  Sum_probs=73.8

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcc--hHHHHHHH----Hh--CCCeEEEeccHHHHH-HHHhC--CC
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVE--VKADVKKI----EE--EGANLLIGTPGRLYD-IMERM--DV   71 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~--~~~~~~~l----~~--~~~~ilV~Tp~~l~~-~~~~~--~~   71 (203)
                      .|+.|+-.+|.-+...+.+-.+.  ......++||..  ..+-...+    .+  .++.++..|.+.+.. ++...  +.
T Consensus        89 Fv~g~~N~~A~aa~~~va~~~g~--~~nplfi~G~~GlGKTHLl~Aign~~~~~~~~a~v~y~~se~f~~~~v~a~~~~~  166 (408)
T COG0593          89 FVVGPSNRLAYAAAKAVAENPGG--AYNPLFIYGGVGLGKTHLLQAIGNEALANGPNARVVYLTSEDFTNDFVKALRDNE  166 (408)
T ss_pred             eeeCCchHHHHHHHHHHHhccCC--cCCcEEEECCCCCCHHHHHHHHHHHHHhhCCCceEEeccHHHHHHHHHHHHHhhh
Confidence            46788888887666666554322  367788888764  33333322    12  235889999988753 22210  11


Q ss_pred             c-----cCCCccEEEEcchhHhhhh-chHHHHHHHHHhCCC-CCcEEEEeeecChhHH
Q 028826           72 L-----DFRNLVILVLDEADRLLDM-GFQKQISYIISRLPK-LRRTGLFSATQTEAVE  122 (203)
Q Consensus        72 ~-----~l~~v~~lViDEad~l~~~-~~~~~~~~il~~~~~-~~q~i~~SAT~~~~v~  122 (203)
                      .     .. ++++++||+++.+-.. ...+.+.+++..+.. ..|+++.|...|.++.
T Consensus       167 ~~~Fk~~y-~~dlllIDDiq~l~gk~~~qeefFh~FN~l~~~~kqIvltsdr~P~~l~  223 (408)
T COG0593         167 MEKFKEKY-SLDLLLIDDIQFLAGKERTQEEFFHTFNALLENGKQIVLTSDRPPKELN  223 (408)
T ss_pred             HHHHHHhh-ccCeeeechHhHhcCChhHHHHHHHHHHHHHhcCCEEEEEcCCCchhhc
Confidence            1     12 7999999999988543 357777777777753 3488888877777654

>PRK08084 DNA replication initiation factor; Provisional

Probab=86.97  E-value=6.2  Score=30.69  Aligned_cols=90  Identities=8%  Similarity=0.039  Sum_probs=47.3

Q ss_pred             CceEEEEEcCc--chHHHHHH----HHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHhhh-hchHHHHHHH
Q 028826           28 DVKSMLLVGGV--EVKADVKK----IEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYI  100 (203)
Q Consensus        28 ~i~~~~~~~g~--~~~~~~~~----l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~~-~~~~~~~~~i  100 (203)
                      +.....++|..  .+.+-...    +...+..+.+.+.+........ -.-.+.+..++++||+|.+-. ....+.+.++
T Consensus        44 ~~~~l~l~Gp~G~GKThLl~a~~~~~~~~~~~v~y~~~~~~~~~~~~-~~~~~~~~dlliiDdi~~~~~~~~~~~~lf~l  122 (235)
T PRK08084         44 HSGYIYLWSREGAGRSHLLHAACAELSQRGRAVGYVPLDKRAWFVPE-VLEGMEQLSLVCIDNIECIAGDELWEMAIFDL  122 (235)
T ss_pred             CCCeEEEECCCCCCHHHHHHHHHHHHHhCCCeEEEEEHHHHhhhhHH-HHHHhhhCCEEEEeChhhhcCCHHHHHHHHHH
Confidence            34567778753  33333332    2234567777777664332211 000134467999999998753 2345556666


Q ss_pred             HHhCCC--CCcEEEEeeecCh
Q 028826          101 ISRLPK--LRRTGLFSATQTE  119 (203)
Q Consensus       101 l~~~~~--~~q~i~~SAT~~~  119 (203)
                      +.....  ..++++.|. .|+
T Consensus       123 ~n~~~e~g~~~li~ts~-~~p  142 (235)
T PRK08084        123 YNRILESGRTRLLITGD-RPP  142 (235)
T ss_pred             HHHHHHcCCCeEEEeCC-CCh
Confidence            655432  235555544 443

>PRK11131 ATP-dependent RNA helicase HrpA; Provisional

Probab=86.81  E-value=3.4  Score=40.17  Aligned_cols=71  Identities=8%  Similarity=0.136  Sum_probs=54.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHh-CCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEE-EGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~-~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +||.+|+++-+..+.+.+++..  .+...+..++|+.+..++.+.... +...|||+|.     .. . .++++.+++++
T Consensus       289 ILVFLpg~~EIe~lae~L~~~~--~~~~~VlpLhg~Ls~~eQ~~Vf~~~g~rkIIVATN-----IA-E-tSITIpgI~yV  359 (1294)
T PRK11131        289 ILIFMSGEREIRDTADALNKLN--LRHTEILPLYARLSNSEQNRVFQSHSGRRIVLATN-----VA-E-TSLTVPGIKYV  359 (1294)
T ss_pred             EEEEcCCHHHHHHHHHHHHhcC--CCcceEeecccCCCHHHHHHHhcccCCeeEEEecc-----HH-h-hccccCcceEE
Confidence            6899999998888888777642  335668889999988877765532 3568999998     22 3 68999999988


Q ss_pred             E
Q 028826           81 V   81 (203)
Q Consensus        81 V   81 (203)
                      |
T Consensus       360 I  360 (1294)
T PRK11131        360 I  360 (1294)
T ss_pred             E
Confidence            7

>PRK14086 dnaA chromosomal replication initiation protein; Provisional

Probab=86.67  E-value=5.9  Score=35.50  Aligned_cols=93  Identities=14%  Similarity=0.159  Sum_probs=54.1

Q ss_pred             ceEEEEEcCc--chHHHHHHHHh------CCCeEEEeccHHHHHHH-Hh--CCCc-----cCCCccEEEEcchhHhhhhc
Q 028826           29 VKSMLLVGGV--EVKADVKKIEE------EGANLLIGTPGRLYDIM-ER--MDVL-----DFRNLVILVLDEADRLLDMG   92 (203)
Q Consensus        29 i~~~~~~~g~--~~~~~~~~l~~------~~~~ilV~Tp~~l~~~~-~~--~~~~-----~l~~v~~lViDEad~l~~~~   92 (203)
                      .+..+++|+.  .+.+-...+.+      .+..++..|.+.+..-+ ..  .+..     .+.++++|+|||+|.+....
T Consensus       314 ~NpL~LyG~sGsGKTHLL~AIa~~a~~~~~g~~V~Yitaeef~~el~~al~~~~~~~f~~~y~~~DLLlIDDIq~l~gke  393 (617)
T PRK14086        314 YNPLFIYGESGLGKTHLLHAIGHYARRLYPGTRVRYVSSEEFTNEFINSIRDGKGDSFRRRYREMDILLVDDIQFLEDKE  393 (617)
T ss_pred             CCcEEEECCCCCCHHHHHHHHHHHHHHhCCCCeEEEeeHHHHHHHHHHHHHhccHHHHHHHhhcCCEEEEehhccccCCH
Confidence            3456777743  34444433321      25788888888765332 21  0111     14578999999999885432


Q ss_pred             -hHHHHHHHHHhCCC-CCcEEEEeeecChhH
Q 028826           93 -FQKQISYIISRLPK-LRRTGLFSATQTEAV  121 (203)
Q Consensus        93 -~~~~~~~il~~~~~-~~q~i~~SAT~~~~v  121 (203)
                       ..+.+.+++..+.. ..|+|+.|-..|..+
T Consensus       394 ~tqeeLF~l~N~l~e~gk~IIITSd~~P~eL  424 (617)
T PRK14086        394 STQEEFFHTFNTLHNANKQIVLSSDRPPKQL  424 (617)
T ss_pred             HHHHHHHHHHHHHHhcCCCEEEecCCChHhh
Confidence             34556666666643 567777665555444

>PRK09751 putative ATP-dependent helicase Lhr; Provisional

Probab=86.38  E-value=5.3  Score=39.56  Aligned_cols=75  Identities=9%  Similarity=0.116  Sum_probs=49.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhc----------------------------CCCceEEEEEcCcchHHHHH---HHHh
Q 028826            1 MGMIISPTRELSAQIYHVAQPFIST----------------------------LPDVKSMLLVGGVEVKADVK---KIEE   49 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~----------------------------~~~i~~~~~~~g~~~~~~~~---~l~~   49 (203)
                      .+||+++||..|..+...++++...                            .+...+...+||.+.++...   .+++
T Consensus       246 stLVFvNSR~~AE~La~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ia~~HHGsLSkeeR~~IE~~fK~  325 (1490)
T PRK09751        246 STIVFTNSRGLAEKLTARLNELYAARLQRSPSIAVDAAHFESTSGATSNRVQSSDVFIARSHHGSVSKEQRAITEQALKS  325 (1490)
T ss_pred             CEEEECCCHHHHHHHHHHHHHhhhhhccccccccchhhhhhhccccchhccccccceeeeeccccCCHHHHHHHHHHHHh
Confidence            3699999999999888888776321                            00122456678877665443   4455


Q ss_pred             CCCeEEEeccHHHHHHHHhCCCccCCCccEEEE
Q 028826           50 EGANLLIGTPGRLYDIMERMDVLDFRNLVILVL   82 (203)
Q Consensus        50 ~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lVi   82 (203)
                      +...+||+|..-     .  -.+|+.+++++|.
T Consensus       326 G~LrvLVATssL-----E--LGIDIg~VDlVIq  351 (1490)
T PRK09751        326 GELRCVVATSSL-----E--LGIDMGAVDLVIQ  351 (1490)
T ss_pred             CCceEEEeCcHH-----H--ccCCcccCCEEEE
Confidence            778999998632     1  3566777776665

>smart00488 DEXDc2 DEAD-like helicases superfamily

Probab=86.21  E-value=0.63  Score=37.58  Aligned_cols=40  Identities=25%  Similarity=0.224  Sum_probs=28.1

Q ss_pred             CCCeEEEeccHHHHHHHH-hCCCccCCCccEEEEcchhHhhh
Q 028826           50 EGANLLIGTPGRLYDIME-RMDVLDFRNLVILVLDEADRLLD   90 (203)
Q Consensus        50 ~~~~ilV~Tp~~l~~~~~-~~~~~~l~~v~~lViDEad~l~~   90 (203)
                      ..+||||++-.-|++-.. ..-.+.+ .-.++||||||.+.+
T Consensus       210 ~~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00488      210 EFANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             hcCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            358999999888875442 2112344 468999999999864

>smart00489 DEXDc3 DEAD-like helicases superfamily

Probab=86.21  E-value=0.63  Score=37.58  Aligned_cols=40  Identities=25%  Similarity=0.224  Sum_probs=28.1

Q ss_pred             CCCeEEEeccHHHHHHHH-hCCCccCCCccEEEEcchhHhhh
Q 028826           50 EGANLLIGTPGRLYDIME-RMDVLDFRNLVILVLDEADRLLD   90 (203)
Q Consensus        50 ~~~~ilV~Tp~~l~~~~~-~~~~~~l~~v~~lViDEad~l~~   90 (203)
                      ..+||||++-.-|++-.. ..-.+.+ .-.++||||||.+.+
T Consensus       210 ~~Adivi~ny~yll~~~~r~~~~~~l-~~~~lIiDEAHnL~d  250 (289)
T smart00489      210 EFANVVVLPYQYLLDPKIRQALSIEL-KDSIVIFDEAHNLDN  250 (289)
T ss_pred             hcCCEEEECHHHHhcHHHHHHhcccc-cccEEEEeCccChHH
Confidence            358999999888875442 2112344 468999999999864

>PRK07413 hypothetical protein; Validated

Probab=86.14  E-value=10  Score=31.92  Aligned_cols=54  Identities=15%  Similarity=0.262  Sum_probs=45.4

Q ss_pred             CCCccEEEEcchhHhhhhch--HHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHh
Q 028826           74 FRNLVILVLDEADRLLDMGF--QKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (203)
Q Consensus        74 l~~v~~lViDEad~l~~~~~--~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~  127 (203)
                      -...+++|+||+-..++.|+  .+++..+++.-|...-+|+..-..|+++.++++.
T Consensus       123 sg~ydlvILDEi~~Al~~gll~~eevl~~L~~rP~~~evVLTGR~ap~~Lie~ADl  178 (382)
T PRK07413        123 SGLYSVVVLDELNPVLDLGLLPVDEVVNTLKSRPEGLEIIITGRAAPQSLLDIADL  178 (382)
T ss_pred             CCCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEeCCCCCHHHHHhCCe
Confidence            35788999999998888884  6677788888888889999999999988888773

>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA

Probab=86.04  E-value=4.3  Score=39.48  Aligned_cols=71  Identities=11%  Similarity=0.173  Sum_probs=54.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhC-CCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEE-GANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~-~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +||++|+++-+.++.+.+++..  .+++.+..++|+.+..++.+..... +-.|||+|.     .. . .++++.+++++
T Consensus       282 ILVFLpg~~EI~~l~~~L~~~~--~~~~~VlpLhg~Ls~~eQ~~vf~~~~~rkIVLATN-----IA-E-tSLTIpgV~yV  352 (1283)
T TIGR01967       282 ILIFLPGEREIRDAAEILRKRN--LRHTEILPLYARLSNKEQQRVFQPHSGRRIVLATN-----VA-E-TSLTVPGIHYV  352 (1283)
T ss_pred             EEEeCCCHHHHHHHHHHHHhcC--CCCcEEEeccCCCCHHHHHHHhCCCCCceEEEecc-----HH-H-hccccCCeeEE
Confidence            6899999998888888887653  2367889999999988887765432 358999997     22 2 57888999987


Q ss_pred             E
Q 028826           81 V   81 (203)
Q Consensus        81 V   81 (203)
                      |
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.

>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=85.99  E-value=0.8  Score=34.21  Aligned_cols=96  Identities=16%  Similarity=0.173  Sum_probs=37.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      .+|-+|+.+=+..+++.+.+-.... +++...    .........+...+..|-.-.|+.+...-        ...+++|
T Consensus        29 I~vtAP~~~~~~~lf~~~~~~l~~~-~~~~~~----~~~~~~~~~~~~~~~~i~f~~Pd~l~~~~--------~~~Dlli   95 (177)
T PF05127_consen   29 ILVTAPSPENVQTLFEFAEKGLKAL-GYKEEK----KKRIGQIIKLRFNKQRIEFVAPDELLAEK--------PQADLLI   95 (177)
T ss_dssp             EEEE-SS--S-HHHHHCC-------------------------------CCC--B--HHHHCCT------------SCEE
T ss_pred             EEEecCCHHHHHHHHHHHHhhcccc-cccccc----ccccccccccccccceEEEECCHHHHhCc--------CCCCEEE
Confidence            4677899887777766665543332 222200    00000111111234566666676654321        1347999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecC
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  118 (203)
                      ||||=.+    -.+.+..+++    ..-.++||.|..
T Consensus        96 VDEAAaI----p~p~L~~ll~----~~~~vv~stTi~  124 (177)
T PF05127_consen   96 VDEAAAI----PLPLLKQLLR----RFPRVVFSTTIH  124 (177)
T ss_dssp             ECTGGGS-----HHHHHHHHC----CSSEEEEEEEBS
T ss_pred             EechhcC----CHHHHHHHHh----hCCEEEEEeecc
Confidence            9999765    2344444443    334677788864

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.

>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins

Probab=85.93  E-value=3.2  Score=25.81  Aligned_cols=51  Identities=16%  Similarity=0.264  Sum_probs=38.9

Q ss_pred             CceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcch
Q 028826           28 DVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEA   85 (203)
Q Consensus        28 ~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEa   85 (203)
                      ++++..++|+.+..+....+   .....+|||+|- .+.      ..+|+..++.+|+=+.
T Consensus         7 ~~~~~~i~~~~~~~~r~~~~~~f~~~~~~vli~t~-~~~------~Gid~~~~~~vi~~~~   60 (78)
T PF00271_consen    7 GIKVAIIHGDMSQKERQEILKKFNSGEIRVLIATD-ILG------EGIDLPDASHVIFYDP   60 (78)
T ss_dssp             TSSEEEESTTSHHHHHHHHHHHHHTTSSSEEEESC-GGT------TSSTSTTESEEEESSS
T ss_pred             CCcEEEEECCCCHHHHHHHHHHhhccCceEEEeec-ccc------cccccccccccccccc
Confidence            89999999988877665544   346789999994 222      5899999999988555

It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....

>PF03354 Terminase_1: Phage Terminase ; InterPro: IPR005021 This entry is represented by Lactococcus phage bIL285, Orf41 (terminase)

Probab=85.89  E-value=1.6  Score=37.87  Aligned_cols=104  Identities=14%  Similarity=0.180  Sum_probs=56.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHh-CCCccCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMER-MDVLDFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~-~~~~~l~~v~~l   80 (203)
                      .++.+++++-|..+++.++++....|.++...  +.     ..  .....-.|..-..+.....+.. .+..+=.+..++
T Consensus        57 i~~~A~~~~QA~~~f~~~~~~i~~~~~l~~~~--~~-----~~--~~~~~~~i~~~~~~s~~~~~s~~~~~~dG~~~~~~  127 (477)
T PF03354_consen   57 IYCAANTRDQAKIVFDEAKKMIEASPELRKRK--KP-----KI--IKSNKKEIEFPKTGSFFKALSSDADSLDGLNPSLA  127 (477)
T ss_pred             EEEEeCCHHHHHHHHHHHHHHHHhChhhccch--hh-----hh--hhhhceEEEEcCCCcEEEEEecCCCCccCCCCceE
Confidence            56889999999999999999987654333211  00     00  0001112222222222222111 133444567899


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEee
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSA  115 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SA  115 (203)
                      |+||+|.+-+....+.+..-.... .++|+++.|.
T Consensus       128 i~DE~h~~~~~~~~~~l~~g~~~r-~~pl~~~IST  161 (477)
T PF03354_consen  128 IFDELHAHKDDELYDALESGMGAR-PNPLIIIIST  161 (477)
T ss_pred             EEeCCCCCCCHHHHHHHHhhhccC-CCceEEEEeC
Confidence            999999885544444444444443 4566655543

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]

Probab=85.83  E-value=3.6  Score=36.22  Aligned_cols=84  Identities=12%  Similarity=0.156  Sum_probs=54.3

Q ss_pred             CccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhcc
Q 028826           76 NLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLAS  155 (203)
Q Consensus        76 ~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~  155 (203)
                      ....+||||+|.=++..-...+-.-++.++...|+++.|-  -|.|...+..++    .|.-...               
T Consensus       453 ~~ptlIFDEVD~GIsG~~A~aVg~~L~~Ls~~~QVl~VTH--lPQVAa~ad~H~----~V~K~~~---------------  511 (557)
T COG0497         453 DTPTLIFDEVDTGISGRVAQAVGKKLRRLSEHHQVLCVTH--LPQVAAMADTHF----LVEKESE---------------  511 (557)
T ss_pred             CCCeEEEecccCCCChHHHHHHHHHHHHHhcCceEEEEec--HHHHHhhhcceE----EEEEecC---------------
Confidence            4669999999976655567777888999999999998853  344544444332    2211111               


Q ss_pred             CCCCCceeEEEEEcCCCCcHHHHHHHHh
Q 028826          156 SKTPLGLHLEYLECESDKKPSQLVDLLI  183 (203)
Q Consensus       156 ~~~~~~i~~~~~~~~~~~k~~~l~~ll~  183 (203)
                         -....-.+..++.++|.+.+..+|-
T Consensus       512 ---~~~T~s~V~~L~~eeRveEiARMl~  536 (557)
T COG0497         512 ---DGRTESRVRPLDKEERVEEIARMLG  536 (557)
T ss_pred             ---CCceEEeeeeCCHhHHHHHHHHHhc
Confidence               1222344555677888888888873

>PF13086 AAA_11: AAA domain; PDB: 2XZL_A 2XZO_A 2WJY_A 2WJV_A 2XZP_A 2GK6_A 2GK7_A 2GJK_A

Probab=84.88  E-value=3.2  Score=31.45  Aligned_cols=36  Identities=19%  Similarity=0.399  Sum_probs=22.1

Q ss_pred             CCCeEEEeccHHHHHHHHhCCCcc-C-CCccEEEEcchhHhhh
Q 028826           50 EGANLLIGTPGRLYDIMERMDVLD-F-RNLVILVLDEADRLLD   90 (203)
Q Consensus        50 ~~~~ilV~Tp~~l~~~~~~~~~~~-l-~~v~~lViDEad~l~~   90 (203)
                      ..++||++|+......     .+. . ..++++|||||-++..
T Consensus       169 ~~~~vi~~T~~~~~~~-----~~~~~~~~~d~vIvDEAsq~~e  206 (236)
T PF13086_consen  169 KEADVIFTTLSSAASP-----FLSNFKEKFDVVIVDEASQITE  206 (236)
T ss_dssp             HT-SEEEEETCGGG-C-----CGTT-----SEEEETTGGGS-H
T ss_pred             ccccccccccccchhh-----HhhhhcccCCEEEEeCCCCcch
Confidence            4689999999887321     222 2 2789999999987643

>PRK12900 secA preprotein translocase subunit SecA; Reviewed

Probab=84.63  E-value=0.46  Score=44.35  Aligned_cols=76  Identities=11%  Similarity=0.053  Sum_probs=46.0

Q ss_pred             cEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcC--C
Q 028826          109 RTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKN--K  186 (203)
Q Consensus       109 q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~--~  186 (203)
                      ...+.|.|...+..+|.+.|--+-+.  ++...              +....... ..++.+..+|..++.+.+...  .
T Consensus       535 kLaGMTGTA~te~~Ef~~iY~L~Vv~--IPTnr--------------P~~R~D~~-d~vy~t~~eK~~Ali~~I~~~~~~  597 (1025)
T PRK12900        535 KLAGMTGTAETEASEFFEIYKLDVVV--IPTNK--------------PIVRKDMD-DLVYKTRREKYNAIVLKVEELQKK  597 (1025)
T ss_pred             hhcccCCCChhHHHHHHHHhCCcEEE--CCCCC--------------CcceecCC-CeEecCHHHHHHHHHHHHHHHhhC
Confidence            45567777766666676555333322  32221              11111111 233356678999999999643  6


Q ss_pred             CCeEEEEeccCCccc
Q 028826          187 SKKIIMYVQHGNFSE  201 (203)
Q Consensus       187 ~~~~lIF~ns~~~~e  201 (203)
                      ++|+||||+|++.+|
T Consensus       598 grpVLIft~Sve~sE  612 (1025)
T PRK12900        598 GQPVLVGTASVEVSE  612 (1025)
T ss_pred             CCCEEEEeCcHHHHH
Confidence            789999999988765

>PRK01172 ski2-like helicase; Provisional

Probab=84.47  E-value=8.2  Score=35.01  Aligned_cols=77  Identities=6%  Similarity=0.120  Sum_probs=49.8

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCC--------------------ceEEEEEcCcchHHHHHH---HHhCCCeEEEe
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPD--------------------VKSMLLVGGVEVKADVKK---IEEEGANLLIG   57 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~--------------------i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~   57 (203)
                      .+||.+|||.-+..+...+.+.......                    ..+...+||.+..++...   ..++...|||+
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            4799999999888887777654332111                    246778888876654442   23467899999


Q ss_pred             ccHHHHHHHHhCCCccCCCccEEEEcch
Q 028826           58 TPGRLYDIMERMDVLDFRNLVILVLDEA   85 (203)
Q Consensus        58 Tp~~l~~~~~~~~~~~l~~v~~lViDEa   85 (203)
                      |..--       .++++... .+|++..
T Consensus       318 T~~la-------~Gvnipa~-~VII~~~  337 (674)
T PRK01172        318 TPTLA-------AGVNLPAR-LVIVRDI  337 (674)
T ss_pred             cchhh-------ccCCCcce-EEEEcCc
Confidence            97332       35666554 5666554

>PRK07414 cob(I)yrinic acid a,c-diamide adenosyltransferase; Validated

Probab=84.47  E-value=2.6  Score=31.49  Aligned_cols=53  Identities=15%  Similarity=0.249  Sum_probs=44.9

Q ss_pred             CCCccEEEEcchhHhhhhch--HHHHHHHHHhCCCCCcEEEEeeecChhHHHHHH
Q 028826           74 FRNLVILVLDEADRLLDMGF--QKQISYIISRLPKLRRTGLFSATQTEAVEELSK  126 (203)
Q Consensus        74 l~~v~~lViDEad~l~~~~~--~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~  126 (203)
                      -...+++|+||+-..++.|+  .+++..+++.-|...-+|+..-..|+++.++++
T Consensus       113 ~~~~dlvVLDEi~~Al~~gli~~eeVl~~L~~rp~~~evILTGR~~p~~Lie~AD  167 (178)
T PRK07414        113 EGRYSLVVLDELSLAIQFGLIPETEVLEFLEKRPSHVDVILTGPEMPESLLAIAD  167 (178)
T ss_pred             CCCCCEEEEehhHHHHHCCCccHHHHHHHHHhCCCCCEEEEECCCCCHHHHHhCC
Confidence            35788999999988888884  677888888888888999999999988887766

>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]

Probab=84.38  E-value=8.5  Score=29.26  Aligned_cols=74  Identities=15%  Similarity=0.278  Sum_probs=46.7

Q ss_pred             CceEEEEEcCcchHHHHHHHHh----CCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHhhhhchHHHHHHHHHh
Q 028826           28 DVKSMLLVGGVEVKADVKKIEE----EGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISR  103 (203)
Q Consensus        28 ~i~~~~~~~g~~~~~~~~~l~~----~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~~~~~~~~~~~il~~  103 (203)
                      +.++..+....+.......+.+    +-+-++|-.+..+.+.+.. ..-+ .+++.+.||||. +++......+..+...
T Consensus        32 g~~v~vfkp~iD~R~~~~~V~Sr~G~~~~A~~i~~~~~i~~~i~~-~~~~-~~~~~v~IDEaQ-F~~~~~v~~l~~lad~  108 (201)
T COG1435          32 GMKVLVFKPAIDTRYGVGKVSSRIGLSSEAVVIPSDTDIFDEIAA-LHEK-PPVDCVLIDEAQ-FFDEELVYVLNELADR  108 (201)
T ss_pred             CCeEEEEecccccccccceeeeccCCcccceecCChHHHHHHHHh-cccC-CCcCEEEEehhH-hCCHHHHHHHHHHHhh
Confidence            6777777766554433332211    2356777778888887765 2222 228899999996 4566666777777776


Q ss_pred             C
Q 028826          104 L  104 (203)
Q Consensus       104 ~  104 (203)
                      +
T Consensus       109 l  109 (201)
T COG1435         109 L  109 (201)
T ss_pred             c
Confidence            5

>PRK06835 DNA replication protein DnaC; Validated

Probab=84.33  E-value=10  Score=31.31  Aligned_cols=110  Identities=13%  Similarity=0.199  Sum_probs=62.9

Q ss_pred             HHHHHHHHHHHHHhhhcCC-CceEEEEEcC--cchHHHHH----HHHhCCCeEEEeccHHHHHHHHhC---CC-------
Q 028826            9 RELSAQIYHVAQPFISTLP-DVKSMLLVGG--VEVKADVK----KIEEEGANLLIGTPGRLYDIMERM---DV-------   71 (203)
Q Consensus         9 reLa~Qi~~~~~~l~~~~~-~i~~~~~~~g--~~~~~~~~----~l~~~~~~ilV~Tp~~l~~~~~~~---~~-------   71 (203)
                      ++-+.++...+.++...+. +-....++|.  .....-..    .+...+..|++.|...+...+...   ..       
T Consensus       162 ~~~~~~~~~~~~~f~~~f~~~~~~Lll~G~~GtGKThLa~aIa~~l~~~g~~V~y~t~~~l~~~l~~~~~~~~~~~~~~~  241 (329)
T PRK06835        162 RKNMEKILEKCKNFIENFDKNNENLLFYGNTGTGKTFLSNCIAKELLDRGKSVIYRTADELIEILREIRFNNDKELEEVY  241 (329)
T ss_pred             HHHHHHHHHHHHHHHHHHhccCCcEEEECCCCCcHHHHHHHHHHHHHHCCCeEEEEEHHHHHHHHHHHHhccchhHHHHH
Confidence            5566677776776665321 2255677774  33333332    233467889999988887765330   11       


Q ss_pred             ccCCCccEEEEcchhHhhhhc-hHHHHHHHHHhCC-CCCcEEEEeeecCh
Q 028826           72 LDFRNLVILVLDEADRLLDMG-FQKQISYIISRLP-KLRRTGLFSATQTE  119 (203)
Q Consensus        72 ~~l~~v~~lViDEad~l~~~~-~~~~~~~il~~~~-~~~q~i~~SAT~~~  119 (203)
                      -.+.++++||||+........ ....+..++...- ....+|+. +.+++
T Consensus       242 ~~l~~~DLLIIDDlG~e~~t~~~~~~Lf~iin~R~~~~k~tIiT-SNl~~  290 (329)
T PRK06835        242 DLLINCDLLIIDDLGTEKITEFSKSELFNLINKRLLRQKKMIIS-TNLSL  290 (329)
T ss_pred             HHhccCCEEEEeccCCCCCCHHHHHHHHHHHHHHHHCCCCEEEE-CCCCH
Confidence            124689999999997664222 3445555655443 33445554 44443

>PRK08727 hypothetical protein; Validated

Probab=84.32  E-value=1.9  Score=33.55  Aligned_cols=90  Identities=8%  Similarity=-0.039  Sum_probs=49.1

Q ss_pred             eEEEEEcCcc--hHHHHHH----HHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHhhhhc-hHHHHHHHHH
Q 028826           30 KSMLLVGGVE--VKADVKK----IEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMG-FQKQISYIIS  102 (203)
Q Consensus        30 ~~~~~~~g~~--~~~~~~~----l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~~~~-~~~~~~~il~  102 (203)
                      ....++|+..  +.+-...    +.+.+..+++.+.+.+...+.. ..-.+.+..++|+||+|.+.... ....+.+++.
T Consensus        42 ~~l~l~G~~G~GKThL~~a~~~~~~~~~~~~~y~~~~~~~~~~~~-~~~~l~~~dlLiIDDi~~l~~~~~~~~~lf~l~n  120 (233)
T PRK08727         42 DWLYLSGPAGTGKTHLALALCAAAEQAGRSSAYLPLQAAAGRLRD-ALEALEGRSLVALDGLESIAGQREDEVALFDFHN  120 (233)
T ss_pred             CeEEEECCCCCCHHHHHHHHHHHHHHcCCcEEEEeHHHhhhhHHH-HHHHHhcCCEEEEeCcccccCChHHHHHHHHHHH
Confidence            4567777543  3333332    3345677777776665543332 11135677899999999875432 2334445555


Q ss_pred             hCCC-CCcEEEEeeecChh
Q 028826          103 RLPK-LRRTGLFSATQTEA  120 (203)
Q Consensus       103 ~~~~-~~q~i~~SAT~~~~  120 (203)
                      .... ..++++.|...|..
T Consensus       121 ~~~~~~~~vI~ts~~~p~~  139 (233)
T PRK08727        121 RARAAGITLLYTARQMPDG  139 (233)
T ss_pred             HHHHcCCeEEEECCCChhh
Confidence            4432 33555555544443

>PF02572 CobA_CobO_BtuR: ATP:corrinoid adenosyltransferase BtuR/CobO/CobP; InterPro: IPR003724 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2

Probab=83.77  E-value=3.1  Score=30.95  Aligned_cols=56  Identities=16%  Similarity=0.251  Sum_probs=39.5

Q ss_pred             ccCCCccEEEEcchhHhhhhc--hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHh
Q 028826           72 LDFRNLVILVLDEADRLLDMG--FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (203)
Q Consensus        72 ~~l~~v~~lViDEad~l~~~~--~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~  127 (203)
                      +.-...+++|+||+-..++.+  -.+++..+++.-|...-+|+..-..|+++.+.++.
T Consensus        92 i~~~~~dlvILDEi~~a~~~gll~~~~v~~~l~~rp~~~evVlTGR~~~~~l~e~ADl  149 (172)
T PF02572_consen   92 ISSGEYDLVILDEINYAVDYGLLSEEEVLDLLENRPESLEVVLTGRNAPEELIEAADL  149 (172)
T ss_dssp             TT-TT-SEEEEETHHHHHHTTSS-HHHHHHHHHTS-TT-EEEEE-SS--HHHHHH-SE
T ss_pred             HhCCCCCEEEEcchHHHhHCCCccHHHHHHHHHcCCCCeEEEEECCCCCHHHHHhCCe
Confidence            334678899999998888887  46778888888888899999999999988888773

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.

>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated

Probab=83.49  E-value=1.8  Score=40.72  Aligned_cols=40  Identities=18%  Similarity=0.205  Sum_probs=29.4

Q ss_pred             CCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHhhh
Q 028826           50 EGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLD   90 (203)
Q Consensus        50 ~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~~   90 (203)
                      ..+||||+.-.-|+..+.. +.--+.+-.++||||||+|-+
T Consensus       430 ~~AdivItNHalLl~dl~~-~~~ilp~~~~lViDEAH~l~d  469 (928)
T PRK08074        430 KFADLVITNHALLLTDLTS-EEPLLPSYEHIIIDEAHHFEE  469 (928)
T ss_pred             hcCCEEEECHHHHHHHHhh-hcccCCCCCeEEEECCchHHH
Confidence            4689999999887765533 222245578999999999864

>COG0653 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking and secretion]

Probab=83.20  E-value=2.4  Score=39.05  Aligned_cols=83  Identities=17%  Similarity=0.245  Sum_probs=60.5

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHH-HHHHhC-----CCccCCC
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-DIMERM-----DVLDFRN   76 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~-~~~~~~-----~~~~l~~   76 (203)
                      .++...--||..=..++.++-..+ |+.++....+.+..++....   .+||..+|-..+- ++++.+     ...-...
T Consensus       125 hvVTvNdYLA~RDae~m~~l~~~L-GlsvG~~~~~m~~~ek~~aY---~~DItY~TnnElGFDYLRDNm~~~~ee~vqr~  200 (822)
T COG0653         125 HVVTVNDYLARRDAEWMGPLYEFL-GLSVGVILAGMSPEEKRAAY---ACDITYGTNNELGFDYLRDNMVTSQEEKVQRG  200 (822)
T ss_pred             EEeeehHHhhhhCHHHHHHHHHHc-CCceeeccCCCChHHHHHHH---hcCceeccccccCcchhhhhhhccHHHhhhcc
Confidence            355566667777788888888888 99999999999776665544   5899999998873 444431     0111346


Q ss_pred             ccEEEEcchhHhh
Q 028826           77 LVILVLDEADRLL   89 (203)
Q Consensus        77 v~~lViDEad~l~   89 (203)
                      ..+-|+||+|.++
T Consensus       201 ~~faIvDEvDSIL  213 (822)
T COG0653         201 LNFAIVDEVDSIL  213 (822)
T ss_pred             CCeEEEcchhhee
Confidence            8899999999875

>PF12340 DUF3638: Protein of unknown function (DUF3638); InterPro: IPR022099 This domain family is found in eukaryotes, and is approximately 230 amino acids in length

Probab=82.96  E-value=4.2  Score=31.66  Aligned_cols=89  Identities=16%  Similarity=0.274  Sum_probs=47.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEE--cCcchH----HHHHHHH---hCCCeEEEeccHHHHHHHHh----
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLV--GGVEVK----ADVKKIE---EEGANLLIGTPGRLYDIMER----   68 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~--~g~~~~----~~~~~l~---~~~~~ilV~Tp~~l~~~~~~----   68 (203)
                      +-+++| +.|..|....++.-.+..-+-++..+.  ......    +....+.   ...-.|+++||+.++.+.-.    
T Consensus        73 vrviVp-k~Ll~q~~~~L~~~lg~l~~r~i~~lpFsR~~~~~~~~~~~~~~l~~~~~~~~gill~~PEhilSf~L~~le~  151 (229)
T PF12340_consen   73 VRVIVP-KALLEQMRQMLRSRLGGLLNRRIYHLPFSRSTPLTPETLEKIRQLLEECMRSGGILLATPEHILSFKLKGLER  151 (229)
T ss_pred             EEEEcC-HHHHHHHHHHHHHHHHHHhCCeeEEecccCCCCCCHHHHHHHHHHHHHHHHcCCEEEeChHHHHHHHHHHHHH
Confidence            446666 568888888876654444244444332  222211    1122111   23456999999998764321    


Q ss_pred             --CCCcc-----------CCCccEEEEcchhHhhhh
Q 028826           69 --MDVLD-----------FRNLVILVLDEADRLLDM   91 (203)
Q Consensus        69 --~~~~~-----------l~~v~~lViDEad~l~~~   91 (203)
                        .+...           +.+...=|+||.|..++.
T Consensus       152 l~~~~~~~~~~l~~~q~~l~~~~rdilDEsDe~L~~  187 (229)
T PF12340_consen  152 LQDGKPEEARELLKIQKWLDEHSRDILDESDEILSV  187 (229)
T ss_pred             HHhcCHHHHHHHHHHHHHHHhcCCeEeECchhccCc
Confidence              01110           334555688888887653

There are two conserved sequence motifs: LLE and NMG.

>KOG0964 consensus Structural maintenance of chromosome protein 3 (sister chromatid cohesion complex Cohesin, subunit SMC3) [Cell cycle control, cell division, chromosome partitioning]

Probab=82.53  E-value=1.2  Score=41.42  Aligned_cols=54  Identities=15%  Similarity=0.154  Sum_probs=47.1

Q ss_pred             CCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCC
Q 028826           75 RNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLR  130 (203)
Q Consensus        75 ~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~  130 (203)
                      +.--+.++||+|.-+|..|+..+..++..++...|+|.  .|+-|++...+.+|+.
T Consensus      1118 DPAPFYlfDEIDAaLDaQyR~aVa~lIkelS~~aQFI~--TTFRpEll~vAdKfyg 1171 (1200)
T KOG0964|consen 1118 DPAPFYLFDEIDAALDAQYRTAVADLIKELSDSAQFIT--TTFRPELLSVADKFYG 1171 (1200)
T ss_pred             CCcchhhHhHHhhhccHHHHHHHHHHHHHHhhccceEe--ecccHHHHHHHHhhhc
Confidence            34458899999999999999999999999999999886  5888999998888876

>PRK04195 replication factor C large subunit; Provisional

Probab=82.17  E-value=25  Score=30.52  Aligned_cols=80  Identities=14%  Similarity=0.173  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHHhhhcCCCceEEEEEcCc--chHHHHHHHHh-CCCeEEEeccH------HHHHHHHhC-CCcc-C-CCc
Q 028826           10 ELSAQIYHVAQPFISTLPDVKSMLLVGGV--EVKADVKKIEE-EGANLLIGTPG------RLYDIMERM-DVLD-F-RNL   77 (203)
Q Consensus        10 eLa~Qi~~~~~~l~~~~~~i~~~~~~~g~--~~~~~~~~l~~-~~~~ilV~Tp~------~l~~~~~~~-~~~~-l-~~v   77 (203)
                      +...++..++..+..+. ..+...++|..  ....-...+.+ -+.+++..++.      .+...+... .... + .+-
T Consensus        21 ~~~~~l~~~l~~~~~g~-~~~~lLL~GppG~GKTtla~ala~el~~~~ielnasd~r~~~~i~~~i~~~~~~~sl~~~~~   99 (482)
T PRK04195         21 KAKEQLREWIESWLKGK-PKKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVIERVAGEAATSGSLFGARR   99 (482)
T ss_pred             HHHHHHHHHHHHHhcCC-CCCeEEEECCCCCCHHHHHHHHHHHcCCCEEEEcccccccHHHHHHHHHHhhccCcccCCCC
Confidence            34456666666654333 25667777743  33444444422 34566665542      233333320 1111 2 257


Q ss_pred             cEEEEcchhHhhh
Q 028826           78 VILVLDEADRLLD   90 (203)
Q Consensus        78 ~~lViDEad~l~~   90 (203)
                      ++|||||+|.+..
T Consensus       100 kvIiIDEaD~L~~  112 (482)
T PRK04195        100 KLILLDEVDGIHG  112 (482)
T ss_pred             eEEEEecCccccc
Confidence            8999999999865

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

Probab=81.86  E-value=3.8  Score=38.62  Aligned_cols=74  Identities=18%  Similarity=0.293  Sum_probs=52.1

Q ss_pred             EEEEcCc---HHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCcc-CCCc
Q 028826            2 GMIISPT---RELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLD-FRNL   77 (203)
Q Consensus         2 alil~Pt---reLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~-l~~v   77 (203)
                      .||.+|+   +|.|..+.+.+++.     |+++..++.+.  .+.......+..|++||....-.-+++   .+| +..+
T Consensus       338 gLIfV~~d~G~e~aeel~e~Lr~~-----Gi~a~~~~a~~--~~~le~F~~GeidvLVGvAsyYG~lVR---GlDLP~ri  407 (1187)
T COG1110         338 GLIFVPIDYGREKAEELAEYLRSH-----GINAELIHAEK--EEALEDFEEGEVDVLVGVASYYGVLVR---GLDLPHRI  407 (1187)
T ss_pred             eEEEEEcHHhHHHHHHHHHHHHhc-----CceEEEeeccc--hhhhhhhccCceeEEEEecccccceee---cCCchhhe
Confidence            6899999   88887777777665     78988888765  334444456889999999876655553   344 4566


Q ss_pred             cEEEEcch
Q 028826           78 VILVLDEA   85 (203)
Q Consensus        78 ~~lViDEa   85 (203)
                      ++.|+=.+
T Consensus       408 rYaIF~Gv  415 (1187)
T COG1110         408 RYAVFYGV  415 (1187)
T ss_pred             eEEEEecC
Confidence            66666443

>PRK13766 Hef nuclease; Provisional

Probab=81.85  E-value=9.2  Score=35.24  Aligned_cols=73  Identities=16%  Similarity=0.312  Sum_probs=52.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcC--------cchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGG--------VEVKADVKK---IEEEGANLLIGTPGRLYDIMERMD   70 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g--------~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~   70 (203)
                      +||++.+++-+.++.+.+.+.     ++++..++|.        .+..++.+.   ...+..+++|+|.     .. . .
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            689999999999999888553     6777777775        333333332   2346689999997     22 2 5


Q ss_pred             CccCCCccEEEEcchh
Q 028826           71 VLDFRNLVILVLDEAD   86 (203)
Q Consensus        71 ~~~l~~v~~lViDEad   86 (203)
                      ++|+.+++++|+=+.+
T Consensus       436 Gldi~~~~~VI~yd~~  451 (773)
T PRK13766        436 GLDIPSVDLVIFYEPV  451 (773)
T ss_pred             CCCcccCCEEEEeCCC
Confidence            7899999999986553

>PF13173 AAA_14: AAA domain

Probab=81.79  E-value=3.7  Score=28.54  Aligned_cols=41  Identities=10%  Similarity=0.174  Sum_probs=29.4

Q ss_pred             CccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecCh
Q 028826           76 NLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (203)
Q Consensus        76 ~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  119 (203)
                      .-.++++||++.+-  ++...++.+...- .+.++++.++....
T Consensus        61 ~~~~i~iDEiq~~~--~~~~~lk~l~d~~-~~~~ii~tgS~~~~  101 (128)
T PF13173_consen   61 GKKYIFIDEIQYLP--DWEDALKFLVDNG-PNIKIILTGSSSSL  101 (128)
T ss_pred             CCcEEEEehhhhhc--cHHHHHHHHHHhc-cCceEEEEccchHH
Confidence            56799999999884  4567777777755 45677777665543

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

Probab=81.78  E-value=7.8  Score=35.40  Aligned_cols=73  Identities=18%  Similarity=0.310  Sum_probs=53.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEc--------CcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVG--------GVEVKADVKKI---EEEGANLLIGTPGRLYDIMERM   69 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~--------g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~   69 (203)
                      .++|.+-||+.|..+..++.++...  +++...+.|        |.+...|...+   .++..+|||+|.      +.+ 
T Consensus       415 R~IIFve~R~sa~~l~~~l~~~~~~--~ir~~~fiGq~~s~~~~gmtqk~Q~evl~~Fr~G~~NvLVATS------V~E-  485 (746)
T KOG0354|consen  415 RTIIFVETRESALALKKWLLQLHEL--GIKAEIFIGQGKSTQSTGMTQKEQKEVLDKFRDGEINVLVATS------VAE-  485 (746)
T ss_pred             cEEEEEehHHHHHHHHHHHHhhhhc--ccccceeeeccccccccccCHHHHHHHHHHHhCCCccEEEEec------chh-
Confidence            3799999999999999999985333  678777776        44555555544   347899999995      223 


Q ss_pred             CCccCCCccEEEE
Q 028826           70 DVLDFRNLVILVL   82 (203)
Q Consensus        70 ~~~~l~~v~~lVi   82 (203)
                      .++|...+.++|-
T Consensus       486 EGLDI~ec~lVIc  498 (746)
T KOG0354|consen  486 EGLDIGECNLVIC  498 (746)
T ss_pred             ccCCcccccEEEE
Confidence            5788888888774

>KOG0298 consensus DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair]

Probab=81.60  E-value=5.3  Score=38.45  Aligned_cols=114  Identities=16%  Similarity=0.166  Sum_probs=69.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchH-HHHHHHHhCCCeEEEeccHHHHHHHHhC-----------
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVK-ADVKKIEEEGANLLIGTPGRLYDIMERM-----------   69 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~-~~~~~l~~~~~~ilV~Tp~~l~~~~~~~-----------   69 (203)
                      .|||+|.- +..|++.++.+-++.  ++++....|-.... -+...+  ..+|||++|-.-|..=+...           
T Consensus       423 TLII~P~a-Il~QW~~EI~kH~~~--~lKv~~Y~Girk~~~~~~~el--~~yDIVlTtYdiLr~El~hte~~~~~R~lR~  497 (1394)
T KOG0298|consen  423 TLIICPNA-ILMQWFEEIHKHISS--LLKVLLYFGIRKTFWLSPFEL--LQYDIVLTTYDILRNELYHTEDFGSDRQLRH  497 (1394)
T ss_pred             eEEECcHH-HHHHHHHHHHHhccc--cceEEEEechhhhcccCchhh--hccCEEEeehHHHHhHhhcccccCChhhhhc
Confidence            48999965 678999998887665  47877766633211 111233  36899999998886433220           


Q ss_pred             --CCccC----CCcc--EEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHH
Q 028826           70 --DVLDF----RNLV--ILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEE  123 (203)
Q Consensus        70 --~~~~l----~~v~--~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~  123 (203)
                        +..++    -.+.  .+++|||-. +.. -.....+++.+++ .....+.|.|.-..+.+
T Consensus       498 qsr~~~~~SPL~~v~wWRIclDEaQM-ves-ssS~~a~M~~rL~-~in~W~VTGTPiq~Idd  556 (1394)
T KOG0298|consen  498 QSRYMRPNSPLLMVNWWRICLDEAQM-VES-SSSAAAEMVRRLH-AINRWCVTGTPIQKIDD  556 (1394)
T ss_pred             ccCCCCCCCchHHHHHHHHhhhHHHh-hcc-hHHHHHHHHHHhh-hhceeeecCCchhhhhh
Confidence              11111    1222  478999964 444 4556667777774 44556777774433443

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

Probab=81.52  E-value=8.6  Score=35.82  Aligned_cols=70  Identities=17%  Similarity=0.095  Sum_probs=47.3

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHH-----HHH---Hh----C-------CCeEEEeccHH
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADV-----KKI---EE----E-------GANLLIGTPGR   61 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~-----~~l---~~----~-------~~~ilV~Tp~~   61 (203)
                      .+||+++|++-|..+++.+++.     ++  ..++|+....+..     ..+   .+    +       +..|||+|-  
T Consensus       274 ~vLVF~NTv~~Aq~L~~~L~~~-----g~--~lLHG~m~q~dR~~~~~~~il~~Fk~~~~~g~~~~~~~g~~ILVATd--  344 (844)
T TIGR02621       274 AILVFCRTVKHVRKVFAKLPKE-----KF--ELLTGTLRGAERDDLVKKEIFNRFLPQMLSGSRARPQQGTVYLVCTS--  344 (844)
T ss_pred             cEEEEECCHHHHHHHHHHHHhc-----CC--eEeeCCCCHHHHhhHHHHHHHHHHhccccccccccccccceEEeccc--
Confidence            3799999999999999988764     34  7888887766554     111   11    1       267999993  


Q ss_pred             HHHHHHhCCCccCCCccEEEEcch
Q 028826           62 LYDIMERMDVLDFRNLVILVLDEA   85 (203)
Q Consensus        62 l~~~~~~~~~~~l~~v~~lViDEa   85 (203)
                         .+.  .++|++. ..+|.|.+
T Consensus       345 ---Vae--rGLDId~-d~VI~d~a  362 (844)
T TIGR02621       345 ---AGE--VGVNISA-DHLVCDLA  362 (844)
T ss_pred             ---hhh--hcccCCc-ceEEECCC
Confidence               222  4677764 67776543

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.

>PRK06620 hypothetical protein; Validated

Probab=81.49  E-value=22  Score=27.28  Aligned_cols=106  Identities=13%  Similarity=0.074  Sum_probs=52.7

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCc--chHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGV--EVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~--~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .|+.++-+.|.+....+.+-....|.-+...++|..  .+.+-.... ...+...+.+.....+-       ...+...+
T Consensus        18 Fvvg~~N~~a~~~~~~~~~~~~~~~~~~~l~l~Gp~G~GKThLl~a~-~~~~~~~~~~~~~~~~~-------~~~~~d~l   89 (214)
T PRK06620         18 FIVSSSNDQAYNIIKNWQCGFGVNPYKFTLLIKGPSSSGKTYLTKIW-QNLSNAYIIKDIFFNEE-------ILEKYNAF   89 (214)
T ss_pred             hEecccHHHHHHHHHHHHHccccCCCcceEEEECCCCCCHHHHHHHH-HhccCCEEcchhhhchh-------HHhcCCEE
Confidence            467776776665555444311111112557778753  344444443 33444444433222110       12345789


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCC-CCCcEEEEeeecChh
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLP-KLRRTGLFSATQTEA  120 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~-~~~q~i~~SAT~~~~  120 (203)
                      ++||+|.+-+    ..+..++..+. ...|+++.|.|.|+.
T Consensus        90 liDdi~~~~~----~~lf~l~N~~~e~g~~ilits~~~p~~  126 (214)
T PRK06620         90 IIEDIENWQE----PALLHIFNIINEKQKYLLLTSSDKSRN  126 (214)
T ss_pred             EEeccccchH----HHHHHHHHHHHhcCCEEEEEcCCCccc
Confidence            9999995422    23445544443 345666666666654

>COG2109 BtuR ATP:corrinoid adenosyltransferase [Coenzyme metabolism]

Probab=81.41  E-value=5.5  Score=30.10  Aligned_cols=54  Identities=15%  Similarity=0.226  Sum_probs=45.0

Q ss_pred             CCccEEEEcchhHhhhhch--HHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhc
Q 028826           75 RNLVILVLDEADRLLDMGF--QKQISYIISRLPKLRRTGLFSATQTEAVEELSKAG  128 (203)
Q Consensus        75 ~~v~~lViDEad~l~~~~~--~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~  128 (203)
                      ...+++|+||.-..+..|+  .+++..++..-|....+|+..-..|+.+.+++...
T Consensus       121 ~~ydlviLDEl~~al~~g~l~~eeV~~~l~~kP~~~~vIiTGr~ap~~lie~ADlV  176 (198)
T COG2109         121 GKYDLVILDELNYALRYGLLPLEEVVALLKARPEHTHVIITGRGAPPELIELADLV  176 (198)
T ss_pred             CCCCEEEEehhhHHHHcCCCCHHHHHHHHhcCCCCcEEEEECCCCCHHHHHHHHHH
Confidence            3688999999999988874  66777888888888889999988999988888753

>KOG1015 consensus Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription]

Probab=81.17  E-value=17  Score=34.48  Aligned_cols=117  Identities=15%  Similarity=0.171  Sum_probs=64.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcC---CCceEEEEEcCcchHHHHHHHH---hCCCeEEEeccHHHHHHHHhCCC----
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTL---PDVKSMLLVGGVEVKADVKKIE---EEGANLLIGTPGRLYDIMERMDV----   71 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~---~~i~~~~~~~g~~~~~~~~~l~---~~~~~ilV~Tp~~l~~~~~~~~~----   71 (203)
                      ||||+|-.-+ .-+.+++.+....+   ..+.|..+..-...++....|.   ..+.=.||| -+.+..+... +.    
T Consensus       731 aLvV~PlNt~-~NW~~EFekWm~~~e~~~~leV~eL~~vkr~e~R~~~L~~W~~~ggVmIiG-YdmyRnLa~g-r~vk~r  807 (1567)
T KOG1015|consen  731 ALVVCPLNTA-LNWMNEFEKWMEGLEDDEKLEVSELATVKRPEERSYMLQRWQEDGGVMIIG-YDMYRNLAQG-RNVKSR  807 (1567)
T ss_pred             EEEEcchHHH-HHHHHHHHHhcccccccccceeehhhhccChHHHHHHHHHHHhcCCEEEEe-hHHHHHHhcc-cchhhh
Confidence            7999996643 44566666665432   1456655554444455544442   244445555 2222222111 00    


Q ss_pred             ---------ccCCCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHH
Q 028826           72 ---------LDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEE  123 (203)
Q Consensus        72 ---------~~l~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~  123 (203)
                               +-=..-+++|-||+|.|=..  ...+...+..+...+.+++.+..+-+++.+
T Consensus       808 k~ke~f~k~lvdpGPD~vVCDE~HiLKNe--ksa~Skam~~irtkRRI~LTGTPLQNNLmE  866 (1567)
T KOG1015|consen  808 KLKEIFNKALVDPGPDFVVCDEGHILKNE--KSAVSKAMNSIRTKRRIILTGTPLQNNLME  866 (1567)
T ss_pred             HHHHHHHHhccCCCCCeEEecchhhhccc--hHHHHHHHHHHHhheeEEeecCchhhhhHH
Confidence                     00123569999999987322  445555666665667777777777766554

>COG3587 Restriction endonuclease [Defense mechanisms]

Probab=81.06  E-value=9.8  Score=35.33  Aligned_cols=113  Identities=14%  Similarity=0.120  Sum_probs=56.7

Q ss_pred             EEEcCcHHHH---HHHHHHHHHhh--hcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHH------HHHh---
Q 028826            3 MIISPTRELS---AQIYHVAQPFI--STLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYD------IMER---   68 (203)
Q Consensus         3 lil~PtreLa---~Qi~~~~~~l~--~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~------~~~~---   68 (203)
                      ||||||.+.-   .+..+.+.+-.  +.+.+.+.-.+.-....... ..-.++.|.+++.|-.....      ++..   
T Consensus       108 IivVPs~AIkeGv~~~s~~~~ehF~k~~Yent~~e~~i~~~~~~~~-~~~~~~~~~vLl~~~~Afnk~~inan~iN~~s~  186 (985)
T COG3587         108 IIVVPSLAIKEGVFLTSKETTEHFFKSEYENTRLESYIYDEDIEKF-KFKSNNKPCVLLIFVSAFNKEEINANMINSESM  186 (985)
T ss_pred             EEEeccHHHHhhhHHHHHHHHHHHhhhhccCcceeEEeechHHHHH-hhccCCCceEEEEehhhhccccccccccchhhh
Confidence            7999997653   33333333322  22323443333333222111 11225678888888665532      1211   


Q ss_pred             -CCCcc---------CCCcc-EEEEcchhHhhhh-chHHHHHHHHHhCCCCCc-EEEEeeecChhHH
Q 028826           69 -MDVLD---------FRNLV-ILVLDEADRLLDM-GFQKQISYIISRLPKLRR-TGLFSATQTEAVE  122 (203)
Q Consensus        69 -~~~~~---------l~~v~-~lViDEad~l~~~-~~~~~~~~il~~~~~~~q-~i~~SAT~~~~v~  122 (203)
                       ....+         +..++ ++|+||-|+|... .....+..    +  ++| ++=||||+++...
T Consensus       187 ~~~~~~~~~~spvd~la~~rPIvIvDEPh~f~~~~k~~~~i~~----l--~pl~ilRfgATfkd~y~  247 (985)
T COG3587         187 ENTNLFNGATSPVDALASMRPIVIVDEPHRFLGDDKTYGAIKQ----L--NPLLILRFGATFKDEYN  247 (985)
T ss_pred             cccCccccccCHHHHHHhcCCEEEecChhhcccchHHHHHHHh----h--CceEEEEecccchhhhc
Confidence             01100         22233 7899999999753 22322222    2  344 4559999987755

>PRK11747 dinG ATP-dependent DNA helicase DinG; Provisional

Probab=80.99  E-value=1.8  Score=39.48  Aligned_cols=41  Identities=22%  Similarity=0.267  Sum_probs=28.4

Q ss_pred             CCCeEEEeccHHHHHHHHh-CCCccCC-CccEEEEcchhHhhh
Q 028826           50 EGANLLIGTPGRLYDIMER-MDVLDFR-NLVILVLDEADRLLD   90 (203)
Q Consensus        50 ~~~~ilV~Tp~~l~~~~~~-~~~~~l~-~v~~lViDEad~l~~   90 (203)
                      ..+||||+.-.-|+.-+.. .+.+-.. +-.++||||||+|-+
T Consensus       218 ~~AdivVtNH~LLladl~~~~~~iLp~~~~~~lViDEAH~L~d  260 (697)
T PRK11747        218 DEADVVVANHDLVLADLELGGGVVLPDPENLLYVLDEGHHLPD  260 (697)
T ss_pred             hhCCEEEECcHHHHhhhhccCCcccCCCCCCEEEEECccchHH
Confidence            4689999998877654432 1222222 468899999999864

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	203
2pl3_A	236	Human Dead-Box Rna Helicase Ddx10, Dead Domain In C		3e-23
3ly5_A	262	Ddx18 Dead-Domain Length = 262		2e-21
3ber_A	249	Human Dead-Box Rna-Helicase Ddx47, Conserved Domain		3e-21
2i4i_A	417	Crystal Structure Of Human Dead-Box Rna Helicase Dd		6e-19
2zu6_A	388	Crystal Structure Of The Eif4a-Pdcd4 Complex Length		2e-18
3eiq_A	414	Crystal Structure Of Pdcd4-eif4a Length = 414		2e-18
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		6e-18
1wrb_A	253	Crystal Structure Of The N-Terminal Reca-Like Domai		1e-17
3bor_A	237	Crystal Structure Of The Deadc Domain Of Human Tran		3e-17
2gxq_A	207	Hera N-Terminal Domain In Complex With Amp, Crystal		3e-16
3mwj_A	207	Q28e Mutant Of Hera N-Terminal Reca-Like Domain, Ap		3e-16
2j0u_B	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		3e-16
2vso_A	395	Crystal Structure Of A Translation Initiation Compl		7e-16
1qde_A	224	Crystal Structure Of The Atpase Domain Of Translati		7e-16
2hyi_C	413	Structure Of The Human Exon Junction Complex With A		8e-16
2hxy_A	391	Crystal Structure Of Human Apo-Eif4aiii Length = 39		9e-16
2xb2_A	411	Crystal Structure Of The Core Mago-Y14-Eif4aiii-Bar		9e-16
2j0q_A	410	The Crystal Structure Of The Exon Junction Complex		9e-16
2g9n_A	221	Structure Of The Dead Domain Of Human Eukaryotic In		1e-15
2j0u_A	374	The Crystal Structure Of Eif4aiii-Barentsz Complex		1e-15
1qva_A	223	Yeast Initiation Factor 4a N-Terminal Domain Length		1e-15
1q0u_A	219	Crystal Structure Of The Bstdead N-Terminal Domain		3e-15
1fuu_A	394	Yeast Initiation Factor 4a Length = 394		1e-14
2db3_A	434	Structural Basis For Rna Unwinding By The Dead-Box		3e-14
2z0m_A	337	Crystal Structure Of Hypothetical Atp-Dependent Rna		3e-14
1s2m_A	400	Crystal Structure Of The Dead Box Protein Dhh1p Len		4e-14
1xtk_A	390	Structure Of Decd To Dead Mutation Of Human Uap56 L		5e-14
1xtj_A	386	Structure Of Human Uap56 In Complex With Adp Length		1e-13
1xti_A	391	Structure Of Wildtype Human Uap56 Length = 391		1e-13
3iuy_A	228	Crystal Structure Of Ddx53 Dead-Box Domain Length =		2e-13
1vec_A	206	Crystal Structure Of The N-Terminal Domain Of RckP5		3e-13
2oxc_A	230	Human Dead-Box Rna Helicase Ddx20, Dead Domain In C		5e-13
1hv8_A	367	Crystal Structure Of A Dead Box Protein From The Hy		2e-12
3sqw_A	579	Structure Of Mss116p (Nte Deletion) Bound To Ssrna		3e-12
3i5x_A	563	Structure Of Mss116p Bound To Ssrna And Amp-Pnp Len		3e-12
1t6n_A	220	Crystal Structure Of The N-Terminal Domain Of Human		3e-12
3sqx_A	512	Structure Of Mss116p (Nte And C-Tail Double Deletio		3e-12
3fho_B	508	Structure Of S. Pombe Dbp5 Length = 508		9e-11
3pey_A	395	S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length		2e-09
3pew_A	395	S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3		2e-09
2kbe_A	226	Solution Structure Of Amino-Terminal Domain Of Dbp5		2e-09
3fht_A	412	Crystal Structure Of Human Dbp5 In Complex With Amp		1e-08
3g0h_A	424	Human Dead-box Rna Helicase Ddx19, In Complex With		1e-08
3fmp_B	479	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-08
3ews_A	445	Human Dead-Box Rna-Helicase Ddx19 In Complex With A		1e-08
3fhc_B	235	Crystal Structure Of Human Dbp5 In Complex With Nup		1e-08
3fmo_B	300	Crystal Structure Of The Nucleoporin Nup214 In Comp		1e-08
3dkp_A	245	Human Dead-Box Rna-Helicase Ddx52, Conserved Domain		3e-06

>pdb|2PL3|A Chain A, Human Dead-Box Rna Helicase Ddx10, Dead Domain In Complex With Adp Length = 236

Iteration: 1
 Score =  104 bits (260), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 57/135 (42%), Positives = 88/135 (65%), Gaps = 3/135 (2%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +IISPTREL+ Q + V +  +    D  + L++GG ++K + ++I     N+L+ TPGRL
Sbjct: 101 LIISPTRELAYQTFEVLRK-VGKNHDFSAGLIIGGKDLKHEAERIN--NINILVCTPGRL 157
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
              M+        +L +LVLDEADR+LDMGF   ++ +I  LPK R+T LFSATQT++V+
Sbjct: 158 LQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVK 217
Query: 123 ELSKAGLRNPVRIEV 137
           +L++  L+NP  + V
Sbjct: 218 DLARLSLKNPEYVWV 232

>pdb|3LY5|A Chain A, Ddx18 Dead-Domain Length = 262

Iteration: 1
 Score = 98.6 bits (244), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 53/128 (41%), Positives = 83/128 (64%), Gaps = 2/128 (1%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I+SPTREL+ Q + V +  ++        L++GG    A+ +K+   G N+++ TPGRL
Sbjct: 130 LILSPTRELAMQTFGVLKELMTHHVHTYG-LIMGGSNRSAEAQKLGN-GINIIVATPGRL 187
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 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|3BER|A Chain A, Human Dead-Box Rna-Helicase Ddx47, Conserved Domain I In Complex With Amp Length = 249

Iteration: 1
 Score = 98.2 bits (243), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 51/139 (36%), Positives = 90/139 (64%), Gaps = 2/139 (1%)
Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             ++++PTREL+ QI    +   S++  V+S ++VGG++  +    + ++  +++I TPG
Sbjct: 113 FALVLTPTRELAFQISEQFEALGSSI-GVQSAVIVGGIDSMSQSLALAKK-PHIIIATPG 170
Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL D +E     + R L  LV+DEADR+L+M F+ ++  I+  +P+ R+T LFSAT T+ 
Sbjct: 171 RLIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKK 230
Query: 121 VEELSKAGLRNPVRIEVRA 139
           V++L +A L+NPV+  V +
Sbjct: 231 VQKLQRAALKNPVKCAVSS 249

>pdb|2I4I|A Chain A, Crystal Structure Of Human Dead-Box Rna Helicase Ddx3x Length = 417

Iteration: 1
 Score = 90.5 bits (223), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 55/131 (41%), Positives = 85/131 (64%), Gaps = 9/131 (6%)
Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           + ++++PTREL+ QIY  A+ F S    V+  ++ GG ++   ++ +E  G +LL+ TPG
Sbjct: 103 ISLVLAPTRELAVQIYEEARKF-SYRSRVRPCVVYGGADIGQQIRDLER-GCHLLVATPG 160
Query: 61  RLYDIMERMDV-LDFRNLVILVLDEADRLLDMGFQKQISYIISR---LPK-LRRTGLFSA 115
           RL D+MER  + LDF     LVLDEADR+LDMGF+ QI  I+ +    PK +R T +FSA
Sbjct: 161 RLVDMMERGKIGLDF--CKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSA 218
Query: 116 TQTEAVEELSK 126
           T  + ++ L++
Sbjct: 219 TFPKEIQMLAR 229

>pdb|2ZU6|A Chain A, Crystal Structure Of The Eif4a-Pdcd4 Complex Length = 388

Iteration: 1
 Score = 89.0 bits (219), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 51/142 (35%), Positives = 84/142 (59%), Gaps = 8/142 (5%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPD---VKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            ++++PTREL+ QI    Q  +  L D         +GG  V+A+V+K++ E  ++++GT
Sbjct: 85  ALVLAPTRELAQQI----QKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGT 140
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  + + + VLDEAD +L  GF+ QI  I  +L    +  L SAT  
Sbjct: 141 PGRVFDMLNRR-YLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMP 199
Query: 119 EAVEELSKAGLRNPVRIEVRAE 140
             V E++K  +R+P+RI V+ E
Sbjct: 200 SDVLEVTKKFMRDPIRILVKKE 221

>pdb|3EIQ|A Chain A, Crystal Structure Of Pdcd4-eif4a Length = 414

Iteration: 1
 Score = 88.6 bits (218), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 51/142 (35%), Positives = 84/142 (59%), Gaps = 8/142 (5%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPD---VKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            ++++PTREL+ QI    Q  +  L D         +GG  V+A+V+K++ E  ++++GT
Sbjct: 111 ALVLAPTRELAQQI----QKVVMALGDYMGASCHACIGGTNVRAEVQKLQMEAPHIIVGT 166
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  + + + VLDEAD +L  GF+ QI  I  +L    +  L SAT  
Sbjct: 167 PGRVFDMLNRR-YLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMP 225
Query: 119 EAVEELSKAGLRNPVRIEVRAE 140
             V E++K  +R+P+RI 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 = 87.4 bits (215), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 49/137 (35%), Positives = 80/137 (58%), Gaps = 3/137 (2%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           ++++PTREL+ Q+  VA  +      +KS  + GG      ++ +E  G  + I TPGRL
Sbjct: 120 LVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLER-GVEICIATPGRL 177
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D +E     + R    LVLDEADR+LDMGF+ QI  I+ ++   R+T ++SAT  + V 
Sbjct: 178 IDFLE-CGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVR 236
Query: 123 ELSKAGLRNPVRIEVRA 139
           +L++  L++ + I + 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 = 6e-18,   Method: Compositional matrix adjust.
 Identities = 49/137 (35%), Positives = 80/137 (58%), Gaps = 3/137 (2%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           ++++PTREL+ Q+  VA  +      +KS  + GG      ++ +E  G  + I TPGRL
Sbjct: 106 LVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLER-GVEICIATPGRL 163
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D +E     + R    LVLDEADR+LDMGF+ QI  I+ ++   R+T ++SAT  + V 
Sbjct: 164 IDFLE-CGKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKEVR 222
Query: 123 ELSKAGLRNPVRIEVRA 139
           +L++  L++ + I + 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 = 86.3 bits (212), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 54/140 (38%), Positives = 89/140 (63%), Gaps = 9/140 (6%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTREL+ QI   +Q F    P ++S ++ GG +  + +++++  G +LL+ TPGRL
Sbjct: 104 LILAPTRELAIQILSESQKFSLNTP-LRSCVVYGGADTHSQIREVQM-GCHLLVATPGRL 161
Query: 63  YDIMERMDV-LDFRNLVILVLDEADRLLDMGFQKQISYII--SRLPK--LRRTGLFSATQ 117
            D +E+  + L+F   +  VLDEADR+LDMGF+ QI  II  S +P    R+T +FSAT 
Sbjct: 162 VDFIEKNKISLEFCKYI--VLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATF 219
Query: 118 TEAVEELSKAGLRNPVRIEV 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 = 85.1 bits (209), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 50/142 (35%), Positives = 83/142 (58%), Gaps = 8/142 (5%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPD---VKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            ++++PTREL+ QI    Q  I  L D         +GG  V+ +++K++ E  ++++GT
Sbjct: 101 ALVLAPTRELAQQI----QKVILALGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGT 156
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  + + + VLDEAD +L  GF+ QI  I  +L    +  L SAT  
Sbjct: 157 PGRVFDMLNR-RYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMP 215
Query: 119 EAVEELSKAGLRNPVRIEVRAE 140
             V E++K  +R+P+RI 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 = 81.6 bits (200), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 49/136 (36%), Positives = 78/136 (57%), Gaps = 5/136 (3%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ Q   VA    +  P +K + + GG       K+    GA+ ++ TPGR
Sbjct: 75  ALVLTPTRELALQ---VASELTAVAPHLKVVAVYGGTGYGKQ-KEALLRGADAVVATPGR 130
Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
             D + R  VLD   + + VLDEAD +L MGF++++  ++S  P  R+T LFSAT     
Sbjct: 131 ALDYL-RQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWA 189
Query: 122 EELSKAGLRNPVRIEV 137
           + L++  ++NPV I 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 = 81.6 bits (200), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 49/136 (36%), Positives = 78/136 (57%), Gaps = 5/136 (3%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ Q   VA    +  P +K + + GG       K+    GA+ ++ TPGR
Sbjct: 75  ALVLTPTRELALQ---VASELTAVAPHLKVVAVYGGTGYGKQ-KEALLRGADAVVATPGR 130
Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
             D + R  VLD   + + VLDEAD +L MGF++++  ++S  P  R+T LFSAT     
Sbjct: 131 ALDYL-RQGVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWA 189
Query: 122 EELSKAGLRNPVRIEV 137
           + L++  ++NPV I 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 = 81.6 bits (200), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 51/142 (35%), Positives = 85/142 (59%), Gaps = 9/142 (6%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPD---VKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTREL+ Q+    Q  +  L D   V+S   +GG  V  D++K++  G +++ GT
Sbjct: 72  ALILAPTRELAVQV----QKGLLALGDYMNVQSHACIGGTNVGEDIRKLDY-GQHVVAGT 126
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  R + +LVLDEAD +L+ GF++QI  +   LP   +  L SAT  
Sbjct: 127 PGRVFDMIRRRS-LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 185
Query: 119 EAVEELSKAGLRNPVRIEVRAE 140
             V E++   + +P+RI V+ +
Sbjct: 186 HEVLEMTNKFMTDPIRILVKRD 207

>pdb|2VSO|A Chain A, Crystal Structure Of A Translation Initiation Complex Length = 395

Iteration: 1
 Score = 80.1 bits (196), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 49/141 (34%), Positives = 80/141 (56%), Gaps = 8/141 (5%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V       + D+K    +GG     D + + +  A +++GTPGR
Sbjct: 93  ALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--AQIVVGTPGR 149
Query: 62  LYDIMERMDVLDFRN--LVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE 119
           ++D ++R     FR   + + +LDEAD +L  GF++QI  I + LP   +  L SAT   
Sbjct: 150 VFDNIQRRR---FRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPN 206
Query: 120 AVEELSKAGLRNPVRIEVRAE 140
            V E++   +RNPVRI V+ +
Sbjct: 207 DVLEVTTKFMRNPVRILVKKD 227

>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 = 80.1 bits (196), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 49/141 (34%), Positives = 80/141 (56%), Gaps = 8/141 (5%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V       + D+K    +GG     D + + +  A +++GTPGR
Sbjct: 85  ALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--AQIVVGTPGR 141
Query: 62  LYDIMERMDVLDFRN--LVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE 119
           ++D ++R     FR   + + +LDEAD +L  GF++QI  I + LP   +  L SAT   
Sbjct: 142 VFDNIQRRR---FRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPN 198
Query: 120 AVEELSKAGLRNPVRIEVRAE 140
            V E++   +RNPVRI V+ +
Sbjct: 199 DVLEVTTKFMRNPVRILVKKD 219

>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 = 80.1 bits (196), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 50/140 (35%), Positives = 83/140 (59%), Gaps = 9/140 (6%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPD---VKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTREL+ QI    Q  +  L D   V+    +GG  V  D++K++  G +++ GT
Sbjct: 109 ALILAPTRELAVQI----QKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGT 163
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  R + +LVLDEAD +L+ GF++QI  +   LP   +  L SAT  
Sbjct: 164 PGRVFDMIRRRS-LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 222
Query: 119 EAVEELSKAGLRNPVRIEVR 138
             + E++   + +P+RI V+
Sbjct: 223 HEILEMTNKFMTDPIRILVK 242

>pdb|2HXY|A Chain A, Crystal Structure Of Human Apo-Eif4aiii Length = 391

Iteration: 1
 Score = 80.1 bits (196), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 50/140 (35%), Positives = 83/140 (59%), Gaps = 9/140 (6%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPD---VKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTREL+ QI    Q  +  L D   V+    +GG  V  D++K++  G +++ GT
Sbjct: 87  ALILAPTRELAVQI----QKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGT 141
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  R + +LVLDEAD +L+ GF++QI  +   LP   +  L SAT  
Sbjct: 142 PGRVFDMIRRRS-LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 200
Query: 119 EAVEELSKAGLRNPVRIEVR 138
             + E++   + +P+RI V+
Sbjct: 201 HEILEMTNKFMTDPIRILVK 220

>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 = 80.1 bits (196), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 50/140 (35%), Positives = 83/140 (59%), Gaps = 9/140 (6%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPD---VKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTREL+ QI    Q  +  L D   V+    +GG  V  D++K++  G +++ GT
Sbjct: 109 ALILAPTRELAVQI----QKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGT 163
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  R + +LVLDEAD +L+ GF++QI  +   LP   +  L SAT  
Sbjct: 164 PGRVFDMIRRRS-LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 222
Query: 119 EAVEELSKAGLRNPVRIEVR 138
             + E++   + +P+RI V+
Sbjct: 223 HEILEMTNKFMTDPIRILVK 242

>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 = 9e-16,   Method: Compositional matrix adjust.
 Identities = 50/140 (35%), Positives = 83/140 (59%), Gaps = 9/140 (6%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPD---VKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTREL+ QI    Q  +  L D   V+    +GG  V  D++K++  G +++ GT
Sbjct: 108 ALILAPTRELAVQI----QKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGT 162
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  R + +LVLDEAD +L+ GF++QI  +   LP   +  L SAT  
Sbjct: 163 PGRVFDMIRRRS-LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 221
Query: 119 EAVEELSKAGLRNPVRIEVR 138
             + E++   + +P+RI V+
Sbjct: 222 HEILEMTNKFMTDPIRILVK 241

>pdb|2G9N|A Chain A, Structure Of The Dead Domain Of Human Eukaryotic Initiation Factor 4a, Eif4a Length = 221

Iteration: 1
 Score = 79.7 bits (195), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 48/139 (34%), Positives = 77/139 (55%), Gaps = 8/139 (5%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPD---VKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            ++++PTREL+ QI    Q  +  L D         +GG  V+A+V+ ++ E  ++++GT
Sbjct: 86  ALVLAPTRELAQQI----QXVVMALGDYMGASCHACIGGTNVRAEVQXLQMEAPHIIVGT 141
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L    + + VLDEAD +L  GF  QI  I   L    +  L SAT  
Sbjct: 142 PGRVFDMLNR-RYLSPXYIXMFVLDEADEMLSRGFXDQIYDIFQXLNSNTQVVLLSATMP 200
Query: 119 EAVEELSKAGLRNPVRIEV 137
             V E++   +R+P+RI V
Sbjct: 201 SDVLEVTXXFMRDPIRILV 219

>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 = 49/142 (34%), Positives = 84/142 (59%), Gaps = 9/142 (6%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPD---VKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTREL+ Q+    Q  +  L D   V+    +GG  V  D++K++  G +++ GT
Sbjct: 72  ALILAPTRELAVQV----QKGLLALGDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGT 126
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR++D++ R   L  R + +LVLDEAD +L+ GF++QI  +   LP   +  L SAT  
Sbjct: 127 PGRVFDMIRRRS-LRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLP 185
Query: 119 EAVEELSKAGLRNPVRIEVRAE 140
             + E++   + +P+RI V+ +
Sbjct: 186 HEILEMTNKFMTDPIRILVKRD 207

>pdb|1QVA|A Chain A, Yeast Initiation Factor 4a N-Terminal Domain Length = 223

Iteration: 1
 Score = 79.3 bits (194), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 49/138 (35%), Positives = 78/138 (56%), Gaps = 8/138 (5%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V       + D+K    +GG     D + + +  A +++GTPGR
Sbjct: 92  ALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLRD--AQIVVGTPGR 148
Query: 62  LYDIMERMDVLDFRN--LVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE 119
           ++D ++R     FR   + + +LDEAD +L  GF++QI  I + LP   +  L SAT   
Sbjct: 149 VFDNIQRRR---FRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPN 205
Query: 120 AVEELSKAGLRNPVRIEV 137
            V E++   +RNPVRI V
Sbjct: 206 DVLEVTTKFMRNPVRILV 223

>pdb|1Q0U|A Chain A, Crystal Structure Of The Bstdead N-Terminal Domain Length = 219

Iteration: 1
 Score = 77.8 bits (190), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 49/139 (35%), Positives = 75/139 (53%), Gaps = 5/139 (3%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSML---LVGGVEVKADVKKIEEEGANLLIGT 58
            +I +PTREL+ QIYH         P  + ++   L+GG + +  ++K+  +  +++IGT
Sbjct: 75  AVITAPTRELATQIYHETLKITKFCPKDRXIVARCLIGGTDKQKALEKLNVQ-PHIVIGT 133
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR+ D + R   LD     ILV+DEAD  LD GF   +  I +R PK  +  +FSAT  
Sbjct: 134 PGRINDFI-REQALDVHTAHILVVDEADLXLDXGFITDVDQIAARXPKDLQXLVFSATIP 192
Query: 119 EAVEELSKAGLRNPVRIEV 137
           E ++   K    NP  + V
Sbjct: 193 EKLKPFLKKYXENPTFVHV 211

>pdb|1FUU|A Chain A, Yeast Initiation Factor 4a Length = 394

Iteration: 1
 Score = 76.3 bits (186), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 49/141 (34%), Positives = 77/141 (54%), Gaps = 8/141 (5%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            + ++PTREL+ QI  V    ++   D+K    +GG     D + + +  A +++GTPGR
Sbjct: 92  ALXLAPTRELALQIQKVVXA-LAFHXDIKVHACIGGTSFVEDAEGLRD--AQIVVGTPGR 148
Query: 62  LYDIMERMDVLDFRN--LVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE 119
           ++D ++R     FR   +   +LDEAD  L  GF++QI  I + LP   +  L SAT   
Sbjct: 149 VFDNIQRRR---FRTDKIKXFILDEADEXLSSGFKEQIYQIFTLLPPTTQVVLLSATXPN 205
Query: 120 AVEELSKAGLRNPVRIEVRAE 140
            V E++    RNPVRI 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 = 74.7 bits (182), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 48/138 (34%), Positives = 84/138 (60%), Gaps = 7/138 (5%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I+SPTREL+ QI++ A+ F +    +K  ++ GG   +   + I   G +++I TPGRL
Sbjct: 133 VIVSPTRELAIQIFNEARKF-AFESYLKIGIVYGGTSFRHQNECITR-GCHVVIATPGRL 190
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRL---PKLRRTGLFSATQTE 119
            D ++R   + F +   +VLDEADR+LDMGF + +  I++ +   P+  +T +FSAT  E
Sbjct: 191 LDFVDRT-FITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPE-HQTLMFSATFPE 248
Query: 120 AVEELSKAGLRNPVRIEV 137
            ++ ++   L+N V + +
Sbjct: 249 EIQRMAGEFLKNYVFVAI 266

>pdb|2Z0M|A Chain A, Crystal Structure Of Hypothetical Atp-Dependent Rna Helicase From Sulfolobus Tokodaii Length = 337

Iteration: 1
 Score = 74.7 bits (182), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 45/135 (33%), Positives = 78/135 (57%), Gaps = 6/135 (4%)
Query: 3   MIISPTRELSAQIY-HVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
           ++++PTREL+ Q+  H+    I    D K   + GG+  KA + ++    A++++ TPGR
Sbjct: 60  LVVTPTRELTRQVASHIRD--IGRYMDTKVAEVYGGMPYKAQINRVR--NADIVVATPGR 115
Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           L D+  +  V+D  +  I+++DEAD + +MGF   I  I+++    + TGLFSAT  E +
Sbjct: 116 LLDLWSK-GVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEEI 174
Query: 122 EELSKAGLRNPVRIE 136
            ++ K  + N   IE
Sbjct: 175 RKVVKDFITNYEEIE 189

>pdb|1S2M|A Chain A, Crystal Structure Of The Dead Box Protein Dhh1p Length = 400

Iteration: 1
 Score = 74.7 bits (182), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 45/139 (32%), Positives = 74/139 (53%), Gaps = 3/139 (2%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +I+ PTREL+ Q   V +  +     +  M+  GG  ++ D+ ++ E   ++L+GTPGR
Sbjct: 92  ALIMVPTRELALQTSQVVRT-LGKHCGISCMVTTGGTNLRDDILRLNET-VHILVGTPGR 149
Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           + D+  R  V D  +  + ++DEAD++L   F+  I  I+S LP   ++ LFSAT    V
Sbjct: 150 VLDLASR-KVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTV 208
Query: 122 EELSKAGLRNPVRIEVRAE 140
           +E     L  P  I +  E
Sbjct: 209 KEFMVKHLHKPYEINLMEE 227

>pdb|1XTK|A Chain A, Structure Of Decd To Dead Mutation Of Human Uap56 Length = 390

Iteration: 1
 Score = 74.3 bits (181), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 47/194 (24%), Positives = 104/194 (53%), Gaps = 16/194 (8%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR+
Sbjct: 79  LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 138
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
              + R   L+ +++   +LDEAD++L+ +  ++ +  I    P  ++  +FSAT ++ +
Sbjct: 139 L-ALARNKSLNLKHIKHFILDEADKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEI 197
Query: 122 EELSKAGLRNPVRIEVRAEXXXXXXXXXXXXXXXXXTPLGLHLEYLECESDKKPSQLVDL 181
             + +  +++P+ I V  E                 T  GL   Y++ + ++K  +L DL
Sbjct: 198 RPVCRKFMQDPMEIFVDDE--------------TKLTLHGLQQYYVKLKDNEKNRKLFDL 243
Query: 182 LIKNKSKKIIMYVQ 195
           L   +  +++++V+
Sbjct: 244 LDVLEFNQVVIFVK 257

>pdb|1XTJ|A Chain A, Structure Of Human Uap56 In Complex With Adp Length = 386

Iteration: 1
 Score = 72.8 bits (177), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/194 (23%), Positives = 103/194 (53%), Gaps = 16/194 (8%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR+
Sbjct: 80  LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 139
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
              + R   L+ +++   +LDE D++L+ +  ++ +  I    P  ++  +FSAT ++ +
Sbjct: 140 L-ALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEI 198
Query: 122 EELSKAGLRNPVRIEVRAEXXXXXXXXXXXXXXXXXTPLGLHLEYLECESDKKPSQLVDL 181
             + +  +++P+ I V  E                 T  GL   Y++ + ++K  +L DL
Sbjct: 199 RPVCRKFMQDPMEIFVDDE--------------TKLTLHGLQQYYVKLKDNEKNRKLFDL 244
Query: 182 LIKNKSKKIIMYVQ 195
           L   +  +++++V+
Sbjct: 245 LDVLEFNQVVIFVK 258

>pdb|1XTI|A Chain A, Structure Of Wildtype Human Uap56 Length = 391

Iteration: 1
 Score = 72.8 bits (177), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 46/194 (23%), Positives = 103/194 (53%), Gaps = 16/194 (8%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR+
Sbjct: 80  LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 139
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
              + R   L+ +++   +LDE D++L+ +  ++ +  I    P  ++  +FSAT ++ +
Sbjct: 140 L-ALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEI 198
Query: 122 EELSKAGLRNPVRIEVRAEXXXXXXXXXXXXXXXXXTPLGLHLEYLECESDKKPSQLVDL 181
             + +  +++P+ I V  E                 T  GL   Y++ + ++K  +L DL
Sbjct: 199 RPVCRKFMQDPMEIFVDDE--------------TKLTLHGLQQYYVKLKDNEKNRKLFDL 244
Query: 182 LIKNKSKKIIMYVQ 195
           L   +  +++++V+
Sbjct: 245 LDVLEFNQVVIFVK 258

>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 = 42/135 (31%), Positives = 82/135 (60%), Gaps = 4/135 (2%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           ++++PTREL+  +      +  +   +KS+ + GG      ++ I + G +++I TPGRL
Sbjct: 98  LVLTPTRELALHVEAECSKY--SYKGLKSICIYGGRNRNGQIEDISK-GVDIIIATPGRL 154
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D ++  + ++ R++  LV+DEAD++LDM F+ QI  I+  +   R+T + SAT  + V 
Sbjct: 155 ND-LQMNNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDTVR 213
Query: 123 ELSKAGLRNPVRIEV 137
           +L+ + L++P+ + V
Sbjct: 214 QLALSYLKDPMIVYV 228

>pdb|1VEC|A Chain A, Crystal Structure Of The N-Terminal Domain Of RckP54, A Human Dead-Box Protein Length = 206

Iteration: 1
 Score = 71.6 bits (174), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 43/134 (32%), Positives = 76/134 (56%), Gaps = 2/134 (1%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            M+I PTREL+ Q+  +       +   K M   GG  ++ D+ ++++   +++I TPGR
Sbjct: 74  AMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDT-VHVVIATPGR 132
Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           + D++++  V    ++ ++VLDEAD+LL   F + +  II  LPK R+  L+SAT   +V
Sbjct: 133 ILDLIKK-GVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSV 191
Query: 122 EELSKAGLRNPVRI 135
           ++   + L  P  I
Sbjct: 192 QKFMNSHLEKPYEI 205

>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 = 5e-13,   Method: Compositional matrix adjust.
 Identities = 40/138 (28%), Positives = 82/138 (59%), Gaps = 4/138 (2%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTRE++ QI+ V       +  ++  + +GG  +  D  ++++   ++ +G+PGR+
Sbjct: 96  LILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLKK--CHIAVGSPGRI 153
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDMG-FQKQISYIISRLPKLRRTGLFSATQTEAV 121
             ++E +D L+  ++ + +LDEAD+LL+ G FQ+QI++I S LP  ++    SAT  E +
Sbjct: 154 KQLIE-LDYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEFL 212
Query: 122 EELSKAGLRNPVRIEVRA 139
                  +R+P  + + +
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 = 68.6 bits (166), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 41/125 (32%), Positives = 70/125 (56%), Gaps = 4/125 (3%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +I++PTREL+ Q+    +       ++K   + GG  +   +K ++   AN+++GTPGR
Sbjct: 77  AIILTPTRELAIQVADEIESLKGN-KNLKIAKIYGGKAIYPQIKALK--NANIVVGTPGR 133
Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           + D + R   L+ +N+   +LDEAD  L+ GF K +  I++   K +R  LFSAT    +
Sbjct: 134 ILDHINR-GTLNLKNVKYFILDEADEXLNXGFIKDVEKILNACNKDKRILLFSATXPREI 192
Query: 122 EELSK 126
             L+K
Sbjct: 193 LNLAK 197

>pdb|3SQW|A Chain A, Structure Of Mss116p (Nte Deletion) Bound To Ssrna And Amp-Pnp Length = 579

Iteration: 1
 Score = 68.6 bits (166), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 46/134 (34%), Positives = 74/134 (55%), Gaps = 10/134 (7%)
Query: 2   GMIISPTRELSAQIYHVAQPFIST---LPDVKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTR+L+ QI    +        L     + LVGG + +A + K+ +   N++I T
Sbjct: 98  AVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIAT 157
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYII-------SRLPKLRRTG 111
           PGRL D++E+     FR +   VLDEADRLL++GF+  +  I        S+     +T 
Sbjct: 158 PGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTL 217
Query: 112 LFSATQTEAVEELS 125
           LFSAT  + V++L+
Sbjct: 218 LFSATLDDKVQKLA 231

>pdb|3I5X|A Chain A, Structure Of Mss116p Bound To Ssrna And Amp-Pnp Length = 563

Iteration: 1
 Score = 68.6 bits (166), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 46/134 (34%), Positives = 74/134 (55%), Gaps = 10/134 (7%)
Query: 2   GMIISPTRELSAQIYHVAQPFIST---LPDVKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTR+L+ QI    +        L     + LVGG + +A + K+ +   N++I T
Sbjct: 149 AVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIAT 208
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLR-------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|1T6N|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human Uap56 Length = 220

Iteration: 1
 Score = 68.2 bits (165), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 35/136 (25%), Positives = 79/136 (58%), Gaps = 2/136 (1%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR+
Sbjct: 86  LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 145
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
              + R   L+ +++   +LDE D++L+ +  ++ +  I    P  ++  +FSAT ++ +
Sbjct: 146 L-ALARNKSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEI 204
Query: 122 EELSKAGLRNPVRIEV 137
             + +  +++P+ I V
Sbjct: 205 RPVCRKFMQDPMEIFV 220

>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 = 68.2 bits (165), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 46/134 (34%), Positives = 74/134 (55%), Gaps = 10/134 (7%)
Query: 2   GMIISPTRELSAQIYHVAQPFIST---LPDVKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTR+L+ QI    +        L     + LVGG + +A + K+ +   N++I T
Sbjct: 98  AVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIAT 157
Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLR-------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|3PEY|A Chain A, S. Cerevisiae Dbp5 Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 43/140 (30%), Positives = 73/140 (52%), Gaps = 8/140 (5%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            + ++P+REL+ Q   V Q  +     + S L+V         +K ++  A +++GTPG 
Sbjct: 78  AICLAPSRELARQTLEVVQE-MGKFTKITSQLIVPD-----SFEKNKQINAQVIVGTPGT 131
Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           + D+M R  ++  + + I VLDEAD +LD  G   Q   +   LPK  +  LFSAT  +A
Sbjct: 132 VLDLMRR-KLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADA 190
Query: 121 VEELSKAGLRNPVRIEVRAE 140
           V + +K  + N   +E++  
Sbjct: 191 VRQYAKKIVPNANTLELQTN 210

>pdb|3PEW|A Chain A, S. Cerevisiae Dbp5 L327v Bound To Rna And Adp Bef3 Length = 395

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 43/140 (30%), Positives = 73/140 (52%), Gaps = 8/140 (5%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            + ++P+REL+ Q   V Q  +     + S L+V         +K ++  A +++GTPG 
Sbjct: 78  AICLAPSRELARQTLEVVQE-MGKFTKITSQLIVPD-----SFEKNKQINAQVIVGTPGT 131
Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           + D+M R  ++  + + I VLDEAD +LD  G   Q   +   LPK  +  LFSAT  +A
Sbjct: 132 VLDLMRR-KLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADA 190
Query: 121 VEELSKAGLRNPVRIEVRAE 140
           V + +K  + N   +E++  
Sbjct: 191 VRQYAKKIVPNANTLELQTN 210

>pdb|2KBE|A Chain A, Solution Structure Of Amino-Terminal Domain Of Dbp5p Length = 226

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 43/138 (31%), Positives = 73/138 (52%), Gaps = 8/138 (5%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            + ++P+REL+ Q   V Q  +     + S L+V         +K ++  A +++GTPG 
Sbjct: 95  AICLAPSRELARQTLEVVQE-MGKFTKITSQLIVPD-----SFEKNKQINAQVIVGTPGT 148
Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           + D+M R  ++  + + I VLDEAD +LD  G   Q   +   LPK  +  LFSAT  +A
Sbjct: 149 VLDLMRR-KLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADA 207
Query: 121 VEELSKAGLRNPVRIEVR 138
           V + +K  + N   +E++
Sbjct: 208 VRQYAKKIVPNANTLELQ 225

>pdb|3FHT|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Amppnp And Rna Length = 412

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 42/139 (30%), Positives = 76/139 (54%), Gaps = 5/139 (3%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   +KI E+   ++IGTPG +
Sbjct: 99  LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-QKISEQ---IVIGTPGTV 154
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLL-DMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + + + VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 155 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 214
Query: 122 EELSKAGLRNPVRIEVRAE 140
            + ++  + +P  I+++ E
Sbjct: 215 WKFAQKVVPDPNVIKLKRE 233

>pdb|3G0H|A Chain A, Human Dead-box Rna Helicase Ddx19, In Complex With An Atp-analogue And Rna Length = 424

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 42/139 (30%), Positives = 76/139 (54%), Gaps = 5/139 (3%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   +KI E+   ++IGTPG +
Sbjct: 115 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-QKISEQ---IVIGTPGTV 170
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLL-DMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + + + VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 171 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 230
Query: 122 EELSKAGLRNPVRIEVRAE 140
            + ++  + +P  I+++ E
Sbjct: 231 WKFAQKVVPDPNVIKLKRE 249

>pdb|3FMP|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 479

Iteration: 1
 Score = 56.2 bits (134), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 42/139 (30%), Positives = 76/139 (54%), Gaps = 5/139 (3%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   +KI E+   ++IGTPG +
Sbjct: 166 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-QKISEQ---IVIGTPGTV 221
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLL-DMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + + + VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 222 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 281
Query: 122 EELSKAGLRNPVRIEVRAE 140
            + ++  + +P  I+++ E
Sbjct: 282 WKFAQKVVPDPNVIKLKRE 300

>pdb|3EWS|A Chain A, Human Dead-Box Rna-Helicase Ddx19 In Complex With Adp Length = 445

Iteration: 1
 Score = 56.2 bits (134), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 42/139 (30%), Positives = 76/139 (54%), Gaps = 5/139 (3%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   +KI E+   ++IGTPG +
Sbjct: 136 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-QKISEQ---IVIGTPGTV 191
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLL-DMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + + + VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 192 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 251
Query: 122 EELSKAGLRNPVRIEVRAE 140
            + ++  + +P  I+++ E
Sbjct: 252 WKFAQKVVPDPNVIKLKRE 270

>pdb|3FHC|B Chain B, Crystal Structure Of Human Dbp5 In Complex With Nup214 Length = 235

Iteration: 1
 Score = 56.2 bits (134), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 42/139 (30%), Positives = 76/139 (54%), Gaps = 5/139 (3%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   +KI E+   ++IGTPG +
Sbjct: 99  LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-QKISEQ---IVIGTPGTV 154
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLL-DMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + + + VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 155 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 214
Query: 122 EELSKAGLRNPVRIEVRAE 140
            + ++  + +P  I+++ E
Sbjct: 215 WKFAQKVVPDPNVIKLKRE 233

>pdb|3FMO|B Chain B, Crystal Structure Of The Nucleoporin Nup214 In Complex With The Dead- Box Helicase Ddx19 Length = 300

Iteration: 1
 Score = 56.2 bits (134), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 42/139 (30%), Positives = 76/139 (54%), Gaps = 5/139 (3%)
Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   +KI E+   ++IGTPG +
Sbjct: 166 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERG-QKISEQ---IVIGTPGTV 221
Query: 63  YDIMERMDVLDFRNLVILVLDEADRLL-DMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + + + VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 222 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 281
Query: 122 EELSKAGLRNPVRIEVRAE 140
            + ++  + +P  I+++ E
Sbjct: 282 WKFAQKVVPDPNVIKLKRE 300

>pdb|3DKP|A Chain A, Human Dead-Box Rna-Helicase Ddx52, Conserved Domain I In Complex With Adp Length = 245

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 42/144 (29%), Positives = 72/144 (50%), Gaps = 8/144 (5%)
Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +IISPTREL++QI H     IS     +  ++               +  ++L+ TP R
Sbjct: 101 ALIISPTRELASQI-HRELIKISEGTGFRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNR 159
Query: 62  L-YDIMERMDVLDFRNLVILVLDEADRLLD---MGFQKQIS--YIISRLPKLRRTGLFSA 115
           L Y + +    +D  ++  LV+DE+D+L +    GF+ Q++  ++     K+RR  +FSA
Sbjct: 160 LIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRR-AMFSA 218
Query: 116 TQTEAVEELSKAGLRNPVRIEVRA 139
           T    VE+  K  L N + + + A
Sbjct: 219 TFAYDVEQWCKLNLDNVISVSIGA 242

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	203
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	3e-52
3ly5_A	262	ATP-dependent RNA helicase DDX18; alpha-beta, stru	2e-47
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	5e-47
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	1e-46
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	1e-45
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	4e-41
3bor_A	237	Human initiation factor 4A-II; translation initiat	1e-40
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	2e-40
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	4e-40
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	1e-39
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	3e-39
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	5e-39
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	6e-39
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	1e-38
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	2e-38
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	2e-38
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	8e-38
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	9e-38
1vec_A	206	ATP-dependent RNA helicase P54; DEAD-box protein,	2e-37
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	2e-37
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	2e-37
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	3e-37
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	6e-37
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	1e-36
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	1e-36
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	2e-36
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	2e-36
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	7e-34
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	1e-31
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	8e-31
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	3e-30
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	2e-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 =  166 bits (423), Expect = 3e-52
 Identities = 57/140 (40%), Positives = 90/140 (64%), Gaps = 3/140 (2%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +IISPTREL+ Q + V +  +    D  + L++GG ++K + ++I     N+L+ TPGR
Sbjct: 100 VLIISPTRELAYQTFEVLRK-VGKNHDFSAGLIIGGKDLKHEAERIN--NINILVCTPGR 156

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           L   M+        +L +LVLDEADR+LDMGF   ++ +I  LPK R+T LFSATQT++V
Sbjct: 157 LLQHMDETVSFHATDLQMLVLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSV 216

Query: 122 EELSKAGLRNPVRIEVRAES 141
           ++L++  L+NP  + 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 =  155 bits (394), Expect = 2e-47
 Identities = 54/134 (40%), Positives = 86/134 (64%), Gaps = 3/134 (2%)

Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I+SPTREL+ Q + V +  ++        L++GG    A+ +K+   G N+++ TPGRL
Sbjct: 130 LILSPTRELAMQTFGVLKELMTHH-VHTYGLIMGGSNRSAEAQKLGN-GINIIVATPGRL 187

Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D M+      ++NL  LV+DEADR+LD+GF++++  II  LP  R+T LFSATQT  VE
Sbjct: 188 LDHMQNTPGFMYKNLQCLVIDEADRILDVGFEEELKQIIKLLPTRRQTMLFSATQTRKVE 247

Query: 123 ELSKAGLRN-PVRI 135
           +L++  L+  P+ +
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 = 5e-47
 Identities = 51/197 (25%), Positives = 86/197 (43%), Gaps = 21/197 (10%)

Query: 4   IISPTRELSAQIYHVAQ---PFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           I++PTR+L+ QI    +        L     + LVGG + +A + K+ +   N++I TPG
Sbjct: 151 IVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIATPG 210

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLR-------RTGLF 113
           RL D++E+     FR +   VLDEADRLL++GF+  +  I   L +         +T LF
Sbjct: 211 RLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLF 270

Query: 114 SATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDK 173
           SAT  + V++L+   +     + +    K+                  +    +  E   
Sbjct: 271 SATLDDKVQKLANNIMNKKECLFLDTVDKNEPE-----------AHERIDQSVVISEKFA 319

Query: 174 KPSQLVDLLIKNKSKKI 190
                    IK + K+ 
Sbjct: 320 NSIFAAVEHIKKQIKER 336

>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 =  160 bits (406), Expect = 1e-46
 Identities = 52/209 (24%), Positives = 91/209 (43%), Gaps = 27/209 (12%)

Query: 2   GMIISPTRELSAQIYHVAQ---PFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I++PTR+L+ QI    +        L     + LVGG + +A + K+ +   N++I T
Sbjct: 98  AVIVAPTRDLALQIEAEVKKIHDMNYGLKKYACVSLVGGTDFRAAMNKMNKLRPNIVIAT 157

Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLR-------RTG 111
           PGRL D++E+     FR +   VLDEADRLL++GF+  +  I   L +         +T 
Sbjct: 158 PGRLIDVLEKYSNKFFRFVDYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTL 217

Query: 112 LFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECES 171
           LFSAT  + V++L+   +     + +    K+                  +    +  E 
Sbjct: 218 LFSATLDDKVQKLANNIMNKKECLFLDTVDKNEPE-----------AHERIDQSVVISEK 266

Query: 172 -DKKPSQLVDLLIKN-----KSKKIIMYV 194
                   V+ + K       + K I++ 
Sbjct: 267 FANSIFAAVEHIKKQIKERDSNYKAIIFA 295

>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 =  150 bits (381), Expect = 1e-45
 Identities = 51/138 (36%), Positives = 89/138 (64%), Gaps = 2/138 (1%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI    +   S++  V+S ++VGG++  +    + +   +++I TPGR
Sbjct: 114 ALVLTPTRELAFQISEQFEALGSSIG-VQSAVIVGGIDSMSQSLALAK-KPHIIIATPGR 171

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           L D +E     + R L  LV+DEADR+L+M F+ ++  I+  +P+ R+T LFSAT T+ V
Sbjct: 172 LIDHLENTKGFNLRALKYLVMDEADRILNMDFETEVDKILKVIPRDRKTFLFSATMTKKV 231

Query: 122 EELSKAGLRNPVRIEVRA 139
           ++L +A L+NPV+  V +
Sbjct: 232 QKLQRAALKNPVKCAVSS 249

>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 =  138 bits (351), Expect = 4e-41
 Identities = 36/141 (25%), Positives = 66/141 (46%), Gaps = 6/141 (4%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +IISPTREL++QI+             +  ++               +  ++L+ TP R
Sbjct: 101 ALIISPTRELASQIHRELIKISEGTG-FRIHMIHKAAVAAKKFGPKSSKKFDILVTTPNR 159

Query: 62  LYDIMER-MDVLDFRNLVILVLDEADRLLD---MGFQKQISYIISRL-PKLRRTGLFSAT 116
           L  ++++    +D  ++  LV+DE+D+L +    GF+ Q++ I         R  +FSAT
Sbjct: 160 LIYLLKQDPPGIDLASVEWLVVDESDKLFEDGKTGFRDQLASIFLACTSHKVRRAMFSAT 219

Query: 117 QTEAVEELSKAGLRNPVRIEV 137
               VE+  K  L N + + +
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 =  137 bits (347), Expect = 1e-40
 Identities = 47/139 (33%), Positives = 81/139 (58%), Gaps = 2/139 (1%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V    +           +GG  V+ +++K++ E  ++++GTPGR
Sbjct: 101 ALVLAPTRELAQQIQKVILA-LGDYMGATCHACIGGTNVRNEMQKLQAEAPHIVVGTPGR 159

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           ++D++ R   L  + + + VLDEAD +L  GF+ QI  I  +L    +  L SAT    V
Sbjct: 160 VFDMLNR-RYLSPKWIKMFVLDEADEMLSRGFKDQIYEIFQKLNTSIQVVLLSATMPTDV 218

Query: 122 EELSKAGLRNPVRIEVRAE 140
            E++K  +R+P+RI V+ E
Sbjct: 219 LEVTKKFMRDPIRILVKKE 237

>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 = 2e-40
 Identities = 49/139 (35%), Positives = 82/139 (58%), Gaps = 2/139 (1%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V       +        +GG  V+A+V+K++ E  ++++GTPGR
Sbjct: 111 ALVLAPTRELAQQIQKVVMALGDYM-GASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGR 169

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           ++D++ R   L  + + + VLDEAD +L  GF+ QI  I  +L    +  L SAT    V
Sbjct: 170 VFDMLNR-RYLSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDV 228

Query: 122 EELSKAGLRNPVRIEVRAE 140
            E++K  +R+P+RI V+ E
Sbjct: 229 LEVTKKFMRDPIRILVKKE 247

>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 =  140 bits (355), Expect = 4e-40
 Identities = 54/194 (27%), Positives = 97/194 (50%), Gaps = 22/194 (11%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             +I+SPTREL+ QI++ A+ F      +K  ++ GG   +   + I   G +++I TPG
Sbjct: 131 QVVIVSPTRELAIQIFNEARKFAFES-YLKIGIVYGGTSFRHQNECITR-GCHVVIATPG 188

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIIS--RLPKLRRTGLFSATQT 118
           RL D ++R   + F +   +VLDEADR+LDMGF + +  I++   +    +T +FSAT  
Sbjct: 189 RLLDFVDR-TFITFEDTRFVVLDEADRMLDMGFSEDMRRIMTHVTMRPEHQTLMFSATFP 247

Query: 119 EAVEELSKAGLRNPVRIEV-RAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQ 177
           E ++ ++   L+N V + +         A +  +Q           +         K S+
Sbjct: 248 EEIQRMAGEFLKNYVFVAIGIVGG----ACSDVKQ----------TIYE--VNKYAKRSK 291

Query: 178 LVDLLIKNKSKKII 191
           L+++L +     I+
Sbjct: 292 LIEILSEQADGTIV 305

>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 =  134 bits (339), Expect = 1e-39
 Identities = 42/137 (30%), Positives = 80/137 (58%), Gaps = 4/137 (2%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             ++++PTREL+  +      +      +KS+ + GG      ++ I + G +++I TPG
Sbjct: 96  GMLVLTPTRELALHVEAECSKYSYK--GLKSICIYGGRNRNGQIEDISK-GVDIIIATPG 152

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL D+    + ++ R++  LV+DEAD++LDM F+ QI  I+  +   R+T + SAT  + 
Sbjct: 153 RLNDLQM-NNSVNLRSITYLVIDEADKMLDMEFEPQIRKILLDVRPDRQTVMTSATWPDT 211

Query: 121 VEELSKAGLRNPVRIEV 137
           V +L+ + L++P+ + V
Sbjct: 212 VRQLALSYLKDPMIVYV 228

>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 =  133 bits (338), Expect = 3e-39
 Identities = 51/146 (34%), Positives = 85/146 (58%), Gaps = 7/146 (4%)

Query: 4   IISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLY 63
           I++PTREL+ QI   +Q F    P ++S ++ GG +  + +++++  G +LL+ TPGRL 
Sbjct: 105 ILAPTRELAIQILSESQKFSLNTP-LRSCVVYGGADTHSQIREVQM-GCHLLVATPGRLV 162

Query: 64  DIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIIS--RLPKL--RRTGLFSATQTE 119
           D +E+  +        +VLDEADR+LDMGF+ QI  II    +P    R+T +FSAT  +
Sbjct: 163 DFIEKNKI-SLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPK 221

Query: 120 AVEELSKAGLRNPVRIEVRAESKSHH 145
            +++L+   L N + + V     +  
Sbjct: 222 EIQKLAADFLYNYIFMTVGRVGSTSD 247

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens} Length = 417

 Score =  137 bits (347), Expect = 5e-39
 Identities = 65/199 (32%), Positives = 102/199 (51%), Gaps = 25/199 (12%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QIY  A+ F S    V+  ++ GG ++   ++ +E  G +LL+ TPGR
Sbjct: 104 SLVLAPTRELAVQIYEEARKF-SYRSRVRPCVVYGGADIGQQIRDLER-GCHLLVATPGR 161

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIIS----RLPKLRRTGLFSATQ 117
           L D+MER   +       LVLDEADR+LDMGF+ QI  I+         +R T +FSAT 
Sbjct: 162 LVDMMER-GKIGLDFCKYLVLDEADRMLDMGFEPQIRRIVEQDTMPPKGVRHTMMFSATF 220

Query: 118 TEAVEELSKAGLRNPVRIEV-RAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPS 176
            + ++ L++  L   + + V R  S     S +  Q           + +   E   K S
Sbjct: 221 PKEIQMLARDFLDEYIFLAVGRVGS----TSENITQ----------KVVW--VEESDKRS 264

Query: 177 QLVDLLIK-NKSKKIIMYV 194
            L+DLL    K    +++V
Sbjct: 265 FLLDLLNATGKDSLTLVFV 283

>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 =  132 bits (334), Expect = 6e-39
 Identities = 47/139 (33%), Positives = 77/139 (55%), Gaps = 4/139 (2%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V       + D+K    +GG     D + +    A +++GTPGR
Sbjct: 85  ALMLAPTRELALQIQKVVMALAFHM-DIKVHACIGGTSFVEDAEGLR--DAQIVVGTPGR 141

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           ++D ++R        + + +LDEAD +L  GF++QI  I + LP   +  L SAT    V
Sbjct: 142 VFDNIQR-RRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDV 200

Query: 122 EELSKAGLRNPVRIEVRAE 140
            E++   +RNPVRI V+ +
Sbjct: 201 LEVTTKFMRNPVRILVKKD 219

>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 = 1e-38
 Identities = 47/139 (33%), Positives = 78/139 (56%), Gaps = 4/139 (2%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V    ++   D+K    +GG     D + +    A +++GTPGR
Sbjct: 92  ALMLAPTRELALQIQKVVMA-LAFHMDIKVHACIGGTSFVEDAEGLR--DAQIVVGTPGR 148

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           ++D ++R        + + +LDEAD +L  GF++QI  I + LP   +  L SAT    V
Sbjct: 149 VFDNIQR-RRFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQVVLLSATMPNDV 207

Query: 122 EELSKAGLRNPVRIEVRAE 140
            E++   +RNPVRI V+ +
Sbjct: 208 LEVTTKFMRNPVRILVKKD 226

>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 =  135 bits (342), Expect = 2e-38
 Identities = 45/139 (32%), Positives = 73/139 (52%), Gaps = 3/139 (2%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +I+ PTREL+ Q   V +        +  M+  GG  ++ D+ ++ E   ++L+GTPGR
Sbjct: 92  ALIMVPTRELALQTSQVVRTL-GKHCGISCMVTTGGTNLRDDILRLNE-TVHILVGTPGR 149

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           + D+  R  V D  +  + ++DEAD++L   F+  I  I+S LP   ++ LFSAT    V
Sbjct: 150 VLDLASR-KVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLLFSATFPLTV 208

Query: 122 EELSKAGLRNPVRIEVRAE 140
           +E     L  P  I +  E
Sbjct: 209 KEFMVKHLHKPYEINLMEE 227

>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 =  131 bits (332), Expect = 2e-38
 Identities = 48/137 (35%), Positives = 80/137 (58%), Gaps = 3/137 (2%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           + ++++PTREL+ Q+  VA  +      +KS  + GG      ++ +E  G  + I TPG
Sbjct: 104 ICLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDLER-GVEICIATPG 161

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           RL D +E     + R    LVLDEADR+LDMGF+ QI  I+ ++   R+T ++SAT  + 
Sbjct: 162 RLIDFLEC-GKTNLRRTTYLVLDEADRMLDMGFEPQIRKIVDQIRPDRQTLMWSATWPKE 220

Query: 121 VEELSKAGLRNPVRIEV 137
           V +L++  L++ + I +
Sbjct: 221 VRQLAEDFLKDYIHINI 237

>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 =  129 bits (327), Expect = 8e-38
 Identities = 40/139 (28%), Positives = 80/139 (57%), Gaps = 4/139 (2%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +I++PTRE++ QI+ V       +  ++  + +GG  +  D  +++    ++ +G+PGR
Sbjct: 95  ILILAPTREIAVQIHSVITAIGIKMEGLECHVFIGGTPLSQDKTRLK--KCHIAVGSPGR 152

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMG-FQKQISYIISRLPKLRRTGLFSATQTEA 120
           +  ++E  D L+  ++ + +LDEAD+LL+ G FQ+QI++I S LP  ++    SAT  E 
Sbjct: 153 IKQLIEL-DYLNPGSIRLFILDEADKLLEEGSFQEQINWIYSSLPASKQMLAVSATYPEF 211

Query: 121 VEELSKAGLRNPVRIEVRA 139
           +       +R+P  + + +
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 = 9e-38
 Identities = 47/139 (33%), Positives = 82/139 (58%), Gaps = 3/139 (2%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +I++PTREL+ QI          + +V+    +GG  V  D++K++  G +++ GTPGR
Sbjct: 108 ALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKLDY-GQHVVAGTPGR 165

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           ++D++ R   L  R + +LVLDEAD +L+ GF++QI  +   LP   +  L SAT    +
Sbjct: 166 VFDMIRR-RSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHEI 224

Query: 122 EELSKAGLRNPVRIEVRAE 140
            E++   + +P+RI 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 (323), Expect = 2e-37
 Identities = 43/134 (32%), Positives = 76/134 (56%), Gaps = 2/134 (1%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            M+I PTREL+ Q+  +       +   K M   GG  ++ D+ ++++   +++I TPGR
Sbjct: 74  AMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDD-TVHVVIATPGR 132

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           + D++++  V    ++ ++VLDEAD+LL   F + +  II  LPK R+  L+SAT   +V
Sbjct: 133 ILDLIKK-GVAKVDHVQMIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSV 191

Query: 122 EELSKAGLRNPVRI 135
           ++   + L  P  I
Sbjct: 192 QKFMNSHLEKPYEI 205

>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 =  130 bits (329), Expect = 2e-37
 Identities = 40/139 (28%), Positives = 72/139 (51%), Gaps = 5/139 (3%)

Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   K        ++IGTPG +
Sbjct: 166 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI----SEQIVIGTPGTV 221

Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + + + VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 222 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 281

Query: 122 EELSKAGLRNPVRIEVRAE 140
            + ++  + +P  I+++ E
Sbjct: 282 WKFAQKVVPDPNVIKLKRE 300

>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 =  132 bits (334), Expect = 2e-37
 Identities = 36/142 (25%), Positives = 81/142 (57%), Gaps = 2/142 (1%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR
Sbjct: 79  VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGR 138

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           +  +      L+ +++   +LDE D++L+ +  ++ +  I    P  ++  +FSAT ++ 
Sbjct: 139 ILALARN-KSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKE 197

Query: 121 VEELSKAGLRNPVRIEVRAESK 142
           +  + +  +++P+ I V  E+K
Sbjct: 198 IRPVCRKFMQDPMEIFVDDETK 219

>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 = 3e-37
 Identities = 40/139 (28%), Positives = 72/139 (51%), Gaps = 5/139 (3%)

Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   K        ++IGTPG +
Sbjct: 99  LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI----SEQIVIGTPGTV 154

Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + + + VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 155 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 214

Query: 122 EELSKAGLRNPVRIEVRAE 140
            + ++  + +P  I+++ E
Sbjct: 215 WKFAQKVVPDPNVIKLKRE 233

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19 Length = 219

 Score =  127 bits (321), Expect = 6e-37
 Identities = 51/147 (34%), Positives = 78/147 (53%), Gaps = 5/147 (3%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPD---VKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I +PTREL+ QIYH         P    + +  L+GG + +  ++K+     +++IGT
Sbjct: 75  AVITAPTRELATQIYHETLKITKFCPKDRMIVARCLIGGTDKQKALEKLNV-QPHIVIGT 133

Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT 118
           PGR+ D +     LD     ILV+DEAD +LDMGF   +  I +R+PK  +  +FSAT  
Sbjct: 134 PGRINDFIRE-QALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFSATIP 192

Query: 119 EAVEELSKAGLRNPVRIEVRAESKSHH 145
           E ++   K  + NP  + V      HH
Sbjct: 193 EKLKPFLKKYMENPTFVHVLEHHHHHH 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 = 1e-36
 Identities = 40/139 (28%), Positives = 72/139 (51%), Gaps = 5/139 (3%)

Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + +SPT EL+ Q   V +      P++K    V G +++   K        ++IGTPG +
Sbjct: 166 LCLSPTYELALQTGKVIEQMGKFYPELKLAYAVRGNKLERGQKI----SEQIVIGTPGTV 221

Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D   ++  +D + + + VLDEAD ++   G Q Q   I   LP+  +  LFSAT  ++V
Sbjct: 222 LDWCSKLKFIDPKKIKVFVLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSV 281

Query: 122 EELSKAGLRNPVRIEVRAE 140
            + ++  + +P  I+++ E
Sbjct: 282 WKFAQKVVPDPNVIKLKRE 300

>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 =  126 bits (318), Expect = 1e-36
 Identities = 47/135 (34%), Positives = 78/135 (57%), Gaps = 5/135 (3%)

Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           ++++PTREL+ Q   VA    +  P +K + + GG       + +   GA+ ++ TPGR 
Sbjct: 76  LVLTPTRELALQ---VASELTAVAPHLKVVAVYGGTGYGKQKEALLR-GADAVVATPGRA 131

Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            D + +  VLD   + + VLDEAD +L MGF++++  ++S  P  R+T LFSAT     +
Sbjct: 132 LDYLRQ-GVLDLSRVEVAVLDEADEMLSMGFEEEVEALLSATPPSRQTLLFSATLPSWAK 190

Query: 123 ELSKAGLRNPVRIEV 137
            L++  ++NPV I V
Sbjct: 191 RLAERYMKNPVLINV 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 =  125 bits (316), Expect = 2e-36
 Identities = 34/137 (24%), Positives = 78/137 (56%), Gaps = 2/137 (1%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR
Sbjct: 85  VLVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGR 144

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           +  +      L+ +++   +LDE D++L+ +  ++ +  I    P  ++  +FSAT ++ 
Sbjct: 145 ILALARN-KSLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKE 203

Query: 121 VEELSKAGLRNPVRIEV 137
           +  + +  +++P+ I V
Sbjct: 204 IRPVCRKFMQDPMEIFV 220

>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 (308), Expect = 7e-34
 Identities = 46/136 (33%), Positives = 76/136 (55%), Gaps = 8/136 (5%)

Query: 4   IISPTRELSAQIYHVAQPF--ISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
           +++PTREL+ Q   VA     I    D K   + GG+  KA + ++    A++++ TPGR
Sbjct: 61  VVTPTRELTRQ---VASHIRDIGRYMDTKVAEVYGGMPYKAQINRVR--NADIVVATPGR 115

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           L D+  +  V+D  +  I+++DEAD + +MGF   I  I+++    + TGLFSAT  E +
Sbjct: 116 LLDLWSK-GVIDLSSFEIVIIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEEI 174

Query: 122 EELSKAGLRNPVRIEV 137
            ++ K  + N   IE 
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 =  117 bits (295), Expect = 1e-31
 Identities = 43/139 (30%), Positives = 71/139 (51%), Gaps = 8/139 (5%)

Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           + ++P+REL+ Q   V Q  +     + S L+V     K       +  A +++GTPG +
Sbjct: 79  ICLAPSRELARQTLEVVQE-MGKFTKITSQLIVPDSFEKNK-----QINAQVIVGTPGTV 132

Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDM-GFQKQISYIISRLPKLRRTGLFSATQTEAV 121
            D+M R  ++  + + I VLDEAD +LD  G   Q   +   LPK  +  LFSAT  +AV
Sbjct: 133 LDLMRR-KLMQLQKIKIFVLDEADNMLDQQGLGDQCIRVKRFLPKDTQLVLFSATFADAV 191

Query: 122 EELSKAGLRNPVRIEVRAE 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 =  115 bits (290), Expect = 8e-31
 Identities = 28/207 (13%), Positives = 65/207 (31%), Gaps = 30/207 (14%)

Query: 4   IISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKA---DVKKIEEEGANLLIGTPG 60
           ++ PT  L  Q     Q        VK       ++ +      K  EE+  ++L+ +  
Sbjct: 69  LVFPTVTLVKQTLERLQKLADE--KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQ 126

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
            +       + L  +    + +D+ D +L          ++  +P+      FS  +   
Sbjct: 127 FVSK---NREKLSQKRFDFVFVDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTIKQGK 183

Query: 121 VEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHL------------EYLE 168
           + E  K      + +       S  A     +    +  L   +              + 
Sbjct: 184 IYERPKNLKPGILVV------SSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRIS 237

Query: 169 CESDKKPSQLVDLLIKNKSKKIIMYVQ 195
             S +K  +L+++        I+++ Q
Sbjct: 238 SRSKEKLVELLEIF----RDGILIFAQ 260

>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 =  113 bits (284), Expect = 3e-30
 Identities = 45/146 (30%), Positives = 79/146 (54%), Gaps = 8/146 (5%)

Query: 2   GMIISPTRELSAQIYHVAQPF--ISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTP 59
            +I++PTREL+ Q   VA     +    ++K   + GG  +   +K ++   AN+++GTP
Sbjct: 77  AIILTPTRELAIQ---VADEIESLKGNKNLKIAKIYGGKAIYPQIKALK--NANIVVGTP 131

Query: 60  GRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE 119
           GR+ D + R   L+ +N+   +LDEAD +L+MGF K +  I++   K +R  LFSAT   
Sbjct: 132 GRILDHINR-GTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPR 190

Query: 120 AVEELSKAGLRNPVRIEVRAESKSHH 145
            +  L+K  + +   I+ +  +    
Sbjct: 191 EILNLAKKYMGDYSFIKAKINANIEQ 216

>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 = 49.8 bits (118), Expect = 2e-07
 Identities = 27/139 (19%), Positives = 56/139 (40%), Gaps = 5/139 (3%)

Query: 4   IISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLY 63
           +++PT+ L  Q     +     LP  K + L G  E   + +      A +++ TP  + 
Sbjct: 57  MLAPTKPLVLQHAESFRRLF-NLPPEKIVALTG--EKSPEERSKAWARAKVIVATPQTIE 113

Query: 64  DIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEE 123
           + +     +   ++ ++V DEA R +       I+    R  K       +A+     E+
Sbjct: 114 NDLLA-GRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEK 172

Query: 124 LSKAGLRNPV-RIEVRAES 141
           + +      +  IE R+E+
Sbjct: 173 IMEVINNLGIEHIEYRSEN 191

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	203
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	100.0
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	99.97
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	99.97
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	99.96
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	99.96
3fe2_A	242	Probable ATP-dependent RNA helicase DDX5; DEAD, AD	99.96
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	99.95
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	99.95
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.95
1wrb_A	253	DJVLGB; RNA helicase, DEAD BOX, VASA, structural g	99.95
3fmo_B	300	ATP-dependent RNA helicase DDX19B; nuclear porin,	99.95
3iuy_A	228	Probable ATP-dependent RNA helicase DDX53; REC-A-l	99.95
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	99.95
3ber_A	249	Probable ATP-dependent RNA helicase DDX47; DEAD, A	99.94
3bor_A	237	Human initiation factor 4A-II; translation initiat	99.94
2oxc_A	230	Probable ATP-dependent RNA helicase DDX20; DEAD, s	99.94
1t6n_A	220	Probable ATP-dependent RNA helicase; RECA-like fol	99.94
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	99.94
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	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
2pl3_A	236	Probable ATP-dependent RNA helicase DDX10; DEAD, s	99.94
1q0u_A	219	Bstdead; DEAD protein, RNA binding protein; 1.85A	99.94
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	99.94
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	99.93
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	99.93
2gxq_A	207	Heat resistant RNA dependent ATPase; RNA helicase,	99.93
1qde_A	224	EIF4A, translation initiation factor 4A; DEAD box	99.93
3dkp_A	245	Probable ATP-dependent RNA helicase DDX52; DEAD, A	99.92
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	99.92
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	99.92
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	99.91
3l9o_A	1108	ATP-dependent RNA helicase DOB1; REC-A fold, winge	99.89
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	99.88
2fsf_A	853	Preprotein translocase SECA subunit; ATPase, DNA-R	99.87
1tf5_A	844	Preprotein translocase SECA subunit; ATPase, helic	99.87
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	99.87
2xgj_A	1010	ATP-dependent RNA helicase DOB1; hydrolase-RNA com	99.87
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	99.85
4a4z_A	997	Antiviral helicase SKI2; hydrolase, ATPase, mRNA d	99.85
1nkt_A	922	Preprotein translocase SECA 1 subunit; preprotein	99.85
4a2p_A	556	RIG-I, retinoic acid inducible protein I; hydrolas	99.83
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	99.82
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	99.82
2p6r_A	702	Afuhel308 helicase; protein-DNA complex, SF2 helic	99.81
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.81
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	99.81
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	99.8
4f92_B	1724	U5 small nuclear ribonucleoprotein 200 kDa helica;	99.8
4a2q_A	797	RIG-I, retinoic acid inducible protein I; hydrolas	99.8
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	99.79
4a2w_A	936	RIG-I, retinoic acid inducible protein I; hydrolas	99.76
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	99.75
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	99.74
1gm5_A	780	RECG; helicase, replication restart; HET: DNA ADP;	99.69
4gl2_A	699	Interferon-induced helicase C domain-containing P;	99.69
3llm_A	235	ATP-dependent RNA helicase A; alpha-beta-alpha, st	99.67
3b6e_A	216	Interferon-induced helicase C domain-containing P;	99.66
2fwr_A	472	DNA repair protein RAD25; DNA unwinding, XPB, DNA	99.63
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	99.6
1yks_A	440	Genome polyprotein [contains: flavivirin protease	99.59
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	99.58
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	99.58
1rif_A	282	DAR protein, DNA helicase UVSW; bacteriophage, REC	99.56
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	99.56
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	99.51
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	99.51
3h1t_A	590	Type I site-specific restriction-modification syst	99.5
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	99.48
2ipc_A	997	Preprotein translocase SECA subunit; nucleotide bi	99.43
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	99.42
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	99.33
2fz4_A	237	DNA repair protein RAD25; RECA-like domain, DNA da	99.29
3jux_A	822	Protein translocase subunit SECA; protein transloc	99.11
1z63_A	500	Helicase of the SNF2/RAD54 hamily; protein-DNA com	99.07
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	98.99
3mwy_W	800	Chromo domain-containing protein 1; SWI2/SNF2 ATPa	98.82
3crv_A	551	XPD/RAD3 related DNA helicase; XPD helicase DNA re	98.74
1z3i_X	644	Similar to RAD54-like; recombination ATPase helica	98.57
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	98.33
2vl7_A	540	XPD; helicase, unknown function; 2.25A {Sulfolobus	98.14
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	98.11
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	97.86
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	97.31
1w36_D	608	RECD, exodeoxyribonuclease V alpha chain; recombin	97.1
2hjv_A	163	ATP-dependent RNA helicase DBPA; parallel alpha-be	96.77
2p6n_A	191	ATP-dependent RNA helicase DDX41; DEAD, structural	96.64
1fuk_A	165	Eukaryotic initiation factor 4A; helicase, DEAD-bo	96.48
1t5i_A	172	C_terminal domain of A probable ATP-dependent RNA	96.16
3eaq_A	212	Heat resistant RNA dependent ATPase; DEAD box RNA	96.06
2rb4_A	175	ATP-dependent RNA helicase DDX25; rossmann fold, s	96.04
2jgn_A	185	DBX, DDX3, ATP-dependent RNA helicase DDX3X; phosp	95.86
2db3_A	434	ATP-dependent RNA helicase VASA; DEAD-BOX, protein	95.36
2i4i_A	417	ATP-dependent RNA helicase DDX3X; DEAD, structural	95.32
1hv8_A	367	Putative ATP-dependent RNA helicase MJ0669; RNA-bi	95.08
3i5x_A	563	ATP-dependent RNA helicase MSS116; protein-RNA com	95.02
3i32_A	300	Heat resistant RNA dependent ATPase; RNA helicase,	95.01
3sqw_A	579	ATP-dependent RNA helicase MSS116, mitochondrial;	94.92
2d7d_A	661	Uvrabc system protein B; helicase, protein-DNA-ADP	94.58
1c4o_A	664	DNA nucleotide excision repair enzyme UVRB; uvrabc	94.5
1oyw_A	523	RECQ helicase, ATP-dependent DNA helicase; winged	94.47
2j0s_A	410	ATP-dependent RNA helicase DDX48; mRNA processing,	94.44
3fht_A	412	ATP-dependent RNA helicase DDX19B; DBP5, DEAD-box	94.41
3pey_A	395	ATP-dependent RNA helicase DBP5; RECA, DEAD-BOX, A	94.4
1s2m_A	400	Putative ATP-dependent RNA helicase DHH1; ATP-bind	94.09
1xti_A	391	Probable ATP-dependent RNA helicase P47; alpha-bet	93.81
2v1x_A	591	ATP-dependent DNA helicase Q1; DNA strand annealin	93.73
2yjt_D	170	ATP-dependent RNA helicase SRMB, regulator of ribo	92.66
2eyq_A	1151	TRCF, transcription-repair coupling factor; MFD, S	93.54
2v6i_A	431	RNA helicase; membrane, hydrolase, transmembrane,	92.93
1wp9_A	494	ATP-dependent RNA helicase, putative; ATPase, DNA	92.84
2xau_A	773	PRE-mRNA-splicing factor ATP-dependent RNA helica;	92.37
1yks_A	440	Genome polyprotein [contains: flavivirin protease	92.25
2oca_A	510	DAR protein, ATP-dependent DNA helicase UVSW; ATP-	92.15
3rc3_A	677	ATP-dependent RNA helicase SUPV3L1, mitochondrial;	91.85
3eiq_A	414	Eukaryotic initiation factor 4A-I; PDCD4, anti-onc	91.11
2whx_A	618	Serine protease/ntpase/helicase NS3; transcription	90.79
3oiy_A	414	Reverse gyrase helicase domain; topoisomerase, DNA	90.76
2wv9_A	673	Flavivirin protease NS2B regulatory subunit, FLAV	90.7
3o8b_A	666	HCV NS3 protease/helicase; ntpase, RNA, translocat	89.72
2z0m_A	337	337AA long hypothetical ATP-dependent RNA helicase	89.6
4a15_A	620	XPD helicase, ATP-dependent DNA helicase TA0057; h	88.97
3fmp_B	479	ATP-dependent RNA helicase DDX19B; nuclear porin,	88.59
2jlq_A	451	Serine protease subunit NS3; ribonucleoprotein, nu	88.54
3vkw_A	446	Replicase large subunit; alpha/beta domain, helica	88.11
3tbk_A	555	RIG-I helicase domain; DECH helicase, ATP binding,	86.32
4gl2_A	699	Interferon-induced helicase C domain-containing P;	86.25
4ddu_A	1104	Reverse gyrase; topoisomerase, DNA supercoiling, a	85.96
3dmq_A	968	RNA polymerase-associated protein RAPA; SWF2/SNF2,	85.89
1gku_B	1054	Reverse gyrase, TOP-RG; topoisomerase, DNA superco	84.52
2gno_A	305	DNA polymerase III, gamma subunit-related protein;	82.9
1fuu_A	394	Yeast initiation factor 4A; IF4A, helicase, DEAD-b	82.87
3fho_A	508	ATP-dependent RNA helicase DBP5; mRNA export, ATPa	82.67
2w00_A	1038	HSDR, R.ECOR124I; ATP-binding, DNA-binding, restri	82.65
2ykg_A	696	Probable ATP-dependent RNA helicase DDX58; hydrola	82.19
3bos_A	242	Putative DNA replication factor; P-loop containing	82.08
2z83_A	459	Helicase/nucleoside triphosphatase; hydrolase, mem	81.76
2zj8_A	720	DNA helicase, putative SKI2-type helicase; RECA fo	81.59
2va8_A	715	SSO2462, SKI2-type helicase; hydrolase, DNA repair	80.64

>2db3_A ATP-dependent RNA helicase VASA; DEAD-BOX, protein-RNA complex, ATPase, riken structural genomics/proteomics initiative, RSGI; HET: ANP; 2.20A {Drosophila melanogaster}

Probab=100.00  E-value=7.4e-32  Score=226.76  Aligned_cols=182  Identities=30%  Similarity=0.474  Sum_probs=165.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+|||+||||||.|+++++++++... ++++..++||.....+...+ ..+++|+|+||++|.+++.. +.+++++++++
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            48999999999999999999998776 79999999999988887777 56899999999999999988 78889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhC--CCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRL--PKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKT  158 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~--~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~  158 (203)
                      |+||||+|++++|.+.+..++..+  +..+|+++||||+|+.+..++..++.++..+.+...               ...
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             CCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          159 PLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       159 ~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      ..++.+.+..++..+|...|.+++.....+ +|||||+++.|+
T Consensus       273 ~~~i~~~~~~~~~~~k~~~l~~~l~~~~~~-~lVF~~t~~~a~  314 (434)
T 2db3_A          273 CSDVKQTIYEVNKYAKRSKLIEILSEQADG-TIVFVETKRGAD  314 (434)
T ss_dssp             CTTEEEEEEECCGGGHHHHHHHHHHHCCTT-EEEECSSHHHHH
T ss_pred             ccccceEEEEeCcHHHHHHHHHHHHhCCCC-EEEEEeCcHHHH
Confidence            678999999999999999999999887655 999999998775

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=99.97  E-value=3.3e-29  Score=208.56  Aligned_cols=183  Identities=34%  Similarity=0.540  Sum_probs=161.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++||++|+.|+++.+++++... ++++..++||....++...+ ..+++|+|+||++|.+++.. +.+.+++++++|
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            7999999999999999999998776 89999999999988887777 56899999999999999988 778899999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhC--CC--CCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCC
Q 028826           82 LDEADRLLDMGFQKQISYIISRL--PK--LRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSK  157 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~--~~--~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~  157 (203)
                      +||||.+++++|...+..++...  +.  ..|++++|||+++.+..+...++.++..+.+...               ..
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            99999999999999999999853  33  6899999999999999999999999988888765               45


Q ss_pred             CCCceeEEEEEcCCCCcHHHHHHHHhcC-CCCeEEEEeccCCcccC
Q 028826          158 TPLGLHLEYLECESDKKPSQLVDLLIKN-KSKKIIMYVQHGNFSED  202 (203)
Q Consensus       158 ~~~~i~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lIF~ns~~~~e~  202 (203)
                      .+.++.+.+..++..+|...+.++++.. ..+++|||||+++.|++
T Consensus       246 ~~~~i~~~~~~~~~~~~~~~l~~~l~~~~~~~~~lVf~~~~~~~~~  291 (417)
T 2i4i_A          246 TSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADS  291 (417)
T ss_dssp             CCSSEEEEEEECCGGGHHHHHHHHHHTCCTTCEEEEECSSHHHHHH
T ss_pred             CccCceEEEEEeccHhHHHHHHHHHHhcCCCCeEEEEECCHHHHHH
Confidence            6788999999999999999999999976 56799999999987753

>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=99.97  E-value=2.7e-29  Score=208.88  Aligned_cols=183  Identities=30%  Similarity=0.498  Sum_probs=164.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.+++++... ++++..+.||....++...+ ..+++|+|+||+++.+++.. +.+.+.+++++
T Consensus       107 ~~lil~Pt~~L~~q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~-~~~~~ivv~Tp~~l~~~l~~-~~~~~~~~~~v  183 (410)
T 2j0s_A          107 QALILAPTRELAVQIQKGLLALGDYM-NVQCHACIGGTNVGEDIRKL-DYGQHVVAGTPGRVFDMIRR-RSLRTRAIKML  183 (410)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHTTTT-TCCEEEECTTSCHHHHHHHH-HHCCSEEEECHHHHHHHHHT-TSSCCTTCCEE
T ss_pred             eEEEEcCcHHHHHHHHHHHHHHhccC-CeEEEEEECCCCHHHHHHHh-hcCCCEEEcCHHHHHHHHHh-CCccHhheeEE
Confidence            47999999999999999999998877 89999999999988887777 45789999999999999988 78889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||.+.++++...+..++..+++..|++++|||+++.+.++...++.+|..+.+...               .....
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            999999999999999999999999999999999999999999999999999988877655               45667


Q ss_pred             ceeEEEEEcCCCC-cHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          161 GLHLEYLECESDK-KPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      ++.+.+..++..+ |...+.+++.....+++|||||+++.++
T Consensus       249 ~~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~  290 (410)
T 2j0s_A          249 GIKQFFVAVEREEWKFDTLCDLYDTLTITQAVIFCNTKRKVD  290 (410)
T ss_dssp             TEEEEEEEESSTTHHHHHHHHHHHHHTSSEEEEECSSHHHHH
T ss_pred             CceEEEEEeCcHHhHHHHHHHHHHhcCCCcEEEEEcCHHHHH
Confidence            8889988887765 9999999999888889999999988765

>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=99.96  E-value=3.6e-28  Score=200.53  Aligned_cols=185  Identities=24%  Similarity=0.475  Sum_probs=166.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++||++|+.|+++.++++....+++++..+.||.....+...+....++|+|+||+++..++.. +.+.+.+++++|
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            7999999999999999999998887789999999999888777777667789999999999999988 778899999999


Q ss_pred             EcchhHhhh-hchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           82 LDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        82 iDEad~l~~-~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      +||||.+.+ .++...+..++...+...|++++|||+++.+..++..++.++..+......              .....
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 478899999999999999999999999999999999999999888776552              33556


Q ss_pred             ceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          161 GLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      ++.+++..++..+|...+.++++....+++||||++++.|+
T Consensus       224 ~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~lvf~~~~~~~~  264 (391)
T 1xti_A          224 GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVKSVQRCI  264 (391)
T ss_dssp             TCEEEEEECCGGGHHHHHHHHHHHSCCSEEEEECSCHHHHH
T ss_pred             cceEEEEEcCchhHHHHHHHHHHhcCCCcEEEEeCcHHHHH
Confidence            78889998888999999999999988899999999988765

>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=99.96  E-value=2.3e-28  Score=203.11  Aligned_cols=184  Identities=31%  Similarity=0.517  Sum_probs=166.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.+++++... ++.+..+.||.....+...+...+++|+|+||+++.+++.. +.+.+.+++++
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            37999999999999999999998877 89999999999988888777667899999999999999988 88889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||.+.++++...+..++..+++..|++++|||+++.+..+...++.++..+.....               .....
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            999999999999999999999999999999999999999999999999999988887666               55677


Q ss_pred             ceeEEEEEcCCC-CcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          161 GLHLEYLECESD-KKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~~-~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      .+.+.+..+... .|...+..+++....+++|||||+++.++
T Consensus       253 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~  294 (414)
T 3eiq_A          253 GIRQFYINVEREEWKLDTLCDLYETLTITQAVIFINTRRKVD  294 (414)
T ss_dssp             SCCEEEEECSSSTTHHHHHHHHHHSSCCSSCEEECSCHHHHH
T ss_pred             CceEEEEEeChHHhHHHHHHHHHHhCCCCcEEEEeCCHHHHH
Confidence            888888888665 59999999999998899999999988765

>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=6.6e-28  Score=187.84  Aligned_cols=137  Identities=36%  Similarity=0.588  Sum_probs=127.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++|||+|+.|+++.++++.... ++++..++||.....+...+ ..+++|+|+||+++.+++.. +..++++++++
T Consensus       104 ~~lil~Pt~~L~~Q~~~~~~~~~~~~-~~~~~~~~g~~~~~~~~~~~-~~~~~I~v~Tp~~l~~~l~~-~~~~~~~~~~l  180 (242)
T 3fe2_A          104 ICLVLAPTRELAQQVQQVAAEYCRAC-RLKSTCIYGGAPKGPQIRDL-ERGVEICIATPGRLIDFLEC-GKTNLRRTTYL  180 (242)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHHHHHT-TCCEEEECTTSCHHHHHHHH-HHCCSEEEECHHHHHHHHHH-TSCCCTTCCEE
T ss_pred             EEEEEeCcHHHHHHHHHHHHHHHhhc-CceEEEEECCCChHHHHHHh-cCCCCEEEECHHHHHHHHHc-CCCCcccccEE
Confidence            37999999999999999999999887 89999999999988887777 45799999999999999988 88899999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAE  140 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~  140 (203)
                      |+||||++++++|...+..+++.+++.+|++++|||+|+.+..+++.++++|..|.++..
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            999999999999999999999999999999999999999999999999999999998764

>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=99.95  E-value=2.9e-27  Score=195.12  Aligned_cols=183  Identities=31%  Similarity=0.502  Sum_probs=123.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.++++.... ++++..+.||....++...+.  +++|+|+||+++..++.. +.+.+.+++++
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            37999999999999999999998776 899999999988877766663  589999999999999988 77888999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||.+.++++...+..++..+++..|++++|||+++.+..+...++.++..+.....               .....
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            999999999999999999999999999999999999999999999999999998887665               44566


Q ss_pred             ceeEEEEEcCCCC-cHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          161 GLHLEYLECESDK-KPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       161 ~i~~~~~~~~~~~-k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      ++.+.+..++..+ |...+.++++....+++||||++++.+++
T Consensus       232 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lVf~~~~~~~~~  274 (394)
T 1fuu_A          232 GIKQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCNTRRKVEE  274 (394)
T ss_dssp             -------------------------------------------
T ss_pred             CceEEEEEcCchhhHHHHHHHHHhcCCCCcEEEEECCHHHHHH
Confidence            7777777776654 88889999988888899999999998875

>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=99.95  E-value=5.8e-27  Score=194.10  Aligned_cols=182  Identities=31%  Similarity=0.480  Sum_probs=161.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.++++.... ++++..+.||.....+...+ ..+++|+|+||+++.+++.. +...+.+++++
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            37999999999999999999998877 79999999998877666555 56899999999999999887 77889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||.+.+.++...+..++..+++..|++++|||++..+..++..++..+..+.....                ....
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            999999999989999999999999999999999999999999999999998877655443                3456


Q ss_pred             ceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          161 GLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      ++.+++..++...|...+..+++....+++|||||+++.++
T Consensus       232 ~~~~~~~~~~~~~k~~~l~~~~~~~~~~~~lVf~~~~~~~~  272 (400)
T 1s2m_A          232 GITQYYAFVEERQKLHCLNTLFSKLQINQAIIFCNSTNRVE  272 (400)
T ss_dssp             TEEEEEEECCGGGHHHHHHHHHHHSCCSEEEEECSSHHHHH
T ss_pred             CceeEEEEechhhHHHHHHHHHhhcCCCcEEEEEecHHHHH
Confidence            78888888888899999999999888889999999988765

>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=99.95  E-value=9.6e-28  Score=203.74  Aligned_cols=183  Identities=26%  Similarity=0.361  Sum_probs=119.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+|||+||++|+.|+++.++++....+++.+....++.......    ..+++|+|+||+++.+++.+.+.+++++++++
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            48999999999999999999999887788998888887654332    34689999999999999976467788999999


Q ss_pred             EEcchhHhhh-hchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCC
Q 028826           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTP  159 (203)
Q Consensus        81 ViDEad~l~~-~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (203)
                      |+||||.+++ .++...+..+.+.+++.+|++++|||+++.+..++..++.++..+.+...               ....
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 68999999999999999999999999999999999999999999988776               4567


Q ss_pred             CceeEEEEEcCC-CCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          160 LGLHLEYLECES-DKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       160 ~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      ..+.+.+..++. ..|...+..++.....+++||||++++.|++
T Consensus       305 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvF~~s~~~~~~  348 (479)
T 3fmp_B          305 DTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTASW  348 (479)
T ss_dssp             --------------------------------------------
T ss_pred             CCceEEEEEeCCHHHHHHHHHHHHhhccCCceEEEeCcHHHHHH
Confidence            788888888865 5789999999988888899999999998875

>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=6.3e-27  Score=183.29  Aligned_cols=137  Identities=36%  Similarity=0.586  Sum_probs=123.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++|||+|+.|+++.+++++... ++++..++||.+...+...+ ..+++|+|+||+++.+++.. +.+++++++++
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            37999999999999999999998776 79999999999888777776 56899999999999999988 77889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhC--CC--CCcEEEEeeecChhHHHHHHhcCCCCeEEEeccC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRL--PK--LRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAE  140 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~--~~--~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~  140 (203)
                      |+||||++++++|...+..++..+  +.  .+|++++|||+++++..+++.++.+|..+.+...
T Consensus       179 ViDEah~~~~~~~~~~~~~i~~~~~~~~~~~~q~l~~SAT~~~~~~~~~~~~l~~~~~i~~~~~  242 (253)
T 1wrb_A          179 VLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFPKEIQKLAADFLYNYIFMTVGRV  242 (253)
T ss_dssp             EEETHHHHHHTTCHHHHHHHHHSSCCCCGGGCEEEEEESSCCHHHHHHHHHHCSSCEEEEEC--
T ss_pred             EEeCHHHHHhCchHHHHHHHHhhccCCCCCCcEEEEEEEeCCHHHHHHHHHHcCCCEEEEECCC
Confidence            999999999999999999999954  44  6899999999999999999999999999998776

>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=99.95  E-value=2.1e-27  Score=190.79  Aligned_cols=135  Identities=28%  Similarity=0.412  Sum_probs=122.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +||||+||||||.|+++.+++++...+++++....||.......    ..+++|+||||++|++++.+.+.+++++++++
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            48999999999999999999999887789999999987754332    45789999999999999966467889999999


Q ss_pred             EEcchhHhhh-hchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEecc
Q 028826           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRA  139 (203)
Q Consensus        81 ViDEad~l~~-~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~  139 (203)
                      |+||||+|++ .+|...+..+++.+++.+|+++||||+++.+..+++.++++|..|.+..
T Consensus       240 VlDEad~l~~~~~~~~~~~~i~~~~~~~~q~i~~SAT~~~~v~~~a~~~l~~p~~i~~~~  299 (300)
T 3fmo_B          240 VLDEADVMIATQGHQDQSIRIQRMLPRNCQMLLFSATFEDSVWKFAQKVVPDPNVIKLKR  299 (300)
T ss_dssp             EETTHHHHHHSTTHHHHHHHHHTTSCTTCEEEEEESCCCHHHHHHHHHHSSSCEEEEECC
T ss_pred             EEeCHHHHhhccCcHHHHHHHHHhCCCCCEEEEEeccCCHHHHHHHHHHCCCCeEEEecC
Confidence            9999999998 7899999999999999999999999999999999999999999998754

>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=99.95  E-value=1.3e-26  Score=178.69  Aligned_cols=132  Identities=32%  Similarity=0.556  Sum_probs=116.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++||++|+.|+++.++++...  ++++..++||.....+...+ ..+++|+|+||+++.+++.. +..++++++++|
T Consensus        97 ~lil~Pt~~L~~q~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~-~~~~~iiv~Tp~~l~~~~~~-~~~~~~~~~~lV  172 (228)
T 3iuy_A           97 MLVLTPTRELALHVEAECSKYSYK--GLKSICIYGGRNRNGQIEDI-SKGVDIIIATPGRLNDLQMN-NSVNLRSITYLV  172 (228)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHCCT--TCCEEEECC------CHHHH-HSCCSEEEECHHHHHHHHHT-TCCCCTTCCEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHHhccc--CceEEEEECCCChHHHHHHh-cCCCCEEEECHHHHHHHHHc-CCcCcccceEEE
Confidence            799999999999999999999633  79999999998887777776 56899999999999999988 788899999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEe
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEV  137 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~  137 (203)
                      +||||++++++|...+..++..+++.+|++++|||+|+.+.++++.++++|..+.+
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            99999999999999999999999999999999999999999999999999998754

>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=99.95  E-value=5.6e-27  Score=194.49  Aligned_cols=182  Identities=26%  Similarity=0.372  Sum_probs=159.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.++++....+++++....++.......    ..+++|+|+||+++.+++...+.+++++++++
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            37999999999999999999998887789999998887654332    35689999999999999866467788999999


Q ss_pred             EEcchhHhhh-hchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCC
Q 028826           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTP  159 (203)
Q Consensus        81 ViDEad~l~~-~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (203)
                      |+||||.+++ .++...+..+...+++..|++++|||+++.+..+...++.++..+.+...               ....
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 67889999999999999999999999999999999999999998888766               5567


Q ss_pred             CceeEEEEEcCC-CCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          160 LGLHLEYLECES-DKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       160 ~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      ..+.+.+..+.. .+|...+..++.....+++||||++++.|+
T Consensus       238 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~  280 (412)
T 3fht_A          238 DTIKQYYVLCSSRDEKFQALCNLYGAITIAQAMIFCHTRKTAS  280 (412)
T ss_dssp             TTEEEEEEECSSHHHHHHHHHHHHHHHSSSEEEEECSSHHHHH
T ss_pred             cCceEEEEEcCChHHHHHHHHHHHhhcCCCCEEEEeCCHHHHH
Confidence            788888888765 578999999999888889999999988765

>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=4.8e-26  Score=178.21  Aligned_cols=136  Identities=38%  Similarity=0.650  Sum_probs=124.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++|||+|+.|+++.+++++... ++++..++||.....+...+ ..+++|+|+||+++.+++...+.+++++++++
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            38999999999999999999998877 89999999998877777666 46899999999999999886456789999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEec
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVR  138 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~  138 (203)
                      |+||||++++++|...+..++..+++.+|++++|||+++.+.++++.++++|..+.+.
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            9999999999999999999999999999999999999999999999999999988764

>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=2.1e-26  Score=178.87  Aligned_cols=137  Identities=34%  Similarity=0.583  Sum_probs=113.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.+++++... ++++..+.||.....+...+....++|+|+||+++.+++.. +.+.+++++++
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            47999999999999999999998776 78999999998877777777555699999999999999988 77889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEecc
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRA  139 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~  139 (203)
                      |+||||++++++|...+..+++.++...|++++|||+|+++.++++.++++|..+.+..
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            99999999999999999999999999999999999999999999999999999887643

>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=4e-26  Score=176.44  Aligned_cols=135  Identities=30%  Similarity=0.530  Sum_probs=122.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.+++++...+++++..+.||....++...+  .+++|+|+||+++.+++.. +.+++++++++
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            47999999999999999999998776689999999998877666555  4799999999999999987 77889999999


Q ss_pred             EEcchhHhhhhc-hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEec
Q 028826           81 VLDEADRLLDMG-FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVR  138 (203)
Q Consensus        81 ViDEad~l~~~~-~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~  138 (203)
                      |+||||+++++| |.+.+..+++.++..+|++++|||+|+.+.++++.++++|..+.++
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            999999999987 9999999999999999999999999999999999999999988653

>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=9.2e-26  Score=173.01  Aligned_cols=136  Identities=25%  Similarity=0.531  Sum_probs=124.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.++++....+++++..++||.....+...+....++|+|+||+++..++.. +.+.+++++++
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            37999999999999999999998877789999999999888887777667789999999999999988 77889999999


Q ss_pred             EEcchhHhhh-hchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEe
Q 028826           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEV  137 (203)
Q Consensus        81 ViDEad~l~~-~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~  137 (203)
                      |+||||++++ .++...+..+++.+++.+|++++|||+++.+.++++.++++|..+.+
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 58999999999999999999999999999999999999999988753

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=99.94  E-value=4.2e-26  Score=197.97  Aligned_cols=190  Identities=27%  Similarity=0.392  Sum_probs=150.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhh---cCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFIS---TLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~---~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+|||+||++|+.|+++.++++..   ..+.+.+..+.||.....+...+...+++|+|+||++|.+++.......++++
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   33467899999999988888888667899999999999998876224578899


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCC-------CCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchh
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLP-------KLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASS  150 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~-------~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~  150 (203)
                      +++|+||||++++++|.+.+..++..++       ..+|+++||||+++.+..++..++.++..+.+.....        
T Consensus       177 ~~lViDEah~l~~~gf~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~l~~~~~~~~~~~~~--------  248 (579)
T 3sqw_A          177 DYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDK--------  248 (579)
T ss_dssp             CEEEEETHHHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCS--------
T ss_pred             CEEEEEChHHhhcCCCHHHHHHHHHHhhhhhcccccCceEEEEeccCChHHHHHHHHHcCCCceEEEeecCc--------
Confidence            9999999999999999999999887764       3679999999999999999999999988776644210        


Q ss_pred             hhhccCCCCCceeEEEEEcCCC-CcH----HHHHHHHhc-CCCCeEEEEeccCCccc
Q 028826          151 QQLASSKTPLGLHLEYLECESD-KKP----SQLVDLLIK-NKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       151 ~~~~~~~~~~~i~~~~~~~~~~-~k~----~~l~~ll~~-~~~~~~lIF~ns~~~~e  201 (203)
                         ........+.+.+...+.. .+.    ..+...+.. ....++||||+|++.|+
T Consensus       249 ---~~~~~~~~i~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~t~~~~~  302 (579)
T 3sqw_A          249 ---NEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTS  302 (579)
T ss_dssp             ---SSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSSHHHHH
T ss_pred             ---cccccccccceEEEEecchhhhHHHHHHHHHHHHhhcCCCCcEEEECCcHHHHH
Confidence               0033456677777777653 222    333333333 56779999999988775

>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=99.94  E-value=1.3e-25  Score=183.31  Aligned_cols=176  Identities=28%  Similarity=0.485  Sum_probs=155.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++||++|+.|+.+.++++.... ++++..+.||.....+...+.  +++|+|+||+++..++.. +...+.+++++|
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            7999999999999999999998765 789999999998877776663  689999999999999987 778899999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCc
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLG  161 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (203)
                      +||||.+.++++...+..++..+++..|++++|||+++....+...++.++..+.....                   .+
T Consensus       153 iDEah~~~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~~~~~~~~~~~~~~~~~~~-------------------~~  213 (367)
T 1hv8_A          153 LDEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAKIN-------------------AN  213 (367)
T ss_dssp             EETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECCSS-------------------SS
T ss_pred             EeCchHhhhhchHHHHHHHHHhCCCCceEEEEeeccCHHHHHHHHHHcCCCeEEEecCC-------------------CC
Confidence            99999999999999999999999999999999999999999999989888776654433                   46


Q ss_pred             eeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          162 LHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       162 i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      +.+.+..++..+|...+.++++ ....++||||++++.++
T Consensus       214 ~~~~~~~~~~~~~~~~l~~~l~-~~~~~~lvf~~~~~~~~  252 (367)
T 1hv8_A          214 IEQSYVEVNENERFEALCRLLK-NKEFYGLVFCKTKRDTK  252 (367)
T ss_dssp             SEEEEEECCGGGHHHHHHHHHC-STTCCEEEECSSHHHHH
T ss_pred             ceEEEEEeChHHHHHHHHHHHh-cCCCcEEEEECCHHHHH
Confidence            7788888888899999999997 45568999999988765

>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=1.4e-25  Score=170.25  Aligned_cols=133  Identities=32%  Similarity=0.567  Sum_probs=122.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.++++....+++++..+.||....++...+ ..+++|+|+||+++.+++.. +...+++++++
T Consensus        73 ~~lil~Pt~~L~~q~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~-~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~l  150 (206)
T 1vec_A           73 QAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRL-DDTVHVVIATPGRILDLIKK-GVAKVDHVQMI  150 (206)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHTTTSSSCCEEEECSSSCHHHHHHHT-TSCCSEEEECHHHHHHHHHT-TCSCCTTCCEE
T ss_pred             eEEEEeCcHHHHHHHHHHHHHHHhhcCCceEEEEeCCccHHHHHHhc-CCCCCEEEeCHHHHHHHHHc-CCcCcccCCEE
Confidence            37999999999999999999998877789999999998887776665 56899999999999999988 77889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEE
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRI  135 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i  135 (203)
                      |+||||++.+.+|...+..++..+++..|++++|||+|+.+.++++.++.+|..+
T Consensus       151 ViDEah~~~~~~~~~~l~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~l~~p~~i  205 (206)
T 1vec_A          151 VLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLSVQKFMNSHLEKPYEI  205 (206)
T ss_dssp             EEETHHHHTSTTTHHHHHHHHHHSCTTCEEEEEESCCCHHHHHHHHHHCSSCEEE
T ss_pred             EEEChHHhHhhCcHHHHHHHHHhCCccceEEEEEeeCCHHHHHHHHHHcCCCeEe
Confidence            9999999999999999999999999999999999999999999999999999865

>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=1.1e-25  Score=177.47  Aligned_cols=131  Identities=40%  Similarity=0.642  Sum_probs=119.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++|||+||.|+++.+++++... +.++..++||.....+...+. .+++|+|+||+++.+++.....+.+++++++
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            38999999999999999999998877 789999999998887777774 5699999999999998887445789999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCe
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPV  133 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~  133 (203)
                      |+||||++++++|...+..+++.+++.+|++++|||+|+.+..+++.+++++.
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            99999999999999999999999999999999999999999999999988543

>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=1.8e-25  Score=173.22  Aligned_cols=136  Identities=42%  Similarity=0.648  Sum_probs=121.7

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.+++++... ++++..++||.....+...+  .+++|+|+||+++.+++.....+++.+++++
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            37999999999999999999998776 79999999998877766665  4799999999999999887345788999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEecc
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRA  139 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~  139 (203)
                      |+||||++.+++|...+..++..+++.+|++++|||+++.+.++++.++.+|..+.+..
T Consensus       176 ViDEah~~~~~~~~~~~~~i~~~~~~~~~~l~~SAT~~~~~~~~~~~~~~~p~~i~~~~  234 (236)
T 2pl3_A          176 VLDEADRILDMGFADTMNAVIENLPKKRQTLLFSATQTKSVKDLARLSLKNPEYVWVHE  234 (236)
T ss_dssp             EETTHHHHHHTTTHHHHHHHHHTSCTTSEEEEEESSCCHHHHHHHHHSCSSCEEEECCC
T ss_pred             EEeChHHHhcCCcHHHHHHHHHhCCCCCeEEEEEeeCCHHHHHHHHHhCCCCEEEEeCC
Confidence            99999999999999999999999999999999999999999999999999999988754

>1q0u_A Bstdead; DEAD protein, RNA binding protein; 1.85A {Geobacillus stearothermophilus} SCOP: c.37.1.19

Probab=99.94  E-value=4.6e-26  Score=174.74  Aligned_cols=138  Identities=36%  Similarity=0.574  Sum_probs=122.3

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCC---CceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLP---DVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~---~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||++||++|+.|+++.++++....+   ++++..+.||.+...+.+.+ ..+++|+|+||+++.+++.. +.++++++
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   57888899998766555444 35799999999999999988 78889999


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccC
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAE  140 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~  140 (203)
                      +++|+||||++.++++...+..++..+++..|++++|||+|+++.++++.++++|..+.+...
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            999999999999999999999999999999999999999999999999999999999887664

>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=99.94  E-value=4e-25  Score=178.61  Aligned_cols=177  Identities=29%  Similarity=0.504  Sum_probs=150.8

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.+++++... ++++..++||.....+...+  ..++|+|+||+++..++.. +.+++.+++++
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            37999999999999999999998776 78999999998887776665  3599999999999999887 77889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPL  160 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~  160 (203)
                      |+||||.+.++++...+..++..++...|++++|||+++.+......++.++..+....                  ...
T Consensus       134 ViDEah~~~~~~~~~~~~~~~~~~~~~~~~~~~SAT~~~~~~~~~~~~~~~~~~~~~~~------------------~~~  195 (337)
T 2z0m_A          134 IIDEADLMFEMGFIDDIKIILAQTSNRKITGLFSATIPEEIRKVVKDFITNYEEIEACI------------------GLA  195 (337)
T ss_dssp             EEESHHHHHHTTCHHHHHHHHHHCTTCSEEEEEESCCCHHHHHHHHHHSCSCEEEECSG------------------GGG
T ss_pred             EEEChHHhhccccHHHHHHHHhhCCcccEEEEEeCcCCHHHHHHHHHhcCCceeeeccc------------------ccC
Confidence            99999999999999999999999999999999999999999999999998887664322                  345


Q ss_pred             ceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          161 GLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       161 ~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      ++.+.+..++...+  .....+.....+++||||++++.++
T Consensus       196 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~~lvf~~~~~~~~  234 (337)
T 2z0m_A          196 NVEHKFVHVKDDWR--SKVQALRENKDKGVIVFVRTRNRVA  234 (337)
T ss_dssp             GEEEEEEECSSSSH--HHHHHHHTCCCSSEEEECSCHHHHH
T ss_pred             CceEEEEEeChHHH--HHHHHHHhCCCCcEEEEEcCHHHHH
Confidence            67777777665543  3346777788889999999988765

>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=99.93  E-value=1.4e-25  Score=193.76  Aligned_cols=190  Identities=27%  Similarity=0.393  Sum_probs=149.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhc---CCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFIST---LPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~---~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+|||+||++||.|+++.++++...   .+.+.+..+.||.....+...+...+++|+|+||+++.+++.......++++
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   3357789999999988888877667899999999999998876224468899


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCC-------CCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchh
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLP-------KLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASS  150 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~-------~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~  150 (203)
                      +++|+||||++++++|.+.+..++..++       ...|++++|||+++.+..++..++.++..+.+.....        
T Consensus       228 ~~lViDEah~l~~~~f~~~~~~i~~~l~~~~~~~~~~~~~l~~SAT~~~~v~~~~~~~~~~~~~~~~~~~~~--------  299 (563)
T 3i5x_A          228 DYKVLDEADRLLEIGFRDDLETISGILNEKNSKSADNIKTLLFSATLDDKVQKLANNIMNKKECLFLDTVDK--------  299 (563)
T ss_dssp             CEEEEETHHHHTSTTTHHHHHHHHHHHHHHCSSCTTCCEEEEEESSCCTHHHHHTTTTCCSSEEEEEESSCS--------
T ss_pred             eEEEEeCHHHHhccchHHHHHHHHHhhhhccccCccCceEEEEEccCCHHHHHHHHHhcCCCceEEEeccCC--------
Confidence            9999999999999999999998887763       3679999999999999999999999887776644310        


Q ss_pred             hhhccCCCCCceeEEEEEcCCC-CcH----HHHHHHHhc-CCCCeEEEEeccCCccc
Q 028826          151 QQLASSKTPLGLHLEYLECESD-KKP----SQLVDLLIK-NKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       151 ~~~~~~~~~~~i~~~~~~~~~~-~k~----~~l~~ll~~-~~~~~~lIF~ns~~~~e  201 (203)
                         ........+.+.+...+.. .+.    ..+...+.. ...+++||||+|++.|+
T Consensus       300 ---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~iVF~~s~~~~~  353 (563)
T 3i5x_A          300 ---NEPEAHERIDQSVVISEKFANSIFAAVEHIKKQIKERDSNYKAIIFAPTVKFTS  353 (563)
T ss_dssp             ---SSCSSCTTEEEEEEEESSTTHHHHHHHHHHHHHHHHTTTCCEEEEECSCHHHHH
T ss_pred             ---CCccccccCceEEEECchhHhhHHHHHHHHHHHHhhcCCCCcEEEEcCcHHHHH
Confidence               0033456677777776653 232    233333333 56779999999998775

>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=99.93  E-value=2e-25  Score=183.90  Aligned_cols=179  Identities=28%  Similarity=0.415  Sum_probs=154.8

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.+++++... ++.+....++......     ..+++|+|+||+++..++.. +...+++++++
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            37999999999999999999998766 7888888877553322     34789999999999999988 77889999999


Q ss_pred             EEcchhHhhh-hchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCC
Q 028826           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTP  159 (203)
Q Consensus        81 ViDEad~l~~-~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (203)
                      |+||||.+.+ .++...+..+...+++..|++++|||+++.+..+...++.++..+.....               ....
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 67899999999999999999999999999999999999999988877665               4566


Q ss_pred             CceeEEEEEcCC-CCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          160 LGLHLEYLECES-DKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       160 ~~i~~~~~~~~~-~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      ..+.+.+..+.. ..|...+..++.....+++|||||+++.|+
T Consensus       215 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~lvf~~~~~~~~  257 (395)
T 3pey_A          215 DAIKQLYMDCKNEADKFDVLTELYGLMTIGSSIIFVATKKTAN  257 (395)
T ss_dssp             TTEEEEEEECSSHHHHHHHHHHHHTTTTSSEEEEECSCHHHHH
T ss_pred             ccccEEEEEcCchHHHHHHHHHHHHhccCCCEEEEeCCHHHHH
Confidence            778888887754 568889999998888899999999988765

>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=8.9e-25  Score=165.74  Aligned_cols=133  Identities=33%  Similarity=0.546  Sum_probs=120.7

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.++++..   ++++..++||.....+...+ ..+++|+|+||+++.+++.. +..++++++++
T Consensus        74 ~~lil~P~~~L~~q~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~-~~~~~i~v~T~~~l~~~~~~-~~~~~~~~~~i  148 (207)
T 2gxq_A           74 RALVLTPTRELALQVASELTAVAP---HLKVVAVYGGTGYGKQKEAL-LRGADAVVATPGRALDYLRQ-GVLDLSRVEVA  148 (207)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHHCT---TSCEEEECSSSCSHHHHHHH-HHCCSEEEECHHHHHHHHHH-TSSCCTTCSEE
T ss_pred             cEEEEECCHHHHHHHHHHHHHHhh---cceEEEEECCCChHHHHHHh-hCCCCEEEECHHHHHHHHHc-CCcchhhceEE
Confidence            379999999999999999999864   37788899998877776666 35799999999999999988 88889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEec
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVR  138 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~  138 (203)
                      |+||||.+.+.++...+..++..+++.+|++++|||+++.+.++++.++.+|..+.+.
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            9999999999999999999999999999999999999999999999999999988763

>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=7.1e-25  Score=168.42  Aligned_cols=136  Identities=35%  Similarity=0.591  Sum_probs=114.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++|+.|+++.+++++... ++++..+.||....++...+  ..++|+|+||+++.+++.. +...+++++++
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            37999999999999999999998776 89999999998877666555  2499999999999999988 78889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAE  140 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~  140 (203)
                      |+||||.+.++++...+..++..+++..|++++|||+++.+.++++.++.+|..+.+..+
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            999999999999999999999999999999999999999999999999999999887654

>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=8.2e-25  Score=170.38  Aligned_cols=139  Identities=27%  Similarity=0.385  Sum_probs=117.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhC-CCccCCCccE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM-DVLDFRNLVI   79 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~-~~~~l~~v~~   79 (203)
                      .+||++||++|+.|+++.+++++... ++++..+.||.............+++|+|+||+++..++... ..++++++++
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            38999999999999999999998877 788888887755443332233467899999999999999872 1578999999


Q ss_pred             EEEcchhHhhh---hchHHHHHHHHHhCC-CCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccC
Q 028826           80 LVLDEADRLLD---MGFQKQISYIISRLP-KLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAE  140 (203)
Q Consensus        80 lViDEad~l~~---~~~~~~~~~il~~~~-~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~  140 (203)
                      +|+||||.+++   .+|...+..++..+. ...|++++|||+|+++.++++.++.+|..+.++..
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   468999999887764 57899999999999999999999999999998764

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=99.92  E-value=4.3e-25  Score=184.07  Aligned_cols=174  Identities=18%  Similarity=0.202  Sum_probs=134.8

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcch---HHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEV---KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~---~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||++||++|+.|+++.+++++. . ++++..++||.+.   ..+...+..+.++|+|+||+++.+++..   +.++++
T Consensus        66 ~~lil~Pt~~L~~q~~~~~~~~~~-~-~~~v~~~~g~~~~~~~~~~~~~l~~~~~~Iiv~Tp~~l~~~l~~---~~~~~~  140 (414)
T 3oiy_A           66 KSALVFPTVTLVKQTLERLQKLAD-E-KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK---LSQKRF  140 (414)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHHCC-S-SCCEEECCTTSCHHHHHHHHHHHHHTCCSEEEEEHHHHHHCHHH---HTTCCC
T ss_pred             EEEEEECCHHHHHHHHHHHHHHcc-C-CceEEEEECCCChhhHHHHHHHhhcCCCCEEEECHHHHHHHHHH---hccccc
Confidence            489999999999999999999977 4 8999999999987   5555666555699999999999988764   667899


Q ss_pred             cEEEEcchhHhh----------h-hchHHH-HHHHHHhCC-----------CCCcEEEEeee-cChhHH-HHHHhcCCCC
Q 028826           78 VILVLDEADRLL----------D-MGFQKQ-ISYIISRLP-----------KLRRTGLFSAT-QTEAVE-ELSKAGLRNP  132 (203)
Q Consensus        78 ~~lViDEad~l~----------~-~~~~~~-~~~il~~~~-----------~~~q~i~~SAT-~~~~v~-~~~~~~l~~~  132 (203)
                      +++|+||||++.          + .+|.+. +..++..++           ...|++++||| .|+.+. .+.+.++.  
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            999999997654          4 677777 788888876           78999999999 665544 23333322  


Q ss_pred             eEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          133 VRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       133 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                        +.+...               .....++.+.+..+   +|...+.++++.. ++++|||||+++.|++
T Consensus       219 --~~~~~~---------------~~~~~~i~~~~~~~---~~~~~l~~~l~~~-~~~~lVF~~~~~~~~~  267 (414)
T 3oiy_A          219 --FTVGRL---------------VSVARNITHVRISS---RSKEKLVELLEIF-RDGILIFAQTEEEGKE  267 (414)
T ss_dssp             --CCSSCC---------------CCCCCSEEEEEESS---CCHHHHHHHHHHH-CSSEEEEESSHHHHHH
T ss_pred             --cCcCcc---------------ccccccchheeecc---CHHHHHHHHHHHc-CCCEEEEECCHHHHHH
Confidence              112222               34567788888655   6788888888873 4799999999987753

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=99.91  E-value=3.6e-24  Score=196.72  Aligned_cols=174  Identities=19%  Similarity=0.216  Sum_probs=138.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcch---HHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEV---KADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~---~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+|||+||+|||.|+++.+++++ .. ++++..++||.+.   .++...+..+.++|+|+||++|.+++..   ++++++
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-DE-KVKIFGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREK---LSQKRF  197 (1104)
T ss_dssp             CEEEEESSHHHHHHHHHHHHTTS-CT-TSCEEEECTTCCTTHHHHHHHHHHTSCCSEEEEEHHHHHHSHHH---HHTSCC
T ss_pred             eEEEEechHHHHHHHHHHHHHhh-CC-CCeEEEEeCCCCHHHHHHHHHHHhCCCCCEEEECHHHHHHHHHh---hcccCc
Confidence            48999999999999999999987 44 8999999999987   6666677555699999999999888764   677899


Q ss_pred             cEEEEcchh----------Hhhh-hchHHH-HHHHHHhCC-----------CCCcEEEEeee-cChhHHH-HHHhcCCCC
Q 028826           78 VILVLDEAD----------RLLD-MGFQKQ-ISYIISRLP-----------KLRRTGLFSAT-QTEAVEE-LSKAGLRNP  132 (203)
Q Consensus        78 ~~lViDEad----------~l~~-~~~~~~-~~~il~~~~-----------~~~q~i~~SAT-~~~~v~~-~~~~~l~~~  132 (203)
                      +++|+||||          .+++ +||... +..+++.++           ...|+++|||| .|..+.. +.+..+.  
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            999999995          5556 888888 899999887           88999999999 5655542 3333333  


Q ss_pred             eEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          133 VRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       133 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                        +.+...               ...+.++.+.+..+   +|...|.++++..+ +++|||||+++.|++
T Consensus       276 --i~v~~~---------------~~~~~~i~~~~~~~---~k~~~L~~ll~~~~-~~~LVF~~s~~~a~~  324 (1104)
T 4ddu_A          276 --FTVGRL---------------VSVARNITHVRISS---RSKEKLVELLEIFR-DGILIFAQTEEEGKE  324 (1104)
T ss_dssp             --CCCCBC---------------CCCCCCEEEEEESC---CCHHHHHHHHHHHC-SSEEEEESSSHHHHH
T ss_pred             --EEeccC---------------CCCcCCceeEEEec---CHHHHHHHHHHhcC-CCEEEEECcHHHHHH
Confidence              223333               44677888888766   67888888888743 799999999987763

>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=99.89  E-value=8.1e-23  Score=187.85  Aligned_cols=125  Identities=22%  Similarity=0.190  Sum_probs=107.5

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++|||+|+.|+++.+.++..     .++.++|+.+.        +.+++|+|+||++|.+++.. +...+++++++|
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            79999999999999999999753     57778888763        46799999999999999998 777789999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChh--HHHHHHhcCCCCeEEEeccC
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA--VEELSKAGLRNPVRIEVRAE  140 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~--v~~~~~~~l~~~~~i~~~~~  140 (203)
                      |||||++.++++...+..++..++...|++++|||+|+.  +..++......+..+.....
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  44666667777766655543

>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=99.88  E-value=8.4e-24  Score=193.95  Aligned_cols=173  Identities=17%  Similarity=0.192  Sum_probs=133.3

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCc----eEEEEEcCcchHHHHHHH--HhCCCeEEEeccHHHHHHHHhCCCccC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDV----KSMLLVGGVEVKADVKKI--EEEGANLLIGTPGRLYDIMERMDVLDF   74 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i----~~~~~~~g~~~~~~~~~l--~~~~~~ilV~Tp~~l~~~~~~~~~~~l   74 (203)
                      .+|||+|||+||.|+++.+++++... ++    ++..++||.+..++....  ... ++|+|+||++|.+++..     +
T Consensus       101 ~~lil~PtreLa~Q~~~~l~~l~~~~-~i~~~~~v~~~~Gg~~~~~~~~~~~~l~~-~~IlV~TP~~L~~~l~~-----L  173 (1054)
T 1gku_B          101 RCYVIFPTSLLVIQAAETIRKYAEKA-GVGTENLIGYYHGRIPKREKENFMQNLRN-FKIVITTTQFLSKHYRE-----L  173 (1054)
T ss_dssp             CEEEEESCHHHHHHHHHHHHHHHTTT-CCSGGGSEEECCSSCCSHHHHHHHHSGGG-CSEEEEEHHHHHHCSTT-----S
T ss_pred             eEEEEeccHHHHHHHHHHHHHHHhhc-CCCccceEEEEeCCCChhhHHHHHhhccC-CCEEEEcHHHHHHHHHH-----h
Confidence            48999999999999999999999877 77    899999998877643322  134 99999999999987653     6


Q ss_pred             CCccEEEEcchhHhhhhchHHHHHHHHHhC-----------CCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCccc
Q 028826           75 RNLVILVLDEADRLLDMGFQKQISYIISRL-----------PKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKS  143 (203)
Q Consensus        75 ~~v~~lViDEad~l~~~~~~~~~~~il~~~-----------~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~  143 (203)
                      ++++++|+||||+|+++  ...++.++..+           +..+|++++|||+++. ..+...++.++..+.+...   
T Consensus       174 ~~l~~lViDEah~~l~~--~~~~~~i~~~lgf~~~~~~~~~~~~~q~~l~SAT~t~~-~~~~~~~~~~~~~i~v~~~---  247 (1054)
T 1gku_B          174 GHFDFIFVDDVDAILKA--SKNVDKLLHLLGFHYDLKTKSWVGEARGCLMVSTATAK-KGKKAELFRQLLNFDIGSS---  247 (1054)
T ss_dssp             CCCSEEEESCHHHHHTS--THHHHHHHHHTTEEEETTTTEEEECCSSEEEECCCCSC-CCTTHHHHHHHHCCCCSCC---
T ss_pred             ccCCEEEEeChhhhhhc--cccHHHHHHHhCcchhhhhhhcccCCceEEEEecCCCc-hhHHHHHhhcceEEEccCc---
Confidence            69999999999999984  56777777766           3568999999999987 5444444444433434333   


Q ss_pred             ccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          144 HHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       144 ~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                                  .....++.+.+.   ..+|...|.++++.. .+++||||||++.|++
T Consensus       248 ------------~~~~~~i~~~~~---~~~k~~~L~~ll~~~-~~~~LVF~~t~~~a~~  290 (1054)
T 1gku_B          248 ------------RITVRNVEDVAV---NDESISTLSSILEKL-GTGGIIYARTGEEAEE  290 (1054)
T ss_dssp             ------------EECCCCEEEEEE---SCCCTTTTHHHHTTS-CSCEEEEESSHHHHHH
T ss_pred             ------------ccCcCCceEEEe---chhHHHHHHHHHhhc-CCCEEEEEcCHHHHHH
Confidence                        334567788776   467788888888876 4689999999987763

>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=99.87  E-value=7.5e-23  Score=180.27  Aligned_cols=101  Identities=20%  Similarity=0.274  Sum_probs=73.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHH-HHHHHhCC------Ccc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMD------VLD   73 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l-~~~~~~~~------~~~   73 (203)
                      +|+||+||||||.|+++++.++..++ ++++.+++||.+...+  .+ ..++||+||||++| .++++. +      .+.
T Consensus       117 ~vlVltPTreLA~Q~~e~~~~l~~~l-gl~v~~i~GG~~~~~r--~~-~~~~dIvvgTpgrl~fDyLrd-~~~~~~~~~~  191 (853)
T 2fsf_A          117 GVHVVTVNDYLAQRDAENNRPLFEFL-GLTVGINLPGMPAPAK--RE-AYAADITYGTNNEYGFDYLRD-NMAFSPEERV  191 (853)
T ss_dssp             CCEEEESSHHHHHHHHHHHHHHHHHT-TCCEEECCTTCCHHHH--HH-HHHSSEEEEEHHHHHHHHHHH-TTCSSGGGCC
T ss_pred             cEEEEcCCHHHHHHHHHHHHHHHHhc-CCeEEEEeCCCCHHHH--HH-hcCCCEEEECCchhhHHHHHh-hhhccHhHhc
Confidence            47999999999999999999999998 8999999999886433  33 23699999999999 788886 3      366


Q ss_pred             CCCccEEEEcchhHhh-hh---------------chHHHHHHHHHhCCC
Q 028826           74 FRNLVILVLDEADRLL-DM---------------GFQKQISYIISRLPK  106 (203)
Q Consensus        74 l~~v~~lViDEad~l~-~~---------------~~~~~~~~il~~~~~  106 (203)
                      +++++++|+||||.|+ +.               ++...+..++..+++
T Consensus       192 ~~~l~~lVlDEaD~mLiD~a~tpLIiSg~~~~~~~~y~~i~~iv~~L~~  240 (853)
T 2fsf_A          192 QRKLHYALVDEVDSILIDEARTPLIISGPAEDSSEMYKRVNKIIPHLIR  240 (853)
T ss_dssp             CCSCCEEEESCHHHHTTTTTTCEEEEEEC--------------------
T ss_pred             ccCCcEEEECchHHHHHhcCcccccccCCCccchhHHHHHHHHHHhchh
Confidence            7999999999999998 53               367888899988874

>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=99.87  E-value=3.5e-23  Score=182.64  Aligned_cols=115  Identities=17%  Similarity=0.219  Sum_probs=97.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHH-HHHHHhC-----CCccC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERM-----DVLDF   74 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l-~~~~~~~-----~~~~l   74 (203)
                      +++||+||||||.|+.+++.++..++ ++++.+++||.+...+..   ..++||+||||++| .+++...     +.+.+
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-GLTVGLNLNSMSKDEKRE---AYAADITYSTNNELGFDYLRDNMVLYKEQMVQ  201 (844)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHHHHHT-TCCEEECCTTSCHHHHHH---HHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCC
T ss_pred             CEEEEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHHHH---hcCCCEEEECchhhhHHHHHHhhhcchhhhcc
Confidence            48999999999999999999999998 999999999988654433   24699999999999 6777651     24668


Q ss_pred             CCccEEEEcchhHhh-hhc---------------hHHHHHHHHHhCC---------CCCcEE-----------------E
Q 028826           75 RNLVILVLDEADRLL-DMG---------------FQKQISYIISRLP---------KLRRTG-----------------L  112 (203)
Q Consensus        75 ~~v~~lViDEad~l~-~~~---------------~~~~~~~il~~~~---------~~~q~i-----------------~  112 (203)
                      +.+.++|+||||.|+ +.+               |...+..++..++         +.+|+.                 +
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            899999999999998 653               7889999999997         478888                 9


Q ss_pred             EeeecCh
Q 028826          113 FSATQTE  119 (203)
Q Consensus       113 ~SAT~~~  119 (203)
                      ||||++.
T Consensus       282 fsat~~~  288 (844)
T 1tf5_A          282 FDVKHVA  288 (844)
T ss_dssp             TSGGGHH
T ss_pred             CCCccch
Confidence            9999874

>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=99.87  E-value=1.3e-21  Score=169.95  Aligned_cols=180  Identities=18%  Similarity=0.139  Sum_probs=129.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH-----HhCCCeEEEeccHHHH---HHHHh-CCCc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI-----EEEGANLLIGTPGRLY---DIMER-MDVL   72 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l-----~~~~~~ilV~Tp~~l~---~~~~~-~~~~   72 (203)
                      +|||+|+++|+.|+.+.++++     ++++..+.|+....+.....     ...+++|+|+||++|.   .++.. .+..
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            799999999999999999887     68888999988766554322     2467999999999884   22221 0245


Q ss_pred             cCCCccEEEEcchhHhhhhc--hHHHHHH--HHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccc
Q 028826           73 DFRNLVILVLDEADRLLDMG--FQKQISY--IISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASA  148 (203)
Q Consensus        73 ~l~~v~~lViDEad~l~~~~--~~~~~~~--il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~  148 (203)
                      .+.+++++||||||++.+||  |++.+..  .+....+..|++++|||+++.+...+..++..+....+...        
T Consensus       162 ~~~~i~~iViDEAH~is~~g~dfr~~~~~l~~l~~~~~~~~ii~lSAT~~~~v~~~i~~~l~~~~~~~~~~~--------  233 (591)
T 2v1x_A          162 EARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTAS--------  233 (591)
T ss_dssp             HTTCEEEEEEETGGGGSTTCTTCCGGGGGGGHHHHHCTTSEEEEEESSCCHHHHHHHHHHTTCCSCEEEECC--------
T ss_pred             hccCCcEEEEECcccccccccccHHHHHHHHHHHHhCCCCcEEEEecCCCHHHHHHHHHHhCCCCcEEEecC--------
Confidence            57899999999999999988  7777654  34444457999999999999988877777765433333222        


Q ss_pred             hhhhhccCCCCCceeEEEEEcCC--CCcHHHHHHHHhc-CCCCeEEEEeccCCcccC
Q 028826          149 SSQQLASSKTPLGLHLEYLECES--DKKPSQLVDLLIK-NKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       149 ~~~~~~~~~~~~~i~~~~~~~~~--~~k~~~l~~ll~~-~~~~~~lIF~ns~~~~e~  202 (203)
                              ...+++...+.....  .++...+.++++. ...+++||||+|++.|++
T Consensus       234 --------~~r~nl~~~v~~~~~~~~~~~~~l~~~l~~~~~~~~~IVf~~sr~~~e~  282 (591)
T 2v1x_A          234 --------FNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQ  282 (591)
T ss_dssp             --------CCCTTEEEEEEECCSSHHHHHHHHHHHHTTTTTTCEEEEECSSHHHHHH
T ss_pred             --------CCCcccEEEEEeCCCcHHHHHHHHHHHHHHhccCCCeEEEeCcHHHHHH
Confidence                    234555544443322  2356677777764 467899999999988764

>2xgj_A ATP-dependent RNA helicase DOB1; hydrolase-RNA complex, hydrolase, tramp, exosome, DEAD, nucleotide-binding; HET: ADP; 2.90A {Saccharomyces cerevisiae}

Probab=99.87  E-value=3.3e-21  Score=175.83  Aligned_cols=124  Identities=23%  Similarity=0.216  Sum_probs=102.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++||++|+.|+++.+.++..     +++.++|+...        ..+++|+|+||++|..++.. +...+++++++|
T Consensus       132 vL~l~PtkaLa~Q~~~~l~~~~~-----~vglltGd~~~--------~~~~~IvV~Tpe~L~~~L~~-~~~~l~~l~lVV  197 (1010)
T 2xgj_A          132 VIYTSPIKALSNQKYRELLAEFG-----DVGLMTGDITI--------NPDAGCLVMTTEILRSMLYR-GSEVMREVAWVI  197 (1010)
T ss_dssp             EEEEESSHHHHHHHHHHHHHHHS-----CEEEECSSCEE--------CTTCSEEEEEHHHHHHHHHH-TCTTGGGEEEEE
T ss_pred             EEEECChHHHHHHHHHHHHHHhC-----CEEEEeCCCcc--------CCCCCEEEEcHHHHHHHHHc-CcchhhcCCEEE
Confidence            79999999999999999999863     67778888764        24689999999999999988 778899999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHH--HHHHhcCCCCeEEEecc
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE--ELSKAGLRNPVRIEVRA  139 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~--~~~~~~l~~~~~i~~~~  139 (203)
                      +||||.+.++++...+..++..++...|++++|||+++...  .++......+..+....
T Consensus       198 iDEaH~l~d~~rg~~~e~il~~l~~~~~il~LSATi~n~~e~a~~l~~~~~~~~~vi~~~  257 (1010)
T 2xgj_A          198 FDEVHYMRDKERGVVWEETIILLPDKVRYVFLSATIPNAMEFAEWICKIHSQPCHIVYTN  257 (1010)
T ss_dssp             EETGGGGGCTTTHHHHHHHHHHSCTTCEEEEEECCCTTHHHHHHHHHHHHTSCEEEEEEC
T ss_pred             EechhhhcccchhHHHHHHHHhcCCCCeEEEEcCCCCCHHHHHHHHHhhcCCCeEEEecC
Confidence            99999999998888899999999999999999999987532  33333345565555443

>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=99.85  E-value=8.5e-21  Score=162.85  Aligned_cols=174  Identities=20%  Similarity=0.197  Sum_probs=128.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHH---HHHHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~---~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||++|+++|+.|+.+.++++     ++++..+.|+.+..+..   ..+..++++|+|+||+++...... ..+...+++
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            699999999999999998876     68888888887755443   334457799999999999632222 234557899


Q ss_pred             EEEEcchhHhhhhc--hHHHHHH---HHHhCCCCCcEEEEeeecChhHHH-HHHhc-CCCCeEEEeccCcccccccchhh
Q 028826           79 ILVLDEADRLLDMG--FQKQISY---IISRLPKLRRTGLFSATQTEAVEE-LSKAG-LRNPVRIEVRAESKSHHASASSQ  151 (203)
Q Consensus        79 ~lViDEad~l~~~~--~~~~~~~---il~~~~~~~q~i~~SAT~~~~v~~-~~~~~-l~~~~~i~~~~~~~~~~~~~~~~  151 (203)
                      ++|+||||++.+||  |++.+..   +...+ +..+++++|||.++.+.. +.+.. +.++..+.. ..           
T Consensus       142 ~vViDEaH~i~~~g~~fr~~~~~l~~l~~~~-~~~~~i~lSAT~~~~~~~~i~~~l~~~~~~~~~~-~~-----------  208 (523)
T 1oyw_A          142 LLAVDEAHCISQWGHDFRPEYAALGQLRQRF-PTLPFMALTATADDTTRQDIVRLLGLNDPLIQIS-SF-----------  208 (523)
T ss_dssp             EEEESSGGGGCTTSSCCCHHHHGGGGHHHHC-TTSCEEEEESCCCHHHHHHHHHHHTCCSCEEEEC-CC-----------
T ss_pred             EEEEeCccccCcCCCccHHHHHHHHHHHHhC-CCCCEEEEeCCCCHHHHHHHHHHhCCCCCeEEeC-CC-----------
Confidence            99999999999887  6666544   45555 468999999999998765 33332 345554432 22           


Q ss_pred             hhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          152 QLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       152 ~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                            ..+++  .|...+..++...+.+++.....+++||||+|++.||+
T Consensus       209 ------~r~~l--~~~v~~~~~~~~~l~~~l~~~~~~~~IVf~~sr~~~e~  251 (523)
T 1oyw_A          209 ------DRPNI--RYMLMEKFKPLDQLMRYVQEQRGKSGIIYCNSRAKVED  251 (523)
T ss_dssp             ------CCTTE--EEEEEECSSHHHHHHHHHHHTTTCCEEEECSSHHHHHH
T ss_pred             ------CCCce--EEEEEeCCCHHHHHHHHHHhcCCCcEEEEeCCHHHHHH
Confidence                  23344  34445667889999999998888899999999988763

>4a4z_A Antiviral helicase SKI2; hydrolase, ATPase, mRNA degradation, exosome; HET: ANP; 2.40A {Saccharomyces cerevisiae} PDB: 4a4k_A

Probab=99.85  E-value=6e-21  Score=174.07  Aligned_cols=113  Identities=26%  Similarity=0.276  Sum_probs=97.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++||++|+.|+++.++++.   +++++..++|+...        +..++|+|+||++|..++.. +...+.+++++|
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            7999999999999999998864   26788999998764        35689999999999999988 777889999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHh
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~  127 (203)
                      |||||++.++++...+..++..++...|++++|||+++.. ++.++
T Consensus       153 iDEaH~l~d~~~g~~~e~ii~~l~~~v~iIlLSAT~~n~~-ef~~~  197 (997)
T 4a4z_A          153 FDEVHYVNDQDRGVVWEEVIIMLPQHVKFILLSATVPNTY-EFANW  197 (997)
T ss_dssp             ECCTTCCCTTCTTCCHHHHHHHSCTTCEEEEEECCCTTHH-HHHHH
T ss_pred             EECcccccccchHHHHHHHHHhcccCCCEEEEcCCCCChH-HHHHH
Confidence            9999999999999999999999999999999999998653 44443

>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=99.85  E-value=1.1e-21  Score=173.40  Aligned_cols=115  Identities=17%  Similarity=0.223  Sum_probs=98.8

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHH-HHHHHhC-----CCccC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERM-----DVLDF   74 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l-~~~~~~~-----~~~~l   74 (203)
                      .++||+||++||.|+.+++..+..++ ++++++++||.+...+..   ..++||+||||++| .++++..     +.+.+
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-GLQVGVILATMTPDERRV---AYNADITYGTNNEFGFDYLRDNMAHSLDDLVQ  229 (922)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHHHHHT-TCCEEECCTTCCHHHHHH---HHHSSEEEEEHHHHHHHHHHHTTCSSGGGCCC
T ss_pred             CeEEEeCCHHHHHHHHHHHHHHHhhc-CCeEEEEeCCCCHHHHHH---hcCCCEEEECchHhhHHHHHhhhhccHhhhcc
Confidence            48999999999999999999999998 899999999988544332   23699999999999 7888761     24668


Q ss_pred             CCccEEEEcchhHhh-h---------------hchHHHHHHHHHhCC---------CCCcEE-----------------E
Q 028826           75 RNLVILVLDEADRLL-D---------------MGFQKQISYIISRLP---------KLRRTG-----------------L  112 (203)
Q Consensus        75 ~~v~~lViDEad~l~-~---------------~~~~~~~~~il~~~~---------~~~q~i-----------------~  112 (203)
                      +.+.++|+||||.|+ +               .+|...+..++..++         +.+|+.                 +
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            899999999999998 4               358899999999998         788999                 9


Q ss_pred             EeeecCh
Q 028826          113 FSATQTE  119 (203)
Q Consensus       113 ~SAT~~~  119 (203)
                      ||||.++
T Consensus       310 fsat~~~  316 (922)
T 1nkt_A          310 YEAANSP  316 (922)
T ss_dssp             TCSTTCC
T ss_pred             cCCcchh
Confidence            9999875

>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=99.83  E-value=2.8e-20  Score=159.71  Aligned_cols=116  Identities=13%  Similarity=0.151  Sum_probs=90.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCc-cCCCccE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL-DFRNLVI   79 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~-~l~~v~~   79 (203)
                      .+|||+||++|+.|+++.+++++... ++++..++||.....+...+. .+++|+|+||+++..++.. +.+ .+.++++
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            37999999999999999999998877 899999999987766665553 4699999999999999988 667 7999999


Q ss_pred             EEEcchhHhhhhchHHHH-HHHHHh-C---CCCCcEEEEeeecCh
Q 028826           80 LVLDEADRLLDMGFQKQI-SYIISR-L---PKLRRTGLFSATQTE  119 (203)
Q Consensus        80 lViDEad~l~~~~~~~~~-~~il~~-~---~~~~q~i~~SAT~~~  119 (203)
                      +|+||||++.+++....+ ..++.. +   ++..|++++|||++.
T Consensus       134 vViDEah~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT~~~  178 (556)
T 4a2p_A          134 MIFDECHNTTGNHPYNVLMTRYLEQKFNSASQLPQILGLTASVGV  178 (556)
T ss_dssp             EEEETGGGCSTTSHHHHHHHHHHHHHHCC---CCEEEEEESCCCC
T ss_pred             EEEECCcccCCcchHHHHHHHHHHhhhcccCCCCeEEEEeCCccc
Confidence            999999999877643333 233322 2   356899999999953

>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=99.82  E-value=1.2e-19  Score=161.04  Aligned_cols=171  Identities=16%  Similarity=0.169  Sum_probs=127.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ++|++|+|+||.|+++.++++...  ++++..++|+.......    ..+++|+|+||+++..++.. +...+++++++|
T Consensus        71 ~l~i~P~raLa~q~~~~~~~l~~~--g~~v~~~~G~~~~~~~~----~~~~~Iiv~Tpe~l~~~~~~-~~~~l~~~~~vI  143 (720)
T 2zj8_A           71 AVYIVPLKALAEEKFQEFQDWEKI--GLRVAMATGDYDSKDEW----LGKYDIIIATAEKFDSLLRH-GSSWIKDVKILV  143 (720)
T ss_dssp             EEEECSSGGGHHHHHHHTGGGGGG--TCCEEEECSCSSCCCGG----GGGCSEEEECHHHHHHHHHH-TCTTGGGEEEEE
T ss_pred             EEEEcCcHHHHHHHHHHHHHHHhc--CCEEEEecCCCCccccc----cCCCCEEEECHHHHHHHHHc-ChhhhhcCCEEE
Confidence            799999999999999999877654  79999999986654321    24689999999999999988 666689999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCc
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLG  161 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (203)
                      +||+|.+.++++...+..++..+++..|++++|||+++ ...+.+++ ..+ .+....                  .+..
T Consensus       144 iDE~H~l~~~~r~~~~~~ll~~l~~~~~ii~lSATl~n-~~~~~~~l-~~~-~~~~~~------------------rp~~  202 (720)
T 2zj8_A          144 ADEIHLIGSRDRGATLEVILAHMLGKAQIIGLSATIGN-PEELAEWL-NAE-LIVSDW------------------RPVK  202 (720)
T ss_dssp             EETGGGGGCTTTHHHHHHHHHHHBTTBEEEEEECCCSC-HHHHHHHT-TEE-EEECCC------------------CSSE
T ss_pred             EECCcccCCCcccHHHHHHHHHhhcCCeEEEEcCCcCC-HHHHHHHh-CCc-ccCCCC------------------CCCc
Confidence            99999998888899999999988778999999999986 35666544 321 111111                  1222


Q ss_pred             eeEEEE------EcC-----CCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          162 LHLEYL------ECE-----SDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       162 i~~~~~------~~~-----~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      +...+.      ..+     ...+...+.+.++.  .+++||||++++.|+.
T Consensus       203 l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~LVF~~sr~~~~~  252 (720)
T 2zj8_A          203 LRRGVFYQGFVTWEDGSIDRFSSWEELVYDAIRK--KKGALIFVNMRRKAER  252 (720)
T ss_dssp             EEEEEEETTEEEETTSCEEECSSTTHHHHHHHHT--TCCEEEECSCHHHHHH
T ss_pred             ceEEEEeCCeeeccccchhhhhHHHHHHHHHHhC--CCCEEEEecCHHHHHH
Confidence            222211      112     24566777777754  4699999999988763

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=99.82  E-value=8e-20  Score=156.65  Aligned_cols=116  Identities=13%  Similarity=0.172  Sum_probs=94.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCc-cCCCccE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL-DFRNLVI   79 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~-~l~~v~~   79 (203)
                      .+|||+||++|+.|+++.+++++... ++++..++||.....+...+. .+++|+|+||+++..++.. +.+ .+.++++
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            37999999999999999999999877 899999999987666655553 4699999999999999988 666 7899999


Q ss_pred             EEEcchhHhhhhc-hHHHHHHHHHhC-----CCCCcEEEEeeecCh
Q 028826           80 LVLDEADRLLDMG-FQKQISYIISRL-----PKLRRTGLFSATQTE  119 (203)
Q Consensus        80 lViDEad~l~~~~-~~~~~~~il~~~-----~~~~q~i~~SAT~~~  119 (203)
                      +|+||||++.+.+ +...+...+...     ....|++++|||++.
T Consensus       131 vViDEah~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~lSAT~~~  176 (555)
T 3tbk_A          131 MIFDECHNTSKNHPYNQIMFRYLDHKLGESRDPLPQVVGLTASVGV  176 (555)
T ss_dssp             EEETTGGGCSTTCHHHHHHHHHHHHHTSSCCSCCCEEEEEESCCCC
T ss_pred             EEEECccccCCcchHHHHHHHHHHhhhccccCCCCeEEEEecCccc
Confidence            9999999998765 444444444332     256799999999964

>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=99.81  E-value=2.5e-19  Score=158.60  Aligned_cols=172  Identities=14%  Similarity=0.176  Sum_probs=123.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .++|++|+|+||.|+++.++++.. . ++++..++|+....+..    ..+++|+|+||+++..++.. +...+++++++
T Consensus        70 ~~l~i~P~r~La~q~~~~~~~~~~-~-g~~v~~~~G~~~~~~~~----~~~~~Iiv~Tpe~l~~~l~~-~~~~l~~~~~v  142 (702)
T 2p6r_A           70 KSLYVVPLRALAGEKYESFKKWEK-I-GLRIGISTGDYESRDEH----LGDCDIIVTTSEKADSLIRN-RASWIKAVSCL  142 (702)
T ss_dssp             CEEEEESSHHHHHHHHHHHTTTTT-T-TCCEEEECSSCBCCSSC----STTCSEEEEEHHHHHHHHHT-TCSGGGGCCEE
T ss_pred             cEEEEeCcHHHHHHHHHHHHHHHh-c-CCEEEEEeCCCCcchhh----ccCCCEEEECHHHHHHHHHc-ChhHHhhcCEE
Confidence            379999999999999999976654 3 79999999987654321    24799999999999999987 65668999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhC---CCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCC
Q 028826           81 VLDEADRLLDMGFQKQISYIISRL---PKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSK  157 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~---~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~  157 (203)
                      |+||+|.+.++++...+..++..+   ++..|++++|||+++ ...+.+++ ..+. +....                  
T Consensus       143 IiDE~H~l~~~~r~~~~~~ll~~l~~~~~~~~ii~lSATl~n-~~~~~~~l-~~~~-~~~~~------------------  201 (702)
T 2p6r_A          143 VVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAEWL-DADY-YVSDW------------------  201 (702)
T ss_dssp             EETTGGGGGCTTTHHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHHHHT-TCEE-EECCC------------------
T ss_pred             EEeeeeecCCCCcccHHHHHHHHHHhcCcCceEEEECCCcCC-HHHHHHHh-CCCc-ccCCC------------------
Confidence            999999998877777777776666   578999999999986 46666644 3221 22111                  


Q ss_pred             CCCceeEEEE------EcCCC-------CcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          158 TPLGLHLEYL------ECESD-------KKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       158 ~~~~i~~~~~------~~~~~-------~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      .+..+...+.      ..+..       .+...+.+.++  ..+++||||++++.|++
T Consensus       202 r~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~LVF~~s~~~~~~  257 (702)
T 2p6r_A          202 RPVPLVEGVLCEGTLELFDGAFSTSRRVKFEELVEECVA--ENGGVLVFESTRRGAEK  257 (702)
T ss_dssp             CSSCEEEEEECSSEEEEEETTEEEEEECCHHHHHHHHHH--TTCCEEEECSSHHHHHH
T ss_pred             CCccceEEEeeCCeeeccCcchhhhhhhhHHHHHHHHHh--cCCCEEEEcCCHHHHHH
Confidence            1112222111      11111       15566666665  45699999999987763

>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=99.81  E-value=1e-19  Score=172.86  Aligned_cols=177  Identities=15%  Similarity=0.180  Sum_probs=124.6

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCC--ccCCCccE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDV--LDFRNLVI   79 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~--~~l~~v~~   79 (203)
                      +||++|+|+||+|+++.+++..+.. |++|..++|+.+...+.    ..+++|+|+|||++..+++. ..  -.++++++
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            7999999999999999999887777 89999999987654322    24689999999998777654 22  23789999


Q ss_pred             EEEcchhHhhhhchHHHHHHHHH-------hCCCCCcEEEEeeecChhHHHHHHhcCCCCe--EEEeccCcccccccchh
Q 028826           80 LVLDEADRLLDMGFQKQISYIIS-------RLPKLRRTGLFSATQTEAVEELSKAGLRNPV--RIEVRAESKSHHASASS  150 (203)
Q Consensus        80 lViDEad~l~~~~~~~~~~~il~-------~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~--~i~~~~~~~~~~~~~~~  150 (203)
                      +|+||+|.+-+ +....++.++.       ..++..|++++|||+|+ ..+++++.-.++.  ...+..           
T Consensus       211 vIiDEvH~l~d-~RG~~lE~~l~rl~~~~~~~~~~~riI~LSATl~N-~~dvA~wL~~~~~~~~~~~~~-----------  277 (1724)
T 4f92_B          211 IILDEIHLLHD-DRGPVLEALVARAIRNIEMTQEDVRLIGLSATLPN-YEDVATFLRVDPAKGLFYFDN-----------  277 (1724)
T ss_dssp             EEETTGGGGGS-TTHHHHHHHHHHHHHHHHHHTCCCEEEEEECSCTT-HHHHHHHTTCCHHHHEEECCG-----------
T ss_pred             EEEecchhcCC-ccHHHHHHHHHHHHHHHHhCCCCCcEEEEecccCC-HHHHHHHhCCCCCCCeEEECC-----------
Confidence            99999997644 44444444433       45678999999999985 5677775433321  222222           


Q ss_pred             hhhccCCCCCceeEEEEEcCCCCcHH---H----HHHHHh-cCCCCeEEEEeccCCcccC
Q 028826          151 QQLASSKTPLGLHLEYLECESDKKPS---Q----LVDLLI-KNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       151 ~~~~~~~~~~~i~~~~~~~~~~~k~~---~----l~~ll~-~~~~~~~lIF~ns~~~~e~  202 (203)
                           ...|..+.+.++..+......   .    +...+. ....+++||||+||+.|++
T Consensus       278 -----~~RPvpL~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~LVF~~sR~~~~~  332 (1724)
T 4f92_B          278 -----SFRPVPLEQTYVGITEKKAIKRFQIMNEIVYEKIMEHAGKNQVLVFVHSRKETGK  332 (1724)
T ss_dssp             -----GGCSSCEEEECCEECCCCHHHHHHHHHHHHHHHHTTCCSSCCEEEECSSTTTTHH
T ss_pred             -----CCccCccEEEEeccCCcchhhhhHHHHHHHHHHHHHHhcCCcEEEECCCHHHHHH
Confidence                 235667788777766654322   2    222232 2356799999999999874

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=99.81  E-value=2.5e-19  Score=158.83  Aligned_cols=118  Identities=18%  Similarity=0.190  Sum_probs=98.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ++|++|+|+||.|+.+.++++...  ++++...+|+....+..  +  .+++|+|+||+++..++.. +...+++++++|
T Consensus        78 il~i~P~r~La~q~~~~~~~~~~~--g~~v~~~~G~~~~~~~~--~--~~~~Iiv~Tpe~l~~~~~~-~~~~l~~~~~vI  150 (715)
T 2va8_A           78 AIYVTPLRALTNEKYLTFKDWELI--GFKVAMTSGDYDTDDAW--L--KNYDIIITTYEKLDSLWRH-RPEWLNEVNYFV  150 (715)
T ss_dssp             EEEECSCHHHHHHHHHHHGGGGGG--TCCEEECCSCSSSCCGG--G--GGCSEEEECHHHHHHHHHH-CCGGGGGEEEEE
T ss_pred             EEEEeCcHHHHHHHHHHHHHhhcC--CCEEEEEeCCCCCchhh--c--CCCCEEEEcHHHHHHHHhC-ChhHhhccCEEE
Confidence            799999999999999999766543  78999999887654321  2  3689999999999999988 666689999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhc
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAG  128 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~  128 (203)
                      +||+|.+.+.++...+..++..++ ..|++++|||+++ ...+.+++
T Consensus       151 iDE~H~l~~~~~~~~l~~i~~~~~-~~~ii~lSATl~n-~~~~~~~l  195 (715)
T 2va8_A          151 LDELHYLNDPERGPVVESVTIRAK-RRNLLALSATISN-YKQIAKWL  195 (715)
T ss_dssp             ECSGGGGGCTTTHHHHHHHHHHHH-TSEEEEEESCCTT-HHHHHHHH
T ss_pred             EechhhcCCcccchHHHHHHHhcc-cCcEEEEcCCCCC-HHHHHHHh
Confidence            999999987788888888888886 8999999999986 35666644

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=99.80  E-value=2.8e-20  Score=164.29  Aligned_cols=114  Identities=12%  Similarity=0.172  Sum_probs=92.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCc-cCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL-DFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~-~l~~v~~l   80 (203)
                      +|||+||++|+.|+.+++++++... ++++..++||.....+...+. .+++|+|+||++|.+++.. +.+ .+++++++
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            7999999999999999999998766 899999999987655555553 4699999999999999987 666 79999999


Q ss_pred             EEcchhHhhhhc-hHHHHHHHHHh-----CCCCCcEEEEeeecC
Q 028826           81 VLDEADRLLDMG-FQKQISYIISR-----LPKLRRTGLFSATQT  118 (203)
Q Consensus        81 ViDEad~l~~~~-~~~~~~~il~~-----~~~~~q~i~~SAT~~  118 (203)
                      |+||||++.+.. +...+...+..     .++..|++++|||..
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            999999987554 33333333332     246789999999987

>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=99.80  E-value=4.7e-19  Score=168.34  Aligned_cols=177  Identities=17%  Similarity=0.248  Sum_probs=122.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHH-hhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhC-CCccCCCccE
Q 028826            2 GMIISPTRELSAQIYHVAQP-FISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM-DVLDFRNLVI   79 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~-l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~-~~~~l~~v~~   79 (203)
                      |||++|+|+||.|+++.+++ ++... +++++.++|+.+.+..  .+  .+++|+|+|||++..++++. ..-.++++++
T Consensus       975 avyi~P~raLa~q~~~~~~~~f~~~~-g~~V~~ltGd~~~~~~--~~--~~~~IiV~TPEkld~llr~~~~~~~l~~v~l 1049 (1724)
T 4f92_B          975 CVYITPMEALAEQVYMDWYEKFQDRL-NKKVVLLTGETSTDLK--LL--GKGNIIISTPEKWDILSRRWKQRKNVQNINL 1049 (1724)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHTTTS-CCCEEECCSCHHHHHH--HH--HHCSEEEECHHHHHHHHTTTTTCHHHHSCSE
T ss_pred             EEEEcChHHHHHHHHHHHHHHhchhc-CCEEEEEECCCCcchh--hc--CCCCEEEECHHHHHHHHhCcccccccceeeE
Confidence            79999999999999999876 44445 8999999888654332  22  35899999999998887651 2234789999


Q ss_pred             EEEcchhHhhhhchHHHHHHH-------HHhCCCCCcEEEEeeecChhHHHHHHhcCCCC-eEEEeccCcccccccchhh
Q 028826           80 LVLDEADRLLDMGFQKQISYI-------ISRLPKLRRTGLFSATQTEAVEELSKAGLRNP-VRIEVRAESKSHHASASSQ  151 (203)
Q Consensus        80 lViDEad~l~~~~~~~~~~~i-------l~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~-~~i~~~~~~~~~~~~~~~~  151 (203)
                      +|+||+|.+.+. ....+..+       ....++..|++++|||+++ ..+++++.-.++ ....+...           
T Consensus      1050 vViDE~H~l~d~-rg~~le~il~rl~~i~~~~~~~~riI~lSATl~N-~~dla~WL~~~~~~~~~~~~~----------- 1116 (1724)
T 4f92_B         1050 FVVDEVHLIGGE-NGPVLEVICSRMRYISSQIERPIRIVALSSSLSN-AKDVAHWLGCSATSTFNFHPN----------- 1116 (1724)
T ss_dssp             EEECCGGGGGST-THHHHHHHHHHHHHHHHTTSSCCEEEEEESCBTT-HHHHHHHHTCCSTTEEECCGG-----------
T ss_pred             EEeechhhcCCC-CCccHHHHHHHHHHHHhhcCCCceEEEEeCCCCC-HHHHHHHhCCCCCCeEEeCCC-----------
Confidence            999999988653 34444333       3445778999999999986 477777654433 22223332           


Q ss_pred             hhccCCCCCceeEEEEEcCCCCcHHH-------HHHHHh-cCCCCeEEEEeccCCccc
Q 028826          152 QLASSKTPLGLHLEYLECESDKKPSQ-------LVDLLI-KNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       152 ~~~~~~~~~~i~~~~~~~~~~~k~~~-------l~~ll~-~~~~~~~lIF~ns~~~~e  201 (203)
                           ..|..+++++...+.......       +...+. ....+++||||+|++.|+
T Consensus      1117 -----~RPvpL~~~i~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~lVF~~sR~~~~ 1169 (1724)
T 4f92_B         1117 -----VRPVPLELHIQGFNISHTQTRLLSMAKPVYHAITKHSPKKPVIVFVPSRKQTR 1169 (1724)
T ss_dssp             -----GCSSCEEEEEEEECCCSHHHHHHTTHHHHHHHHHHHCSSSCEEEEESSHHHHH
T ss_pred             -----CCCCCeEEEEEeccCCCchhhhhhhcchHHHHHHHhcCCCCeeeeCCCHHHHH
Confidence                 345667776666555443322       233333 346779999999998876

>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=99.80  E-value=3.5e-19  Score=159.73  Aligned_cols=115  Identities=13%  Similarity=0.171  Sum_probs=90.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCc-cCCCccE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL-DFRNLVI   79 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~-~l~~v~~   79 (203)
                      .+|||+||++|+.|+++.+++++... ++++..++||.....+...+ ..+++|+|+||++|..++.. +.+ .++++++
T Consensus       298 ~~Lvl~Pt~~L~~Q~~~~~~~~~~~~-~~~v~~~~g~~~~~~~~~~~-~~~~~Ivv~Tp~~l~~~l~~-~~~~~~~~~~~  374 (797)
T 4a2q_A          298 KVVFLATKVPVYEQQKNVFKHHFERQ-GYSVQGISGENFSNVSVEKV-IEDSDIIVVTPQILVNSFED-GTLTSLSIFTL  374 (797)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHHHGGG-TCCEEEECCC-----CHHHH-HHTCSEEEECHHHHHHHHHS-SSCCCGGGCSE
T ss_pred             eEEEEeCCHHHHHHHHHHHHHhcccC-CceEEEEeCCcchhhhHHHh-hCCCCEEEEchHHHHHHHHh-ccccccccCCE
Confidence            37999999999999999999998877 89999999998777666655 35799999999999999987 666 7899999


Q ss_pred             EEEcchhHhhhhc-hHHHHHHHHHhC----CCCCcEEEEeeecC
Q 028826           80 LVLDEADRLLDMG-FQKQISYIISRL----PKLRRTGLFSATQT  118 (203)
Q Consensus        80 lViDEad~l~~~~-~~~~~~~il~~~----~~~~q~i~~SAT~~  118 (203)
                      +|+||||++...+ +...+..++...    .+.+|++++|||.+
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            9999999998664 333333443331    46689999999985

>1wp9_A ATP-dependent RNA helicase, putative; ATPase, DNA replication, DNA repair, DNA recombina hydrolase; 2.90A {Pyrococcus furiosus} SCOP: c.37.1.19 c.37.1.19

Probab=99.79  E-value=2e-18  Score=144.94  Aligned_cols=115  Identities=18%  Similarity=0.200  Sum_probs=93.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++||++|+.|+.++++++... ++.++..++|+....+.....  .+++|+|+||+.+...+.. +.+.+.+++++|
T Consensus        55 ~liv~P~~~L~~q~~~~~~~~~~~-~~~~v~~~~g~~~~~~~~~~~--~~~~ivv~T~~~l~~~~~~-~~~~~~~~~~vI  130 (494)
T 1wp9_A           55 VLMLAPTKPLVLQHAESFRRLFNL-PPEKIVALTGEKSPEERSKAW--ARAKVIVATPQTIENDLLA-GRISLEDVSLIV  130 (494)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHBCS-CGGGEEEECSCSCHHHHHHHH--HHCSEEEECHHHHHHHHHT-TSCCTTSCSEEE
T ss_pred             EEEEECCHHHHHHHHHHHHHHhCc-chhheEEeeCCcchhhhhhhc--cCCCEEEecHHHHHHHHhc-CCcchhhceEEE
Confidence            799999999999999999998632 356889999888766544333  3589999999999998887 778899999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChh
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~  120 (203)
                      +||||.+.+......+...+....+..+++++|||.+..
T Consensus       131 iDEaH~~~~~~~~~~~~~~~~~~~~~~~~l~lTaTp~~~  169 (494)
T 1wp9_A          131 FDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGST  169 (494)
T ss_dssp             EETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEESCSCSS
T ss_pred             EECCcccCCCCcHHHHHHHHHhcCCCCeEEEEecCCCCC
Confidence            999999986554455555555566789999999999854

>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=99.76  E-value=2.6e-18  Score=156.22  Aligned_cols=114  Identities=13%  Similarity=0.176  Sum_probs=90.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCc-cCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVL-DFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~-~l~~v~~l   80 (203)
                      +|||+||++|+.|++++++++++.. ++++..++||.....+...+. .+++|+|+||++|.+++.. +.+ .+++++++
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            7999999999999999999998877 899999999987666555553 4689999999999999987 666 78999999


Q ss_pred             EEcchhHhhhhc-hHHHHHHHHHhC----CCCCcEEEEeeecC
Q 028826           81 VLDEADRLLDMG-FQKQISYIISRL----PKLRRTGLFSATQT  118 (203)
Q Consensus        81 ViDEad~l~~~~-~~~~~~~il~~~----~~~~q~i~~SAT~~  118 (203)
                      |+||||++...+ +...+..++...    .+..|++++|||.+
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            999999998664 444444444332    45689999999995

>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=99.75  E-value=8.2e-18  Score=155.44  Aligned_cols=170  Identities=17%  Similarity=0.187  Sum_probs=120.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHH---HHHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~---~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      +++|++||++||.|+++.+++..... ++++..++|+.+..+..   ..+..+.++|+||||+.+.      +.+.++++
T Consensus       654 ~vlvlvPt~~La~Q~~~~~~~~~~~~-~i~v~~l~~~~~~~~~~~~~~~l~~g~~dIvV~T~~ll~------~~~~~~~l  726 (1151)
T 2eyq_A          654 QVAVLVPTTLLAQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ------SDVKFKDL  726 (1151)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH------SCCCCSSE
T ss_pred             eEEEEechHHHHHHHHHHHHHHhhcC-CCeEEEEeCCCCHHHHHHHHHHHhcCCCCEEEECHHHHh------CCcccccc
Confidence            47999999999999999999887766 78998888876654433   3444557999999997652      46788999


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCC
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSK  157 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~  157 (203)
                      +++|+||+|++   +  ......+..++...|++++|||.++....+....+.++..+.....                 
T Consensus       727 ~lvIiDEaH~~---g--~~~~~~l~~l~~~~~vl~lSATp~p~~l~~~~~~~~~~~~i~~~~~-----------------  784 (1151)
T 2eyq_A          727 GLLIVDEEHRF---G--VRHKERIKAMRANVDILTLTATPIPRTLNMAMSGMRDLSIIATPPA-----------------  784 (1151)
T ss_dssp             EEEEEESGGGS---C--HHHHHHHHHHHTTSEEEEEESSCCCHHHHHHHTTTSEEEECCCCCC-----------------
T ss_pred             ceEEEechHhc---C--hHHHHHHHHhcCCCCEEEEcCCCChhhHHHHHhcCCCceEEecCCC-----------------
Confidence            99999999995   2  2334556666678999999999988888877777766554433222                 


Q ss_pred             CCCceeEEEEEcCCCCcHHHHHHHHhc-CCCCeEEEEeccCCcccC
Q 028826          158 TPLGLHLEYLECESDKKPSQLVDLLIK-NKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       158 ~~~~i~~~~~~~~~~~k~~~l~~ll~~-~~~~~~lIF~ns~~~~e~  202 (203)
                      ....+..++...+   +......+++. ..+++++||||+++.+++
T Consensus       785 ~r~~i~~~~~~~~---~~~i~~~il~~l~~g~qvlvf~~~v~~~~~  827 (1151)
T 2eyq_A          785 RRLAVKTFVREYD---SMVVREAILREILRGGQVYYLYNDVENIQK  827 (1151)
T ss_dssp             BCBCEEEEEEECC---HHHHHHHHHHHHTTTCEEEEECCCSSCHHH
T ss_pred             CccccEEEEecCC---HHHHHHHHHHHHhcCCeEEEEECCHHHHHH
Confidence            1223444443322   22333333332 356799999999988763

>3o8b_A HCV NS3 protease/helicase; ntpase, RNA, translocation, protein-RNA compl protease/ntpase/helicase, hydrolase; 1.95A {Hepatitis c virus} PDB: 3o8c_A* 3o8d_A* 3o8r_A* 4b71_A* 4b73_A* 4b74_A* 4b76_A* 4b75_A* 4a92_A* 1cu1_A 4b6e_A* 4b6f_A* 2zjo_A* 1a1v_A* 1hei_A 3kqn_A* 3kql_A* 3kqu_A* 3kqh_A 3kqk_A ...

Probab=99.74  E-value=6.7e-18  Score=147.23  Aligned_cols=103  Identities=14%  Similarity=0.094  Sum_probs=85.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ++||++||||||.|+.+.+.+..    +.++...+|+..        ...+++|+|+||++|   +.. +.+++++++++
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            48999999999999988776554    455667777755        256899999999997   445 77889999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCc--EEEEeeecChh
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRR--TGLFSATQTEA  120 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q--~i~~SAT~~~~  120 (203)
                      |+|||| +++.++...+..+++.++..+|  .+++|||+++.
T Consensus       323 VlDEAH-~l~~~~~~~l~~Il~~l~~~~~~llil~SAT~~~~  363 (666)
T 3o8b_A          323 ICDECH-STDSTTILGIGTVLDQAETAGARLVVLATATPPGS  363 (666)
T ss_dssp             EETTTT-CCSHHHHHHHHHHHHHTTTTTCSEEEEEESSCTTC
T ss_pred             EEccch-hcCccHHHHHHHHHHhhhhcCCceEEEECCCCCcc
Confidence            999995 5688899999999999988777  67779999974

>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=99.69  E-value=1.1e-16  Score=142.45  Aligned_cols=168  Identities=15%  Similarity=0.197  Sum_probs=109.3

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHH---HHHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADV---KKIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~---~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      +++|++||++||.|+++.++++.... ++++..++||.+..+..   ..+..+.++|+||||+.+.+      .+.++++
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            58999999999999999999998877 89999999998766543   34444569999999987742      4678999


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCC
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSK  157 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~  157 (203)
                      +++|+||+|++   |+..  +..+......+|++++|||.++....+..  ..+.....+...               ..
T Consensus       492 ~lVVIDEaHr~---g~~q--r~~l~~~~~~~~vL~mSATp~p~tl~~~~--~g~~~~s~i~~~---------------p~  549 (780)
T 1gm5_A          492 GLVIIDEQHRF---GVKQ--REALMNKGKMVDTLVMSATPIPRSMALAF--YGDLDVTVIDEM---------------PP  549 (780)
T ss_dssp             CEEEEESCCCC----------CCCCSSSSCCCEEEEESSCCCHHHHHHH--TCCSSCEEECCC---------------CS
T ss_pred             ceEEecccchh---hHHH--HHHHHHhCCCCCEEEEeCCCCHHHHHHHH--hCCcceeeeecc---------------CC
Confidence            99999999986   2211  12223334578999999998876555443  222211112111               00


Q ss_pred             CCCceeEEEEEcCCCCcHHHHHHHHhc--CCCCeEEEEeccCCcc
Q 028826          158 TPLGLHLEYLECESDKKPSQLVDLLIK--NKSKKIIMYVQHGNFS  200 (203)
Q Consensus       158 ~~~~i~~~~~~~~~~~k~~~l~~ll~~--~~~~~~lIF~ns~~~~  200 (203)
                      ....+...+   ....+...+...+..  ..+++++|||++.+.+
T Consensus       550 ~r~~i~~~~---~~~~~~~~l~~~i~~~l~~g~qvlVf~~~ie~s  591 (780)
T 1gm5_A          550 GRKEVQTML---VPMDRVNEVYEFVRQEVMRGGQAFIVYPLIEES  591 (780)
T ss_dssp             SCCCCEECC---CCSSTHHHHHHHHHHHTTTSCCBCCBCCCC---
T ss_pred             CCcceEEEE---eccchHHHHHHHHHHHHhcCCcEEEEecchhhh
Confidence            112233222   233445555566643  3567899999987543

>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=99.69  E-value=2.8e-18  Score=151.56  Aligned_cols=114  Identities=14%  Similarity=0.224  Sum_probs=84.4

Q ss_pred             EEEEcCcHHHHHHH-HHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHH------HhCCCccC
Q 028826            2 GMIISPTRELSAQI-YHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIM------ERMDVLDF   74 (203)
Q Consensus         2 alil~PtreLa~Qi-~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~------~~~~~~~l   74 (203)
                      +|||+||++|+.|+ .+++++++..  ++++..++|+....++...+ ..+++|+|+||++|..++      .. +.+.+
T Consensus        59 vlvl~P~~~L~~Q~~~~~l~~~~~~--~~~v~~~~g~~~~~~~~~~~-~~~~~Ilv~Tp~~L~~~l~~~~~~~~-~~~~~  134 (699)
T 4gl2_A           59 VIVLVNKVLLVEQLFRKEFQPFLKK--WYRVIGLSGDTQLKISFPEV-VKSCDIIISTAQILENSLLNLENGED-AGVQL  134 (699)
T ss_dssp             BCCEESCSHHHHHHHHHTHHHHHTT--TSCEEEEC----CCCCHHHH-HHSCSEEEEEHHHHHHHTC---------CCCG
T ss_pred             EEEEECCHHHHHHHHHHHHHHHcCc--CceEEEEeCCcchhhHHHhh-hcCCCEEEECHHHHHHHHhccccccc-cceec
Confidence            68999999999999 9999999765  58999999998766555555 357999999999999888      33 56788


Q ss_pred             CCccEEEEcchhHhhhhc-hHHHHHHHHHhC-------------CCCCcEEEEeeecCh
Q 028826           75 RNLVILVLDEADRLLDMG-FQKQISYIISRL-------------PKLRRTGLFSATQTE  119 (203)
Q Consensus        75 ~~v~~lViDEad~l~~~~-~~~~~~~il~~~-------------~~~~q~i~~SAT~~~  119 (203)
                      .+++++|+||||++...+ +...+..++...             .+.+|++++|||.+.
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 333333332221             156899999999986

>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=99.67  E-value=6.1e-16  Score=119.61  Aligned_cols=119  Identities=16%  Similarity=0.177  Sum_probs=88.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +++++|+++|+.|+.+.+.+......+..++.-......      ....+++|+|+||+++.+++..    .+++++++|
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            688999999999998888765443224444433322211      0124689999999999999876    489999999


Q ss_pred             EcchhHh-hhhchH-HHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCe
Q 028826           82 LDEADRL-LDMGFQ-KQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPV  133 (203)
Q Consensus        82 iDEad~l-~~~~~~-~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~  133 (203)
                      +||||.+ ++.++. ..++.++... +..|++++|||++.+.  +.+.+...|+
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 4799999999999876  6665555554

>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=99.66  E-value=1.1e-16  Score=121.41  Aligned_cols=113  Identities=14%  Similarity=0.217  Sum_probs=77.8

Q ss_pred             CEEEEcCcHHHHHH-HHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCC-----CccC
Q 028826            1 MGMIISPTRELSAQ-IYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMD-----VLDF   74 (203)
Q Consensus         1 ~alil~PtreLa~Q-i~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~-----~~~l   74 (203)
                      .+||++||++|+.| +.+.++++...  ++++..+.|+.........+. .+++|+|+||+++..++....     ...+
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 88889998765  688888888876554444442 368999999999999887621     1668


Q ss_pred             CCccEEEEcchhHhhhhchHHHH-HHHHHhC-------------CCCCcEEEEeee
Q 028826           75 RNLVILVLDEADRLLDMGFQKQI-SYIISRL-------------PKLRRTGLFSAT  116 (203)
Q Consensus        75 ~~v~~lViDEad~l~~~~~~~~~-~~il~~~-------------~~~~q~i~~SAT  116 (203)
                      .+++++|+||||.+.+.++...+ ..++...             .+..+++++|||
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            89999999999999876654444 3333222             157899999998

>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=99.63  E-value=5.4e-17  Score=137.30  Aligned_cols=94  Identities=20%  Similarity=0.147  Sum_probs=75.7

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCce-EEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVK-SMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVI   79 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~-~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~   79 (203)
                      .+|||+||++|+.|+.+.++++     +++ +..+.|+..          ..++|+|+||+.+...+..    ...++++
T Consensus       135 ~~Lvl~P~~~L~~Q~~~~~~~~-----~~~~v~~~~g~~~----------~~~~Ivv~T~~~l~~~~~~----~~~~~~l  195 (472)
T 2fwr_A          135 PTLIVVPTLALAEQWKERLGIF-----GEEYVGEFSGRIK----------ELKPLTVSTYDSAYVNAEK----LGNRFML  195 (472)
T ss_dssp             CEEEEESSHHHHHHHHHHGGGG-----CGGGEEEBSSSCB----------CCCSEEEEEHHHHHHTHHH----HTTTCSE
T ss_pred             CEEEEECCHHHHHHHHHHHHhC-----CCcceEEECCCcC----------CcCCEEEEEcHHHHHHHHH----hcCCCCE
Confidence            4799999999999999999885     677 777777754          3579999999999876653    1245899


Q ss_pred             EEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecC
Q 028826           80 LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (203)
Q Consensus        80 lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  118 (203)
                      +|+||+|.+.+.+|..    ++..+ +..+++++|||.+
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            9999999998877754    45555 5789999999997

>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=99.60  E-value=1.1e-14  Score=129.93  Aligned_cols=170  Identities=14%  Similarity=0.110  Sum_probs=110.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ++|++|+|+|+.|+.+.+.+......+..++.-......       .....+|+++||+++...+..  ...+.+++++|
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 VACTQPRRVAAMSVAQRVAEEMDVKLGEEVGYSIRFENK-------TSNKTILKYMTDGMLLREAME--DHDLSRYSCII  213 (773)
T ss_dssp             EEEEESCHHHHHHHHHHHHHHTTCCBTTTEEEEETTEEE-------CCTTCSEEEEEHHHHHHHHHH--STTCTTEEEEE
T ss_pred             EEecCchHHHHHHHHHHHHHHhCCchhheecceeccccc-------cCCCCCEEEECHHHHHHHHhh--CccccCCCEEE
Confidence            688999999999998766543321112222221111111       124689999999999987766  35689999999


Q ss_pred             EcchhH-hhhhc-hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCC
Q 028826           82 LDEADR-LLDMG-FQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTP  159 (203)
Q Consensus        82 iDEad~-l~~~~-~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~  159 (203)
                      +||+|. .++.. ....+..+.... +..|++++|||++.  ..+.+ ++.+...+.+...                  .
T Consensus       214 lDEah~R~ld~d~~~~~l~~l~~~~-~~~~iIl~SAT~~~--~~l~~-~~~~~~vi~v~gr------------------~  271 (773)
T 2xau_A          214 LDEAHERTLATDILMGLLKQVVKRR-PDLKIIIMSATLDA--EKFQR-YFNDAPLLAVPGR------------------T  271 (773)
T ss_dssp             ECSGGGCCHHHHHHHHHHHHHHHHC-TTCEEEEEESCSCC--HHHHH-HTTSCCEEECCCC------------------C
T ss_pred             ecCccccccchHHHHHHHHHHHHhC-CCceEEEEeccccH--HHHHH-HhcCCCcccccCc------------------c
Confidence            999996 56543 344455555554 57899999999974  44554 4454444544332                  2


Q ss_pred             CceeEEEEEcCCCCcHHH----HHHHHhcCCCCeEEEEeccCCcccC
Q 028826          160 LGLHLEYLECESDKKPSQ----LVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       160 ~~i~~~~~~~~~~~k~~~----l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      ..+.++|...+..++...    +.++......+++|||||+++.+++
T Consensus       272 ~pv~~~~~~~~~~~~~~~~l~~l~~~~~~~~~g~iLVF~~~~~~i~~  318 (773)
T 2xau_A          272 YPVELYYTPEFQRDYLDSAIRTVLQIHATEEAGDILLFLTGEDEIED  318 (773)
T ss_dssp             CCEEEECCSSCCSCHHHHHHHHHHHHHHHSCSCEEEEECSCHHHHHH
T ss_pred             cceEEEEecCCchhHHHHHHHHHHHHHHhcCCCCEEEECCCHHHHHH
Confidence            346777766555555433    3344445567899999999987763

>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=99.59  E-value=8.6e-17  Score=135.27  Aligned_cols=99  Identities=21%  Similarity=0.277  Sum_probs=66.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeE-EEeccHHHHHHHHh-------CCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANL-LIGTPGRLYDIMER-------MDVL   72 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~i-lV~Tp~~l~~~~~~-------~~~~   72 (203)
                      +++|++||++||.|+++.++.+     ++.  . .++               .+ .|+||+++.+++..       ....
T Consensus        39 ~~lil~Ptr~La~Q~~~~l~~~-----~v~--~-~~~---------------~~~~v~Tp~~l~~~l~~~~l~~~~~~~~   95 (440)
T 1yks_A           39 RTLVLAPTRVVLSEMKEAFHGL-----DVK--F-HTQ---------------AFSAHGSGREVIDAMCHATLTYRMLEPT   95 (440)
T ss_dssp             CEEEEESSHHHHHHHHHHTTTS-----CEE--E-ESS---------------CCCCCCCSSCCEEEEEHHHHHHHHTSSS
T ss_pred             eEEEEcchHHHHHHHHHHHhcC-----CeE--E-ecc---------------cceeccCCccceeeecccchhHhhhCcc
Confidence            4899999999999999888754     222  1 111               11 48888877644432       0223


Q ss_pred             cCCCccEEEEcchhHhhhhchHHHHHHHHHhC-CCCCcEEEEeeecChhHHH
Q 028826           73 DFRNLVILVLDEADRLLDMGFQKQISYIISRL-PKLRRTGLFSATQTEAVEE  123 (203)
Q Consensus        73 ~l~~v~~lViDEad~l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~v~~  123 (203)
                      .+++++++|+||+|++ +.++...+..+.... +..+|++++|||+++.+..
T Consensus        96 ~~~~l~~vViDEah~~-~~~~~~~~~~~~~~~~~~~~~~l~~SAT~~~~~~~  146 (440)
T 1yks_A           96 RVVNWEVIIMDEAHFL-DPASIAARGWAAHRARANESATILMTATPPGTSDE  146 (440)
T ss_dssp             CCCCCSEEEETTTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCCS
T ss_pred             cccCccEEEEECcccc-CcchHHHHHHHHHHhccCCceEEEEeCCCCchhhh
Confidence            4899999999999998 444443433333333 3679999999999887543

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=99.58  E-value=1.5e-15  Score=129.49  Aligned_cols=107  Identities=21%  Similarity=0.151  Sum_probs=87.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +|||+||++|+.|+++.+++++... +.++..+.||.+..++    ...+++|+|+||+.+..   . ....+++++++|
T Consensus       160 vlvl~P~~~L~~Q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~----~~~~~~I~i~T~~~l~~---~-~~~~~~~~~liI  230 (510)
T 2oca_A          160 ILIIVPTTALTTQMADDFVDYRLFS-HAMIKKIGGGASKDDK----YKNDAPVVVGTWQTVVK---Q-PKEWFSQFGMMM  230 (510)
T ss_dssp             EEEEESSHHHHHHHHHHHHHTTSSC-GGGEEECGGGCCTTGG----GCTTCSEEEEEHHHHTT---S-CGGGGGGEEEEE
T ss_pred             EEEEECcHHHHHHHHHHHHHhhcCC-ccceEEEecCCccccc----cccCCcEEEEeHHHHhh---c-hhhhhhcCCEEE
Confidence            7999999999999999999985543 6889999998776544    24679999999997643   2 345678999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhH
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV  121 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v  121 (203)
                      +||+|++..    ..+..++..+++..+++++|||.++..
T Consensus       231 iDE~H~~~~----~~~~~il~~~~~~~~~l~lSATp~~~~  266 (510)
T 2oca_A          231 NDECHLATG----KSISSIISGLNNCMFKFGLSGSLRDGK  266 (510)
T ss_dssp             EETGGGCCH----HHHHHHGGGCTTCCEEEEEESCGGGCS
T ss_pred             EECCcCCCc----ccHHHHHHhcccCcEEEEEEeCCCCCc
Confidence            999999855    456778888888899999999997764

>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=99.58  E-value=4.5e-16  Score=135.76  Aligned_cols=107  Identities=17%  Similarity=0.137  Sum_probs=76.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||||||.|+++.++.+       .+. +.++. ..    .....+-.+-+.|.+.+...+..  ...+++++++
T Consensus       217 ~vLvl~PtreLa~Qi~~~l~~~-------~v~-~~~~~-l~----~~~tp~~~i~~~t~~~l~~~l~~--~~~l~~~~~i  281 (618)
T 2whx_A          217 RTLILAPTRVVAAEMEEALRGL-------PIR-YQTPA-VK----SDHTGREIVDLMCHATFTTRLLS--STRVPNYNLI  281 (618)
T ss_dssp             CEEEEESSHHHHHHHHHHTTTS-------CEE-ECCTT-SS----CCCCSSSCEEEEEHHHHHHHHHH--CSSCCCCSEE
T ss_pred             eEEEEcChHHHHHHHHHHhcCC-------cee-Eeccc-ce----eccCCCceEEEEChHHHHHHHhc--cccccCCeEE
Confidence            4899999999999999877632       222 22211 00    00122345666777777765554  3568999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCC-CCCcEEEEeeecChhHHH
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLP-KLRRTGLFSATQTEAVEE  123 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~-~~~q~i~~SAT~~~~v~~  123 (203)
                      |+||||.+ +.++...+..++..++ ..+|+++||||++..+..
T Consensus       282 ViDEah~~-~~~~~~~~~~i~~~l~~~~~q~il~SAT~~~~~~~  324 (618)
T 2whx_A          282 VMDEAHFT-DPCSVAARGYISTRVEMGEAAAIFMTATPPGSTDP  324 (618)
T ss_dssp             EEESTTCC-SHHHHHHHHHHHHHHHHTSCEEEEECSSCTTCCCS
T ss_pred             EEECCCCC-CccHHHHHHHHHHHhcccCccEEEEECCCchhhhh
Confidence            99999998 7778888888887775 689999999999987553

>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=99.56  E-value=2.6e-15  Score=119.00  Aligned_cols=108  Identities=20%  Similarity=0.139  Sum_probs=85.6

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++||++|+.|+++.++++.... +.++..+.||......    .....+|+|+||+++...    ....+.+++++|
T Consensus       160 ~lil~Pt~~L~~q~~~~l~~~~~~~-~~~~~~~~~~~~~~~~----~~~~~~I~v~T~~~l~~~----~~~~~~~~~~vI  230 (282)
T 1rif_A          160 ILIIVPTTALTTQMADDFVDYRLFS-HAMIKKIGGGASKDDK----YKNDAPVVVGTWQTVVKQ----PKEWFSQFGMMM  230 (282)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTSCC-GGGEEECSTTCSSTTC----CCTTCSEEEECHHHHTTS----CGGGGGGEEEEE
T ss_pred             EEEEECCHHHHHHHHHHHHHhcccc-cceEEEEeCCCcchhh----hccCCcEEEEchHHHHhh----HHHHHhhCCEEE
Confidence            7999999999999999999986544 6788888888654321    125689999999886432    334578899999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHH
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE  122 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~  122 (203)
                      +||||++.+    +.+..++..+.+..|++++|||.++...
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            999999964    3677788888789999999999987643

>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=99.56  E-value=2.5e-15  Score=126.70  Aligned_cols=106  Identities=15%  Similarity=0.093  Sum_probs=73.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++|||+||.|+++.+..       +.+..-.+....      ....+..+.++||+.+...+..  ...+++++++
T Consensus        50 ~~lvl~Ptr~La~Q~~~~l~g-------~~v~~~~~~~~~------~~~~~~~i~~~t~~~l~~~l~~--~~~l~~~~~i  114 (451)
T 2jlq_A           50 RTLILAPTRVVAAEMEEALRG-------LPIRYQTPAVKS------DHTGREIVDLMCHATFTTRLLS--STRVPNYNLI  114 (451)
T ss_dssp             CEEEEESSHHHHHHHHHHTTT-------SCEEECCTTCSC------CCCSSCCEEEEEHHHHHHHHHH--CSCCCCCSEE
T ss_pred             cEEEECCCHHHHHHHHHHhcC-------ceeeeeeccccc------cCCCCceEEEEChHHHHHHhhC--cccccCCCEE
Confidence            479999999999999987742       333221211111      0124567999999999888776  3668899999


Q ss_pred             EEcchhHhhhhchHHHHHHHHH-hCCCCCcEEEEeeecChhHH
Q 028826           81 VLDEADRLLDMGFQKQISYIIS-RLPKLRRTGLFSATQTEAVE  122 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~-~~~~~~q~i~~SAT~~~~v~  122 (203)
                      |+||||.+ +.++...+..+.. ..++..|++++|||+|+.+.
T Consensus       115 ViDEah~~-~~~~~~~~~~~~~~~~~~~~~~i~~SAT~~~~~~  156 (451)
T 2jlq_A          115 VMDEAHFT-DPCSVAARGYISTRVEMGEAAAIFMTATPPGSTD  156 (451)
T ss_dssp             EEETTTCC-SHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCC
T ss_pred             EEeCCccC-CcchHHHHHHHHHhhcCCCceEEEEccCCCccch
Confidence            99999977 4444433333332 23467999999999987543

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=99.51  E-value=3.5e-14  Score=119.08  Aligned_cols=104  Identities=16%  Similarity=0.164  Sum_probs=69.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +++|++||++||.|+++.+.       ++.+....|+...      ....+..+.+.|.+.+...+..  ...+++++++
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            48999999999999987664       3445444443221      1123455677788888766654  4568999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhC-CCCCcEEEEeeecChh
Q 028826           81 VLDEADRLLDMGFQKQISYIISRL-PKLRRTGLFSATQTEA  120 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~  120 (203)
                      |+||+|.+ +.++......+.... +..+|++++|||+++.
T Consensus        98 ViDEaH~~-~~~~~~~~~~l~~~~~~~~~~~l~~SAT~~~~  137 (431)
T 2v6i_A           98 IMDEAHFL-DPASVAARGYIETRVSMGDAGAIFMTATPPGT  137 (431)
T ss_dssp             EEESTTCC-SHHHHHHHHHHHHHHHTTSCEEEEEESSCTTC
T ss_pred             EEeCCccC-CccHHHHHHHHHHHhhCCCCcEEEEeCCCCcc
Confidence            99999997 444444444444332 5689999999999974

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=99.51  E-value=1.2e-15  Score=134.17  Aligned_cols=99  Identities=20%  Similarity=0.279  Sum_probs=63.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHh-------CCCcc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMER-------MDVLD   73 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~-------~~~~~   73 (203)
                      ++||++|||+||.|+++.++.+     ++.  . ..+ .       + .     .++||+++++++..       .....
T Consensus       272 ~~lilaPTr~La~Q~~~~l~~~-----~i~--~-~~~-~-------l-~-----~v~tp~~ll~~l~~~~l~~~l~~~~~  329 (673)
T 2wv9_A          272 RTAVLAPTRVVAAEMAEALRGL-----PVR--Y-LTP-A-------V-Q-----REHSGNEIVDVMCHATLTHRLMSPLR  329 (673)
T ss_dssp             CEEEEESSHHHHHHHHHHTTTS-----CCE--E-CCC-----------------CCCCSCCCEEEEEHHHHHHHHHSSSC
T ss_pred             cEEEEccHHHHHHHHHHHHhcC-----Cee--e-ecc-c-------c-c-----ccCCHHHHHHHHHhhhhHHHHhcccc
Confidence            4899999999999999888755     232  1 110 0       0 0     15666555332221       01246


Q ss_pred             CCCccEEEEcchhHhhhhchHHHHHHHHHhC-CCCCcEEEEeeecChhHH
Q 028826           74 FRNLVILVLDEADRLLDMGFQKQISYIISRL-PKLRRTGLFSATQTEAVE  122 (203)
Q Consensus        74 l~~v~~lViDEad~l~~~~~~~~~~~il~~~-~~~~q~i~~SAT~~~~v~  122 (203)
                      +++++++|+||+|++ +..+...+..+...+ +..+|++++|||+++.+.
T Consensus       330 l~~l~lvViDEaH~~-~~~~~~~~~~l~~~~~~~~~~vl~~SAT~~~~i~  378 (673)
T 2wv9_A          330 VPNYNLFVMDEAHFT-DPASIAARGYIATRVEAGEAAAIFMTATPPGTSD  378 (673)
T ss_dssp             CCCCSEEEEESTTCC-CHHHHHHHHHHHHHHHTTSCEEEEECSSCTTCCC
T ss_pred             cccceEEEEeCCccc-CccHHHHHHHHHHhccccCCcEEEEcCCCChhhh
Confidence            899999999999998 333333333343333 267999999999997643

>3h1t_A Type I site-specific restriction-modification system, R (restriction) subunit; hydrolase, restriction enzyme HSDR, ATP-binding; 2.30A {Vibrio vulnificus}

Probab=99.50  E-value=2e-14  Score=124.79  Aligned_cols=103  Identities=12%  Similarity=0.049  Sum_probs=57.1

Q ss_pred             EEEEcCcHHHHHHHH-HHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhC---CCccCCCc
Q 028826            2 GMIISPTRELSAQIY-HVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERM---DVLDFRNL   77 (203)
Q Consensus         2 alil~PtreLa~Qi~-~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~---~~~~l~~v   77 (203)
                      +|||+||++|+.|++ +.++.++     ..+..+.++.         ...+.+|+|+||+++.......   +.+...++
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            799999999999999 7777653     2333333321         1457899999999998876521   34566789


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChh
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~  120 (203)
                      +++|+||||++...+ ...++.++..++ ..+++++|||....
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            999999999986542 355677788885 57899999997643

>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=99.48  E-value=1.5e-14  Score=122.19  Aligned_cols=102  Identities=14%  Similarity=0.132  Sum_probs=67.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++|||+||.|+++.++.+       .+....+.....      ...+-.+.+.|.+.+...+..  ...+++++++
T Consensus        52 ~~lvl~Ptr~La~Q~~~~l~g~-------~v~~~~~~~~~~------~t~~~~i~~~~~~~l~~~l~~--~~~l~~~~~i  116 (459)
T 2z83_A           52 RTAVLAPTRVVAAEMAEALRGL-------PVRYQTSAVQRE------HQGNEIVDVMCHATLTHRLMS--PNRVPNYNLF  116 (459)
T ss_dssp             CEEEEECSHHHHHHHHHHTTTS-------CEEECC--------------CCCSEEEEEHHHHHHHHHS--CC-CCCCSEE
T ss_pred             cEEEECchHHHHHHHHHHhcCc-------eEeEEecccccC------CCCCcEEEEEchHHHHHHhhc--cccccCCcEE
Confidence            3799999999999999887632       222211111100      123345777888887766654  4678999999


Q ss_pred             EEcchhH-----hhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHH
Q 028826           81 VLDEADR-----LLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE  122 (203)
Q Consensus        81 ViDEad~-----l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~  122 (203)
                      |+||||.     ++..++.....     .++..|++++|||++..+.
T Consensus       117 ViDEaH~~~~~~~~~~~~~~~~~-----~~~~~~~il~SAT~~~~~~  158 (459)
T 2z83_A          117 VMDEAHFTDPASIAARGYIATKV-----ELGEAAAIFMTATPPGTTD  158 (459)
T ss_dssp             EESSTTCCSHHHHHHHHHHHHHH-----HTTSCEEEEECSSCTTCCC
T ss_pred             EEECCccCCchhhHHHHHHHHHh-----ccCCccEEEEEcCCCcchh
Confidence            9999998     55555544322     1368999999999997643

>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=119.39  Aligned_cols=101  Identities=18%  Similarity=0.200  Sum_probs=81.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHH-HHHHHhCC------Ccc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL-YDIMERMD------VLD   73 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l-~~~~~~~~------~~~   73 (203)
                      +++|++||++||.|+++++..+..++ ++++..++||.+......   ..++||+||||+++ .++++. +      .+.
T Consensus       122 qv~VvTPTreLA~Qdae~m~~l~~~l-GLsv~~i~Gg~~~~~r~~---ay~~DIvyGTpgrlgfDyLrd-~m~~~~~~l~  196 (997)
T 2ipc_A          122 GVHVVTVNDYLARRDAEWMGPVYRGL-GLSVGVIQHASTPAERRK---AYLADVTYVTNSELGFDYLRD-NMAISPDQLV  196 (997)
T ss_dssp             CCEEEESSHHHHHHHHHHHHHHHHTT-TCCEEECCTTCCHHHHHH---HHTSSEEEEEHHHHHHHHHHH-TSCSSTTTCC
T ss_pred             CEEEEeCCHHHHHHHHHHHHHHHHhc-CCeEEEEeCCCCHHHHHH---HcCCCEEEECchhhhhHHHHH-hhhcchhhcc
Confidence            47999999999999999999999988 899999999988543332   24699999999999 899887 4      356


Q ss_pred             CC---CccEEEEcchhHhh-hhc---------------hHHHHHHHHHhCCC
Q 028826           74 FR---NLVILVLDEADRLL-DMG---------------FQKQISYIISRLPK  106 (203)
Q Consensus        74 l~---~v~~lViDEad~l~-~~~---------------~~~~~~~il~~~~~  106 (203)
                      ++   ++.++|+||+|.|+ +.+               ....+..++..++.
T Consensus       197 ~r~d~~l~~lIIDEaDsmLiDeartPLIISgp~~~~~~lY~~~~~~i~~L~~  248 (997)
T 2ipc_A          197 LRHDHPLHYAIIDEVDSILIDEARTPLIISGPAEKATDLYYKMAEIAKKLER  248 (997)
T ss_dssp             SCSSSSSCEEEETTHHHHTTSSTTSCEEEEESCSSCHHHHHHHHHHHHHSCC
T ss_pred             cccCCCcceEEEechHHHHHhCCCCCeeeeCCCccchHHHHHHHHHHHHhhh
Confidence            77   99999999999997 321               23456677776653

>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=99.42  E-value=4.7e-14  Score=128.81  Aligned_cols=107  Identities=13%  Similarity=0.172  Sum_probs=81.5

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCC-CccCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMD-VLDFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~-~~~l~~v~~l   80 (203)
                      +|||+|+++|+.|+.+.+.+++...       +.++.+.......+...+++|+|+||+++..++.... ...++...++
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            7999999999999999999986431       2345555555556645679999999999999887622 1245678999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecCh
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  119 (203)
                      |+||||++...+   ....+...++ ++++++||||...
T Consensus       406 IiDEAHrs~~~~---~~~~I~~~~p-~a~~lgfTATP~~  440 (1038)
T 2w00_A          406 IFDECHRSQFGE---AQKNLKKKFK-RYYQFGFTGTPIF  440 (1038)
T ss_dssp             EEESCCTTHHHH---HHHHHHHHCS-SEEEEEEESSCCC
T ss_pred             EEEccchhcchH---HHHHHHHhCC-cccEEEEeCCccc
Confidence            999999986433   3456667775 5899999999874

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=99.33  E-value=4.7e-13  Score=117.60  Aligned_cols=109  Identities=17%  Similarity=0.083  Sum_probs=81.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ++|++|||+||.|+++.++++     ++++..++||......   ......+++++|++.+.         ....++++|
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            589999999999999998876     6788888888654100   00012567777775432         246789999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCC-CCCcEEEEeeecChhHHHHHHhc
Q 028826           82 LDEADRLLDMGFQKQISYIISRLP-KLRRTGLFSATQTEAVEELSKAG  128 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~-~~~q~i~~SAT~~~~v~~~~~~~  128 (203)
                      +||+|.+.+.++...+..++..++ ...|++++|||. +.+..+....
T Consensus       245 IDEaH~l~d~~~g~~~~~~l~~l~~~~i~il~~SAT~-~~i~~l~~~~  291 (677)
T 3rc3_A          245 IDEIQMIRDPARGWAWTRALLGLCAEEVHLCGEPAAI-DLVMELMYTT  291 (677)
T ss_dssp             ECSGGGGGCTTTHHHHHHHHHHCCEEEEEEEECGGGH-HHHHHHHHHH
T ss_pred             EecceecCCccchHHHHHHHHccCccceEEEeccchH-HHHHHHHHhc
Confidence            999999999899999999999887 778999999995 3455555543

>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=99.29  E-value=1.3e-11  Score=95.52  Aligned_cols=96  Identities=20%  Similarity=0.134  Sum_probs=73.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCce-EEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVK-SMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVI   79 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~-~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~   79 (203)
                      .+||++|+++|+.|+++.+.++     +++ +..+.|+..          ...+|+|+||+.+......    ...++++
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            3799999999999999998884     567 777766643          3579999999998766543    1245899


Q ss_pred             EEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChh
Q 028826           80 LVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (203)
Q Consensus        80 lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~  120 (203)
                      +|+||+|.+.+..+.    .++..+ +..+++++|||.++.
T Consensus       196 lIiDEaH~l~~~~~~----~i~~~~-~~~~~l~LSATp~r~  231 (237)
T 2fz4_A          196 LIFDEVHHLPAESYV----QIAQMS-IAPFRLGLTATFERE  231 (237)
T ss_dssp             EEEECSSCCCTTTHH----HHHHTC-CCSEEEEEEESCC--
T ss_pred             EEEECCccCCChHHH----HHHHhc-cCCEEEEEecCCCCC
Confidence            999999999776654    345555 478899999998753

>3jux_A Protein translocase subunit SECA; protein translocation, ATPase, conformational change, peptide binding, ATP-binding, cell inner membrane; HET: ADP; 3.10A {Thermotoga maritima} PDB: 3din_A*

Probab=99.11  E-value=6.9e-10  Score=97.10  Aligned_cols=85  Identities=14%  Similarity=0.051  Sum_probs=64.8

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcC-------------------------------------------
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGG-------------------------------------------   37 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g-------------------------------------------   37 (203)
                      .+.|++||++||.|-.+++..+...+ |++++++++.                                           
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            36899999999999999999999999 9999999982                                           


Q ss_pred             -------cchHHHHHHHHhCCCeEEEeccHHHH-HHHHhCC-----CccCCCccEEEEcchhHhh
Q 028826           38 -------VEVKADVKKIEEEGANLLIGTPGRLY-DIMERMD-----VLDFRNLVILVLDEADRLL   89 (203)
Q Consensus        38 -------~~~~~~~~~l~~~~~~ilV~Tp~~l~-~~~~~~~-----~~~l~~v~~lViDEad~l~   89 (203)
                             .+..+....   -.+||..||..-+- ++++.+=     ..-.....+.||||+|.++
T Consensus       197 ~~~~~~~~~~~err~a---Y~~DItYgTn~EfgFDYLRDnm~~~~~~~vqR~~~~aIVDEvDSiL  258 (822)
T 3jux_A          197 VEAFQVELKEITRKEA---YLCDVTYGTNNEFGFDYLRDNLVLDYNDKVQRGHFYAIVDEADSVL  258 (822)
T ss_dssp             HTTTCEECCBCCHHHH---HHSSEEEEEHHHHHHHHHHHTSCSSTTSCCCCCCCEEEEETHHHHH
T ss_pred             chhccccCCHHHHHHH---hcCCCEEccCcchhhHhHHhhccCCHHHhccCCCCeEEEeccccee
Confidence                   222222222   24899999999985 6776511     1123578899999999976

>1z63_A Helicase of the SNF2/RAD54 hamily; protein-DNA complex, hydrolase/DNA complex complex; 3.00A {Sulfolobus solfataricus} SCOP: c.37.1.19 c.37.1.19 PDB: 1z6a_A

Probab=99.07  E-value=6.2e-11  Score=100.73  Aligned_cols=101  Identities=17%  Similarity=0.185  Sum_probs=71.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +|||||+ .|+.|+.++++++++   ++++..+.|+...      .....++|+|+||+.+.....    +...+.+++|
T Consensus        89 ~LIv~P~-~l~~qw~~e~~~~~~---~~~v~~~~g~~~~------~~~~~~~ivi~t~~~l~~~~~----l~~~~~~~vI  154 (500)
T 1z63_A           89 SLVICPL-SVLKNWEEELSKFAP---HLRFAVFHEDRSK------IKLEDYDIILTTYAVLLRDTR----LKEVEWKYIV  154 (500)
T ss_dssp             EEEEECS-TTHHHHHHHHHHHCT---TSCEEECSSSTTS------CCGGGSSEEEEEHHHHTTCHH----HHTCCEEEEE
T ss_pred             EEEEccH-HHHHHHHHHHHHHCC---CceEEEEecCchh------ccccCCcEEEeeHHHHhccch----hcCCCcCEEE
Confidence            6999995 589999999999853   5677776666532      112468999999999865432    2334678999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecCh
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  119 (203)
                      +||||.+-..+  ......+..+ +..+.+++|||...
T Consensus       155 vDEaH~~kn~~--~~~~~~l~~l-~~~~~l~LTaTP~~  189 (500)
T 1z63_A          155 IDEAQNIKNPQ--TKIFKAVKEL-KSKYRIALTGTPIE  189 (500)
T ss_dssp             EETGGGGSCTT--SHHHHHHHTS-CEEEEEEECSSCST
T ss_pred             EeCccccCCHh--HHHHHHHHhh-ccCcEEEEecCCCC
Confidence            99999986543  2334455556 35678999999743

>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=98.99  E-value=8.5e-11  Score=107.37  Aligned_cols=112  Identities=20%  Similarity=0.115  Sum_probs=67.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH-HHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK-IEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~-l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +|||||+ .|+.|+..++.+..    ++++..+.|+......... -.....+|+|+|++.+.........+...++.++
T Consensus       203 vLIVvP~-sLl~Qw~~E~~~~f----~l~v~v~~~~~~~~~~~~~~~~~~~~dIvI~T~~~L~~~~~~~~~l~~~~~dlV  277 (968)
T 3dmq_A          203 VLIIVPE-TLQHQWLVEMLRRF----NLRFALFDDERYAEAQHDAYNPFDTEQLVICSLDFARRSKQRLEHLCEAEWDLL  277 (968)
T ss_dssp             EEEECCT-TTHHHHHHHHHHHS----CCCCEECCHHHHHHHHHTTCSSSTTCSEEEECHHHHHTSTTTTHHHHTSCCCEE
T ss_pred             EEEEeCH-HHHHHHHHHHHHHh----CCCEEEEccchhhhhhhhcccccccCCEEEEcHHHHhhCHHHHHHhhhcCCCEE
Confidence            7999999 99999999986653    4565555444322211110 0012569999999988532111012345678899


Q ss_pred             EEcchhHhhhhchH-HHHHHHHHhC-CCCCcEEEEeeecC
Q 028826           81 VLDEADRLLDMGFQ-KQISYIISRL-PKLRRTGLFSATQT  118 (203)
Q Consensus        81 ViDEad~l~~~~~~-~~~~~il~~~-~~~~q~i~~SAT~~  118 (203)
                      |+||||++-..+.. ......+..+ .+.++++++|||..
T Consensus       278 IvDEAH~~kn~~~~~s~~~~~l~~L~~~~~~~L~LTATPi  317 (968)
T 3dmq_A          278 VVDEAHHLVWSEDAPSREYQAIEQLAEHVPGVLLLTATPE  317 (968)
T ss_dssp             EECCSSCCCCBTTBCCHHHHHHHHHHTTCSSEEESCSSCS
T ss_pred             EehhhHhhcCCCCcchHHHHHHHHHhhcCCcEEEEEcCCc
Confidence            99999998543311 1112222222 35567999999974

>3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae}

Probab=98.82  E-value=2.2e-08  Score=89.87  Aligned_cols=106  Identities=16%  Similarity=0.256  Sum_probs=74.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH-----------HhCCCeEEEeccHHHHHHHHhCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI-----------EEEGANLLIGTPGRLYDIMERMD   70 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l-----------~~~~~~ilV~Tp~~l~~~~~~~~   70 (203)
                      +||||| ..|+.|+.+++.+++   |++++..++|+..........           ....++|+|+|++.+......  
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 678899999998885   467888888776655443322           124578999999999764432  


Q ss_pred             CccCCCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeec
Q 028826           71 VLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQ  117 (203)
Q Consensus        71 ~~~l~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~  117 (203)
                       +.-.+..++|+||||++-..  .......+..+ +....+++|||.
T Consensus       363 -l~~~~w~~vIvDEaH~lkn~--~s~~~~~l~~l-~~~~rl~LTgTP  405 (800)
T 3mwy_W          363 -LGSIKWQFMAVDEAHRLKNA--ESSLYESLNSF-KVANRMLITGTP  405 (800)
T ss_dssp             -HHTSEEEEEEETTGGGGCCS--SSHHHHHHTTS-EEEEEEEECSCC
T ss_pred             -HhcCCcceeehhhhhhhcCc--hhHHHHHHHHh-hhccEEEeeCCc
Confidence             22335789999999998432  22344455555 456678899997

>3crv_A XPD/RAD3 related DNA helicase; XPD helicase DNA repair cancer aging, hydrolase; HET: FLC; 2.00A {Sulfolobus acidocaldarius} PDB: 3crw_1*

Probab=98.74  E-value=1.4e-08  Score=87.43  Aligned_cols=87  Identities=21%  Similarity=0.176  Sum_probs=64.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcch---------------------------------HHHHHHH-
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEV---------------------------------KADVKKI-   47 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~---------------------------------~~~~~~l-   47 (203)
                      ++|++||++|+.|+.+++.++.... ++++..+.|+...                                 ......+ 
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            7999999999999999999997766 7888887764321                                 1111111 


Q ss_pred             ----------------HhCCCeEEEeccHHHHHHHHhCCCccC-CCccEEEEcchhHhhh
Q 028826           48 ----------------EEEGANLLIGTPGRLYDIMERMDVLDF-RNLVILVLDEADRLLD   90 (203)
Q Consensus        48 ----------------~~~~~~ilV~Tp~~l~~~~~~~~~~~l-~~v~~lViDEad~l~~   90 (203)
                                      ....+||||+|+..|.+.... ..+.+ .+..++||||||.|.+
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                            124789999999999987554 33433 4678999999999976

>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=98.57  E-value=4.1e-07  Score=79.79  Aligned_cols=109  Identities=19%  Similarity=0.270  Sum_probs=74.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHH--HHHHh-----CCCeEEEeccHHHHHHHHhCCCccC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADV--KKIEE-----EGANLLIGTPGRLYDIMERMDVLDF   74 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~--~~l~~-----~~~~ilV~Tp~~l~~~~~~~~~~~l   74 (203)
                      +|||+|+ .|+.|+.+++.++.+.  .+++..+.||.......  .....     ...+|+|+|++.+....   ..+..
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            6999997 7999999999999765  46777777775433221  11111     14789999999987543   33445


Q ss_pred             CCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecCh
Q 028826           75 RNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (203)
Q Consensus        75 ~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  119 (203)
                      .+..++|+||||.+-...  ......+..+ +....+++|||.-.
T Consensus       191 ~~~~~vI~DEaH~ikn~~--~~~~~al~~l-~~~~rl~LTgTPiq  232 (644)
T 1z3i_X          191 GKVGLVICDEGHRLKNSD--NQTYLALNSM-NAQRRVLISGTPIQ  232 (644)
T ss_dssp             SCCCEEEETTGGGCCTTC--HHHHHHHHHH-CCSEEEEECSSCSG
T ss_pred             CCccEEEEECceecCChh--hHHHHHHHhc-ccCcEEEEecCccc
Confidence            678899999999984332  2223334444 35678999999643

>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=98.33  E-value=5.4e-07  Score=79.22  Aligned_cols=131  Identities=16%  Similarity=0.150  Sum_probs=72.2

Q ss_pred             EcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHhhhh--chHHHH----HHHHHh-----
Q 028826           35 VGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDM--GFQKQI----SYIISR-----  103 (203)
Q Consensus        35 ~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~~~--~~~~~~----~~il~~-----  103 (203)
                      .|+.....+...+ ..+     +||++|++++.. +       .++|+||+|++++.  ++....    ..+...     
T Consensus       304 ~G~e~~~~~~~~~-~~g-----~tpg~LlDyl~~-~-------~llVlDEa~~~l~~~~~~~~~~~~~~~~l~~~G~~lp  369 (661)
T 2d7d_A          304 SGIENYSRHLTLR-PPG-----STPYTLLDYFPD-D-------FMIVVDESHVTIPQVRGMFNGDQARKQVLVDHGFRLP  369 (661)
T ss_dssp             TTGGGGHHHHTTC-CTT-----CCCBCGGGGSCS-S-------CEEEEETHHHHHHHHHHHHHHHHHHHHHHHHTTSSCG
T ss_pred             ccchhHHHHHccc-cCC-----CCccHHHHHccc-C-------cEEEEecHHHHHHHHHHHHHHHHHHHHHHHHccccch
Confidence            4555555555433 223     999999998854 2       28999999998742  122111    111111     


Q ss_pred             -------------CCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcC
Q 028826          104 -------------LPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECE  170 (203)
Q Consensus       104 -------------~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~  170 (203)
                                   .+..+|+++||||.++.....    ........+...               ....+.    +...+
T Consensus       370 ~~l~~~~l~~~e~~~~~~q~i~~SAT~~~~~~~~----~~~~~~~~~r~~---------------~l~~p~----i~v~~  426 (661)
T 2d7d_A          370 SALDNRPLRFEEFEKHMHNIVYVSATPGPYEIEH----TDEMVEQIIRPT---------------GLLDPL----IDVRP  426 (661)
T ss_dssp             GGGGSCCCCHHHHHHTCSEEEEECSSCCHHHHHH----CSSCEEECCCTT---------------CCCCCE----EEEEC
T ss_pred             hhhhcccccHHHHhccCCCEEEEecCCChhHHHh----hhCeeeeeeccc---------------CCCCCe----EEEec
Confidence                         124689999999998654322    111111111111               001111    22234


Q ss_pred             CCCcHHHHHHHHhc--CCCCeEEEEeccCCcccC
Q 028826          171 SDKKPSQLVDLLIK--NKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       171 ~~~k~~~l~~ll~~--~~~~~~lIF~ns~~~~e~  202 (203)
                      ...+...+...+..  ..++++||||+|+..|++
T Consensus       427 ~~~~~~~Ll~~l~~~~~~~~~vlVf~~t~~~ae~  460 (661)
T 2d7d_A          427 IEGQIDDLIGEIQARIERNERVLVTTLTKKMSED  460 (661)
T ss_dssp             STTHHHHHHHHHHHHHTTTCEEEEECSSHHHHHH
T ss_pred             ccchHHHHHHHHHHHHhcCCeEEEEECCHHHHHH
Confidence            44566666565543  356799999999887763

>2vl7_A XPD; helicase, unknown function; 2.25A {Sulfolobus tokodaii}

Probab=98.14  E-value=2.2e-06  Score=73.69  Aligned_cols=82  Identities=21%  Similarity=0.260  Sum_probs=51.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcch--------HH------------------------HHHHH--
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEV--------KA------------------------DVKKI--   47 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~--------~~------------------------~~~~l--   47 (203)
                      ++|++||++|+.|+.+++.++     ++++..+.|....        ..                        ....+  
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            789999999999999988875     3444444432210        00                        00000  


Q ss_pred             ------------HhCCCeEEEeccHHHHHHHHhCCCc-------cCCCccEEEEcchhHhh
Q 028826           48 ------------EEEGANLLIGTPGRLYDIMERMDVL-------DFRNLVILVLDEADRLL   89 (203)
Q Consensus        48 ------------~~~~~~ilV~Tp~~l~~~~~~~~~~-------~l~~v~~lViDEad~l~   89 (203)
                                  ....+||||+|+..+.+.... +.+       .+.+..++||||||.|.
T Consensus       129 ~~~~Cpy~~~r~~~~~adiVV~n~~~l~~~~~~-~~~~~~~~~~~~~~~~~vIiDEAHnl~  188 (540)
T 2vl7_A          129 AVDYCPYYSLRANLKDKDVIAMTYPYLFQKPIR-NSVFCNKDDCLKLEDYLIVIDEAHNLL  188 (540)
T ss_dssp             ----------CTTGGGCSEEEEETHHHHSHHHH-HHHSCSSTTSCCGGGEEEEETTGGGGG
T ss_pred             hcCCChHHHHHHHhhcCCEEEEChHHhcCHHHH-HhhCcccccccCcCCCEEEEEccccHH
Confidence                        013579999999999874433 222       23567899999999994

>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=98.11  E-value=4.8e-06  Score=73.25  Aligned_cols=115  Identities=13%  Similarity=0.135  Sum_probs=63.7

Q ss_pred             eccHHHHHHHHhCCCccCCCccEEEEcchhHhhhh-c--hHHH---HHHHHHh------------------CCCCCcEEE
Q 028826           57 GTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDM-G--FQKQ---ISYIISR------------------LPKLRRTGL  112 (203)
Q Consensus        57 ~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~~~-~--~~~~---~~~il~~------------------~~~~~q~i~  112 (203)
                      +||++|.+++.. +       .++|+||+|++++. +  +...   ...+...                  .+...|+++
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            889999887754 2       38999999998742 1  1111   1111111                  124679999


Q ss_pred             EeeecChhHHHHHHhcCCCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcC--CCCeE
Q 028826          113 FSATQTEAVEELSKAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKN--KSKKI  190 (203)
Q Consensus       113 ~SAT~~~~v~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~--~~~~~  190 (203)
                      ||||.++.....    .  ...+.......             ....+    .+...+...+...+...+...  .+.++
T Consensus       386 ~SAT~~~~~~~~----~--~~~~~~~~r~~-------------~l~~p----~i~v~~~~~~~~~Ll~~l~~~~~~~~~v  442 (664)
T 1c4o_A          386 VSATPGPFELAH----S--GRVVEQIIRPT-------------GLLDP----LVRVKPTENQILDLMEGIRERAARGERT  442 (664)
T ss_dssp             EESSCCHHHHHH----C--SEEEEECSCTT-------------CCCCC----EEEEECSTTHHHHHHHHHHHHHHTTCEE
T ss_pred             EecCCCHHHHHh----h--hCeeeeeeccC-------------CCCCC----eEEEecccchHHHHHHHHHHHHhcCCEE
Confidence            999998654222    1  11122211100             00111    122234455666666666432  56799


Q ss_pred             EEEeccCCcccC
Q 028826          191 IMYVQHGNFSED  202 (203)
Q Consensus       191 lIF~ns~~~~e~  202 (203)
                      ||||+|+..|++
T Consensus       443 lVf~~t~~~ae~  454 (664)
T 1c4o_A          443 LVTVLTVRMAEE  454 (664)
T ss_dssp             EEECSSHHHHHH
T ss_pred             EEEECCHHHHHH
Confidence            999999987763

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=97.86  E-value=5.2e-06  Score=61.72  Aligned_cols=60  Identities=10%  Similarity=0.088  Sum_probs=36.7

Q ss_pred             HhcCCCCeEEEeccCcccccccchhhhhccCCCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          126 KAGLRNPVRIEVRAESKSHHASASSQQLASSKTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       126 ~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      ..|+.+|..+.+...               .....++.|+|+.++.++|...|.+++...+ +++||||++++.++
T Consensus         9 ~~~~~~p~~i~v~~~---------------~~~~~~i~q~~~~~~~~~K~~~L~~~l~~~~-~~~lVF~~~~~~~~   68 (191)
T 2p6n_A            9 SGVDLGTENLYFQSM---------------GAASLDVIQEVEYVKEEAKMVYLLECLQKTP-PPVLIFAEKKADVD   68 (191)
T ss_dssp             ----------------------------------CCSEEEEEECCGGGHHHHHHHHHTTSC-SCEEEECSCHHHHH
T ss_pred             ccccCCCEEEEECCC---------------CCCCcCceEEEEEcChHHHHHHHHHHHHhCC-CCEEEEECCHHHHH
Confidence            468889999988776               4567899999999999999999999998754 58999999988765

>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=97.31  E-value=0.00012  Score=53.92  Aligned_cols=46  Identities=22%  Similarity=0.260  Sum_probs=39.6

Q ss_pred             CCCCCceeEEEEEcCCCCcHHHHHHHHhcC-CCCeEEEEeccCCccc
Q 028826          156 SKTPLGLHLEYLECESDKKPSQLVDLLIKN-KSKKIIMYVQHGNFSE  201 (203)
Q Consensus       156 ~~~~~~i~~~~~~~~~~~k~~~l~~ll~~~-~~~~~lIF~ns~~~~e  201 (203)
                      ...++++.|+|+.++..+|...|.++++.. ..+++||||++++.|+
T Consensus        14 ~~~~~~i~q~~~~v~~~~K~~~L~~ll~~~~~~~k~lVF~~~~~~~~   60 (185)
T 2jgn_A           14 GSTSENITQKVVWVEESDKRSFLLDLLNATGKDSLTLVFVETKKGAD   60 (185)
T ss_dssp             --CCTTEEEEEEECCGGGHHHHHHHHHHHC-CCSCEEEEESCHHHHH
T ss_pred             CCCCCCceEEEEEeCcHHHHHHHHHHHHhcCCCCeEEEEECCHHHHH
Confidence            346789999999999999999999999987 5789999999988765

>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=97.10  E-value=0.00066  Score=59.10  Aligned_cols=99  Identities=20%  Similarity=0.273  Sum_probs=56.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEE-eccHHHHHHHHhCCCccCCCccEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLI-GTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV-~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +++++||+++|.|+.+.+......+ +++.... .+...  .     ....+-++ .+|+.. . +.. ......+++++
T Consensus       199 vll~APTg~AA~~L~e~~~~~~~~l-~l~~~~~-~~~~~--~-----~~Tih~ll~~~~~~~-~-~~~-~~~~~l~~d~l  266 (608)
T 1w36_D          199 IRLAAPTGKAAARLTESLGKALRQL-PLTDEQK-KRIPE--D-----ASTLHRLLGAQPGSQ-R-LRH-HAGNPLHLDVL  266 (608)
T ss_dssp             EEEEBSSHHHHHHHHHHHTHHHHHS-SCCSCCC-CSCSC--C-----CBTTTSCC--------------CTTSCCSCSEE
T ss_pred             EEEEeCChhHHHHHHHHHHHHHhcC-CCCHHHH-hccch--h-----hhhhHhhhccCCCch-H-HHh-ccCCCCCCCEE
Confidence            5789999999999998888776554 3321100 00000  0     00111122 223221 1 112 22233478999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeee
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSAT  116 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT  116 (203)
                      |||||+ |++   .+.+..++..++...|+++++-.
T Consensus       267 IIDEAs-ml~---~~~~~~Ll~~l~~~~~liLvGD~  298 (608)
T 1w36_D          267 VVDEAS-MID---LPMMSRLIDALPDHARVIFLGDR  298 (608)
T ss_dssp             EECSGG-GCB---HHHHHHHHHTCCTTCEEEEEECT
T ss_pred             EEechh-hCC---HHHHHHHHHhCCCCCEEEEEcch
Confidence            999999 555   45678889999999999998754

>2hjv_A ATP-dependent RNA helicase DBPA; parallel alpha-beta, hydrolase; 1.95A {Bacillus subtilis}

Probab=96.77  E-value=0.011  Score=42.13  Aligned_cols=71  Identities=14%  Similarity=0.192  Sum_probs=55.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+++|++-+..+.+.+.+.     ++++..++|+.+..+....+   .++..+|||+|. .    +.  .++|+.+++
T Consensus        38 ~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vlv~T~-~----~~--~Gld~~~~~  105 (163)
T 2hjv_A           38 CIIFCRTKEHVNQLTDELDDL-----GYPCDKIHGGMIQEDRFDVMNEFKRGEYRYLVATD-V----AA--RGIDIENIS  105 (163)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECG-G----GT--TTCCCSCCS
T ss_pred             EEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEECC-h----hh--cCCchhcCC
Confidence            799999999999998888775     68899999998766554433   346789999994 2    22  578999999


Q ss_pred             EEEEcc
Q 028826           79 ILVLDE   84 (203)
Q Consensus        79 ~lViDE   84 (203)
                      ++|.-+
T Consensus       106 ~Vi~~~  111 (163)
T 2hjv_A          106 LVINYD  111 (163)
T ss_dssp             EEEESS
T ss_pred             EEEEeC
Confidence            988743

>2p6n_A ATP-dependent RNA helicase DDX41; DEAD, structural genomics, structural genomic consortium, SGC, hydrolase; 2.60A {Homo sapiens}

Probab=96.64  E-value=0.019  Score=42.14  Aligned_cols=69  Identities=19%  Similarity=0.257  Sum_probs=54.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+++|++-+..+.+.+++.     ++++..++|+.+..++...+   .++..+|+|+|.     .+.  ..+|+.+++
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            799999999999998888775     68899999998766555433   346789999993     233  578999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       125 ~VI~  128 (191)
T 2p6n_A          125 HVIN  128 (191)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9887

>1fuk_A Eukaryotic initiation factor 4A; helicase, DEAD-box protein, translation; 1.75A {Saccharomyces cerevisiae} SCOP: c.37.1.19

Probab=96.48  E-value=0.022  Score=40.61  Aligned_cols=72  Identities=10%  Similarity=0.131  Sum_probs=55.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||+++|++-+..+...+.+.     ++.+..++|+.+..+....+   .++..+|+|+|..     +.  .++|+.++
T Consensus        32 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~--~G~d~~~~   99 (165)
T 1fuk_A           32 QAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDL-----LA--RGIDVQQV   99 (165)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGG-----GT--TTCCCCSC
T ss_pred             CEEEEECCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHcCCCEEEEEcCh-----hh--cCCCcccC
Confidence            3799999999999888887764     67889999998766554433   3467899999942     22  57899999


Q ss_pred             cEEEEcc
Q 028826           78 VILVLDE   84 (203)
Q Consensus        78 ~~lViDE   84 (203)
                      +++|.-+
T Consensus       100 ~~Vi~~~  106 (165)
T 1fuk_A          100 SLVINYD  106 (165)
T ss_dssp             SEEEESS
T ss_pred             CEEEEeC
Confidence            9988743

>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=96.16  E-value=0.021  Score=41.14  Aligned_cols=72  Identities=8%  Similarity=0.110  Sum_probs=55.7

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||.+++++-+..+.+.+.+.     ++++..++|+.+..+....+   .++..+|+|+|..     + . .++|+.++
T Consensus        33 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~hg~~~~~~r~~~~~~f~~g~~~vLvaT~~-----~-~-~Gldi~~~  100 (172)
T 1t5i_A           33 QVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL-----F-G-RGMDIERV  100 (172)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSC-----C-S-TTCCGGGC
T ss_pred             cEEEEECCHHHHHHHHHHHHhc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCcEEEECCc-----h-h-cCcchhhC
Confidence            3799999999999888888775     68889999998766555433   3467899999953     1 2 57899999


Q ss_pred             cEEEEcc
Q 028826           78 VILVLDE   84 (203)
Q Consensus        78 ~~lViDE   84 (203)
                      +++|.-+
T Consensus       101 ~~Vi~~d  107 (172)
T 1t5i_A          101 NIAFNYD  107 (172)
T ss_dssp             SEEEESS
T ss_pred             CEEEEEC
Confidence            9988743

>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=96.06  E-value=0.044  Score=40.80  Aligned_cols=69  Identities=14%  Similarity=0.184  Sum_probs=54.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.+||++-+..+.+.+.+.     ++.+..++|+.+..++...+   .++..+|+|+|.-     + . .++|+.+++
T Consensus        34 ~lVF~~~~~~~~~l~~~L~~~-----~~~~~~lhg~~~~~~r~~~~~~f~~g~~~vlvaT~~-----~-~-~Gidi~~v~  101 (212)
T 3eaq_A           34 AMVFTRTKAETEEIAQGLLRL-----GHPAQALHGDLSQGERERVLGAFRQGEVRVLVATDV-----A-A-RGLDIPQVD  101 (212)
T ss_dssp             EEEECSSHHHHHHHHHHHHHH-----TCCEEEECSSSCHHHHHHHHHHHHSSSCCEEEECTT-----T-T-CSSSCCCBS
T ss_pred             EEEEeCCHHHHHHHHHHHHHc-----CCCEEEEECCCCHHHHHHHHHHHHCCCCeEEEecCh-----h-h-cCCCCccCc
Confidence            799999999999888888775     78899999998876655543   3467899999942     2 2 689999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       102 ~Vi~  105 (212)
T 3eaq_A          102 LVVH  105 (212)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8884

>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=96.04  E-value=0.034  Score=39.99  Aligned_cols=69  Identities=20%  Similarity=0.200  Sum_probs=54.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+++|++-+..+...+.+.     ++++..++|+.+..+....+   .++..+|+|+|..     + . .++|+.++.
T Consensus        37 ~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~R~~~~~~f~~g~~~vLvaT~~-----~-~-~Gid~~~~~  104 (175)
T 2rb4_A           37 AIIFCQTRRNAKWLTVEMIQD-----GHQVSLLSGELTVEQRASIIQRFRDGKEKVLITTNV-----C-A-RGIDVKQVT  104 (175)
T ss_dssp             EEEECSCHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHTTSCSEEEECCS-----C-C-TTTCCTTEE
T ss_pred             EEEEECCHHHHHHHHHHHHHc-----CCcEEEEeCCCCHHHHHHHHHHHHcCCCeEEEEecc-----h-h-cCCCcccCC
Confidence            799999999999888887764     68899999998866555433   3467899999952     2 2 578999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       105 ~Vi~  108 (175)
T 2rb4_A          105 IVVN  108 (175)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9985

>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=95.86  E-value=0.026  Score=41.15  Aligned_cols=69  Identities=10%  Similarity=0.138  Sum_probs=44.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+++|++-+..+.+.++..     ++.+..++|+.+..+...   ...++...|||+|.     .+.  .++|+.++.
T Consensus        49 ~lVF~~~~~~~~~l~~~L~~~-----g~~~~~lhg~~~~~~r~~~~~~f~~g~~~vLvaT~-----~~~--~Gldi~~~~  116 (185)
T 2jgn_A           49 TLVFVETKKGADSLEDFLYHE-----GYACTSIHGDRSQRDREEALHQFRSGKSPILVATA-----VAA--RGLDISNVK  116 (185)
T ss_dssp             EEEEESCHHHHHHHHHHHHHT-----TCCEEEEC--------CHHHHHHHHTSSSEEEEEC-------------CCCSBS
T ss_pred             EEEEECCHHHHHHHHHHHHHc-----CCceEEEeCCCCHHHHHHHHHHHHcCCCeEEEEcC-----hhh--cCCCcccCC
Confidence            799999999999888887764     688999999876554433   33357789999994     222  578889999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       117 ~VI~  120 (185)
T 2jgn_A          117 HVIN  120 (185)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8886

>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=95.36  E-value=0.085  Score=43.63  Aligned_cols=69  Identities=12%  Similarity=0.133  Sum_probs=55.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+++|++-|..+.+.+.+.     ++++..++|+.+..++...+   .++..+|||+|.-     + . .++|+.+++
T Consensus       303 ~lVF~~t~~~a~~l~~~L~~~-----~~~~~~lhg~~~~~~R~~~l~~F~~g~~~vLvaT~v-----~-~-rGlDi~~v~  370 (434)
T 2db3_A          303 TIVFVETKRGADFLASFLSEK-----EFPTTSIHGDRLQSQREQALRDFKNGSMKVLIATSV-----A-S-RGLDIKNIK  370 (434)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEESTTSCHHHHHHHHHHHHTSSCSEEEECGG-----G-T-SSCCCTTCC
T ss_pred             EEEEEeCcHHHHHHHHHHHhC-----CCCEEEEeCCCCHHHHHHHHHHHHcCCCcEEEEchh-----h-h-CCCCcccCC
Confidence            689999999999888888764     78899999998776655543   3467899999972     2 2 689999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       371 ~VI~  374 (434)
T 2db3_A          371 HVIN  374 (434)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9986

>2i4i_A ATP-dependent RNA helicase DDX3X; DEAD, structural genomics, SGC, structural GE consortium, hydrolase; HET: AMP; 2.20A {Homo sapiens}

Probab=95.32  E-value=0.11  Score=42.25  Aligned_cols=69  Identities=10%  Similarity=0.137  Sum_probs=55.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+++|++-+..+++.+++.     ++.+..++|+.+..++...+   .++..+|||+|.     .+.  .++|+.+++
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            699999999999998888774     68899999998866554433   346789999996     333  589999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       347 ~Vi~  350 (417)
T 2i4i_A          347 HVIN  350 (417)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9886

>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=95.08  E-value=0.1  Score=41.40  Aligned_cols=71  Identities=15%  Similarity=0.273  Sum_probs=54.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||++++++-+.++.+.+++.     ++++..++|+.+..+....   ..++..+|+|+|.     .+.  .++|+.+++
T Consensus       241 ~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-----~~~--~Gid~~~~~  308 (367)
T 1hv8_A          241 GLVFCKTKRDTKELASMLRDI-----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATD-----VMS--RGIDVNDLN  308 (367)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECT-----THH--HHCCCSCCS
T ss_pred             EEEEECCHHHHHHHHHHHHhc-----CCCeEEeeCCCCHHHHHHHHHHHHcCCCeEEEECC-----hhh--cCCCcccCC
Confidence            699999999999998888775     6788899998876655443   3356789999995     233  368888999


Q ss_pred             EEEEcc
Q 028826           79 ILVLDE   84 (203)
Q Consensus        79 ~lViDE   84 (203)
                      ++|.-+
T Consensus       309 ~Vi~~~  314 (367)
T 1hv8_A          309 CVINYH  314 (367)
T ss_dssp             EEEESS
T ss_pred             EEEEec
Confidence            988643

>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=95.02  E-value=0.14  Score=43.63  Aligned_cols=74  Identities=14%  Similarity=0.225  Sum_probs=58.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+++|+.-+..+.+.+.+....  ++.+..++|+.+..+....   ..++..+|||+|.-     +.  .++|+.+++
T Consensus       342 ~iVF~~s~~~~~~l~~~L~~~~~~--~~~v~~~h~~~~~~~R~~~~~~f~~g~~~vLvaT~~-----~~--~GiDip~v~  412 (563)
T 3i5x_A          342 AIIFAPTVKFTSFLCSILKNEFKK--DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV-----GA--RGMDFPNVH  412 (563)
T ss_dssp             EEEECSCHHHHHHHHHHHHHHHTT--TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGG-----GT--SSCCCTTCC
T ss_pred             EEEEcCcHHHHHHHHHHHHHhccC--CceEEEecCCCCHHHHHHHHHHHhcCCCCEEEEcch-----hh--cCCCcccCC
Confidence            799999999999999999887543  6889999999887655443   33578999999962     22  689999999


Q ss_pred             EEEEcc
Q 028826           79 ILVLDE   84 (203)
Q Consensus        79 ~lViDE   84 (203)
                      ++|.-.
T Consensus       413 ~VI~~~  418 (563)
T 3i5x_A          413 EVLQIG  418 (563)
T ss_dssp             EEEEES
T ss_pred             EEEEEC
Confidence            998654

>3i32_A Heat resistant RNA dependent ATPase; RNA helicase, dimer, RNA recognition motif, ATP-BIND helicase, nucleotide-binding; 2.80A {Thermus thermophilus}

Probab=95.01  E-value=0.12  Score=40.77  Aligned_cols=69  Identities=14%  Similarity=0.181  Sum_probs=52.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.++|++-+..+...+.+.     ++.+..++|+.+..++...+   .++..+|+|+|.-     + . .++++.++.
T Consensus        31 ~LVF~~t~~~~~~l~~~L~~~-----g~~~~~lhg~l~~~~r~~~~~~f~~g~~~vLVaT~v-----a-~-~Gidi~~v~   98 (300)
T 3i32_A           31 AMVFTRTKAETEEIAQGLLRL-----GHPAQALHGDMSQGERERVMGAFRQGEVRVLVATDV-----A-A-RGLDIPQVD   98 (300)
T ss_dssp             EEEECSSHHHHHHHHHHHHTT-----TCCEEEECSCCCTHHHHHHHHHHHHTSCCEEEECST-----T-T-CSTTCCCCS
T ss_pred             EEEEECCHHHHHHHHHHHHhC-----CCCEEEEeCCCCHHHHHHHHHHhhcCCceEEEEech-----h-h-cCcccccee
Confidence            799999999988887777654     78899999998876655533   3467899999942     2 2 578888888


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus        99 ~VI~  102 (300)
T 3i32_A           99 LVVH  102 (300)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            7774

>3sqw_A ATP-dependent RNA helicase MSS116, mitochondrial; RECA fold, RNA dependent ATPase, RNA helicase; HET: ANP; 1.91A {Saccharomyces cerevisiae S288C}

Probab=94.92  E-value=0.15  Score=43.72  Aligned_cols=75  Identities=13%  Similarity=0.222  Sum_probs=58.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+++|++-+..+.+.+++....  ++.+..++|+.+..+....   ..++..+|||+|.-     +.  .++|+.+++
T Consensus       291 ~iVF~~t~~~~~~l~~~L~~~~~~--~~~v~~~hg~~~~~~R~~~~~~F~~g~~~vLVaT~~-----~~--~GiDip~v~  361 (579)
T 3sqw_A          291 AIIFAPTVKFTSFLCSILKNEFKK--DLPILEFHGKITQNKRTSLVKRFKKDESGILVCTDV-----GA--RGMDFPNVH  361 (579)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHHTT--TSCEEEESTTSCHHHHHHHHHHHHHCSSEEEEECGG-----GT--SSCCCTTCC
T ss_pred             EEEECCcHHHHHHHHHHHHHhhcC--CCcEEEecCCCCHHHHHHHHHHhhcCCCeEEEEcch-----hh--cCCCcccCC
Confidence            799999999999999999887543  6889999999886655443   33578999999962     22  578999999


Q ss_pred             EEEEcch
Q 028826           79 ILVLDEA   85 (203)
Q Consensus        79 ~lViDEa   85 (203)
                      ++|.-..
T Consensus       362 ~VI~~~~  368 (579)
T 3sqw_A          362 EVLQIGV  368 (579)
T ss_dssp             EEEEESC
T ss_pred             EEEEcCC
Confidence            9887553

>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=94.58  E-value=0.33  Score=42.54  Aligned_cols=75  Identities=15%  Similarity=0.278  Sum_probs=59.6

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+++|+.-+..+.+.+.+.     ++++..++|+.+..+....   ...+..+|+|||--     + . .++++.+++
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-----GIKVNYLHSEIKTLERIEIIRDLRLGKYDVLVGINL-----L-R-EGLDIPEVS  515 (661)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHHTSCSEEEESCC-----C-S-TTCCCTTEE
T ss_pred             EEEEECCHHHHHHHHHHHHhc-----CCCeEEEeCCCCHHHHHHHHHHHhcCCeEEEEecch-----h-h-CCcccCCCC
Confidence            789999999999888887775     6888889988776655554   33467899999862     2 2 689999999


Q ss_pred             EEEEcchhHh
Q 028826           79 ILVLDEADRL   88 (203)
Q Consensus        79 ~lViDEad~l   88 (203)
                      ++|+-++|..
T Consensus       516 lVi~~d~d~~  525 (661)
T 2d7d_A          516 LVAILDADKE  525 (661)
T ss_dssp             EEEETTTTCC
T ss_pred             EEEEeCcccc
Confidence            9999998864

>1c4o_A DNA nucleotide excision repair enzyme UVRB; uvrabc, helicase, hypertherm protein, replication; HET: DNA BOG; 1.50A {Thermus thermophilus} SCOP: c.37.1.19 c.37.1.19 PDB: 1d2m_A*

Probab=94.50  E-value=0.51  Score=41.40  Aligned_cols=75  Identities=12%  Similarity=0.165  Sum_probs=59.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.++|+.-+..+.+.+.+.     ++++..++|+.+..+....   ...+..+|+|||---      . .++++.+++
T Consensus       442 vlVf~~t~~~ae~L~~~L~~~-----gi~~~~lh~~~~~~~R~~~~~~f~~g~~~VLvaT~~l------~-~GlDip~v~  509 (664)
T 1c4o_A          442 TLVTVLTVRMAEELTSFLVEH-----GIRARYLHHELDAFKRQALIRDLRLGHYDCLVGINLL------R-EGLDIPEVS  509 (664)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTCCHHHHHHHHHHHHTTSCSEEEESCCC------C-TTCCCTTEE
T ss_pred             EEEEECCHHHHHHHHHHHHhc-----CCCceeecCCCCHHHHHHHHHHhhcCCceEEEccChh------h-cCccCCCCC
Confidence            789999999999888887775     6888889988776655544   334678999998521      2 689999999


Q ss_pred             EEEEcchhHh
Q 028826           79 ILVLDEADRL   88 (203)
Q Consensus        79 ~lViDEad~l   88 (203)
                      ++|+=++|..
T Consensus       510 lVI~~d~d~~  519 (664)
T 1c4o_A          510 LVAILDADKE  519 (664)
T ss_dssp             EEEETTTTSC
T ss_pred             EEEEeCCccc
Confidence            9999888754

>1oyw_A RECQ helicase, ATP-dependent DNA helicase; winged helix, helix-turn-helix, ATP binding, Zn(2+) binding, hydrolase; 1.80A {Escherichia coli} SCOP: a.4.5.43 c.37.1.19 c.37.1.19 PDB: 1oyy_A*

Probab=94.47  E-value=0.15  Score=43.38  Aligned_cols=69  Identities=14%  Similarity=0.203  Sum_probs=53.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.++|++-+.++.+.+++.     ++++..++||.+..+...   ...++..+|||+|..     + . .++|+.+++
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-----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVA-----F-G-MGINKPNVR  306 (523)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTT-----S-C-TTTCCTTCC
T ss_pred             EEEEeCCHHHHHHHHHHHHHC-----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEech-----h-h-CCCCccCcc
Confidence            699999999999888888775     688999999988665444   333577899999972     2 2 478888888


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       307 ~VI~  310 (523)
T 1oyw_A          307 FVVH  310 (523)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8886

>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=94.44  E-value=0.17  Score=41.01  Aligned_cols=69  Identities=13%  Similarity=0.141  Sum_probs=54.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+++|++-+..+.+.+.+.     ++++..++|+.+..++...   ..++..+|||+|..     + . .++|+.+++
T Consensus       279 ~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~-~-~Gidi~~v~  346 (410)
T 2j0s_A          279 AVIFCNTKRKVDWLTEKMREA-----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDV-----W-A-RGLDVPQVS  346 (410)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGG-----G-S-SSCCCTTEE
T ss_pred             EEEEEcCHHHHHHHHHHHHhC-----CCceEEeeCCCCHHHHHHHHHHHHCCCCCEEEECCh-----h-h-CcCCcccCC
Confidence            689999999999888888774     6788899999876654443   33567899999962     2 2 689999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       347 ~Vi~  350 (410)
T 2j0s_A          347 LIIN  350 (410)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9986

>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=94.41  E-value=0.2  Score=40.46  Aligned_cols=69  Identities=19%  Similarity=0.211  Sum_probs=54.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||+++|++-+..+++.+.+.     ++++..++|+.+..++...+   .++..+|||+|.-     +.  .++|+.+++
T Consensus       269 ~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~--~Gidip~~~  336 (412)
T 3fht_A          269 AMIFCHTRKTASWLAAELSKE-----GHQVALLSGEMMVEQRAAVIERFREGKEKVLVTTNV-----CA--RGIDVEQVS  336 (412)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHTTSCSEEEECGG-----GT--SSCCCTTEE
T ss_pred             EEEEeCCHHHHHHHHHHHHhC-----CCeEEEecCCCCHHHHHHHHHHHHCCCCcEEEEcCc-----cc--cCCCccCCC
Confidence            699999999999998888875     67888999998766555433   3467899999962     22  689999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       337 ~Vi~  340 (412)
T 3fht_A          337 VVIN  340 (412)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9885

>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=94.40  E-value=0.74  Score=36.69  Aligned_cols=73  Identities=15%  Similarity=0.226  Sum_probs=56.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||++++++-+..+++.+++.     ++++..++|+.+..++...   ..++..+|||+|.-     + . .++|+.+++
T Consensus       246 ~lvf~~~~~~~~~l~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~-~-~Gidip~~~  313 (395)
T 3pey_A          246 SIIFVATKKTANVLYGKLKSE-----GHEVSILHGDLQTQERDRLIDDFREGRSKVLITTNV-----L-A-RGIDIPTVS  313 (395)
T ss_dssp             EEEECSCHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHTTSCCEEEECGG-----G-S-SSCCCTTEE
T ss_pred             EEEEeCCHHHHHHHHHHHHhc-----CCcEEEeCCCCCHHHHHHHHHHHHCCCCCEEEECCh-----h-h-cCCCcccCC
Confidence            689999999999888888775     6788899999876655443   33467899999962     2 2 689999999


Q ss_pred             EEEEcchh
Q 028826           79 ILVLDEAD   86 (203)
Q Consensus        79 ~lViDEad   86 (203)
                      ++|.-+..
T Consensus       314 ~Vi~~~~p  321 (395)
T 3pey_A          314 MVVNYDLP  321 (395)
T ss_dssp             EEEESSCC
T ss_pred             EEEEcCCC
Confidence            99976554

>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=94.09  E-value=0.22  Score=40.14  Aligned_cols=70  Identities=6%  Similarity=0.091  Sum_probs=54.6

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||++++++-+..+.+.+++.     ++.+..++|+.+..++...   ..++..+|||+|.     .+.  .++|+.+++
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            699999999999998888876     6788899999876655443   3346789999995     222  579999999


Q ss_pred             EEEEc
Q 028826           79 ILVLD   83 (203)
Q Consensus        79 ~lViD   83 (203)
                      ++|.-
T Consensus       329 ~Vi~~  333 (400)
T 1s2m_A          329 VVINF  333 (400)
T ss_dssp             EEEES
T ss_pred             EEEEe
Confidence            98863

>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=93.81  E-value=0.29  Score=39.25  Aligned_cols=72  Identities=8%  Similarity=0.121  Sum_probs=55.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHH---HHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKK---IEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~---l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||++++++-+..+++.+.+.     ++.+..++|+.+..++...   ..++..+|||+|..     +.  .++|+.+++
T Consensus       253 ~lvf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~~-----~~--~Gidi~~~~  320 (391)
T 1xti_A          253 VVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNL-----FG--RGMDIERVN  320 (391)
T ss_dssp             EEEECSCHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTCCSEEEESCC-----CS--SCBCCTTEE
T ss_pred             EEEEeCcHHHHHHHHHHHHhC-----CCcEEEEeCCCCHHHHHHHHHHHhcCCCcEEEECCh-----hh--cCCCcccCC
Confidence            699999999999998888774     6788999999876555443   33467899999952     22  579999999


Q ss_pred             EEEEcch
Q 028826           79 ILVLDEA   85 (203)
Q Consensus        79 ~lViDEa   85 (203)
                      ++|.-+.
T Consensus       321 ~Vi~~~~  327 (391)
T 1xti_A          321 IAFNYDM  327 (391)
T ss_dssp             EEEESSC
T ss_pred             EEEEeCC
Confidence            9987543

>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=93.73  E-value=0.27  Score=42.47  Aligned_cols=69  Identities=12%  Similarity=0.133  Sum_probs=53.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.++|+.-+.++...+++.     ++.+..++||.+..++...+   ..+..+|||+|-.     + . .++|+.+++
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-----GIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVA-----F-G-MGIDKPDVR  337 (591)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEECTT-----S-C-TTCCCSCEE
T ss_pred             eEEEeCcHHHHHHHHHHHHHC-----CCCEEEecCCCCHHHHHHHHHHHHcCCCeEEEEech-----h-h-cCCCccccc
Confidence            689999999999998888775     78899999998876655433   3467899999952     2 2 467888888


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       338 ~VI~  341 (591)
T 2v1x_A          338 FVIH  341 (591)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            8875

>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=92.66  E-value=0.013  Score=42.07  Aligned_cols=71  Identities=14%  Similarity=0.189  Sum_probs=51.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.++|++-+..+.+.+++.     ++.+..++|+.+..+....+   .++..+|||+|.     .+.  .++|+.+++
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            689999999998888877765     67888889887655444333   345688999993     222  468888888


Q ss_pred             EEEEcc
Q 028826           79 ILVLDE   84 (203)
Q Consensus        79 ~lViDE   84 (203)
                      ++|.-+
T Consensus       101 ~Vi~~~  106 (170)
T 2yjt_D          101 HVFNFD  106 (170)
Confidence            887633

>2eyq_A TRCF, transcription-repair coupling factor; MFD, SF2 ATPase, hydrolase; HET: EPE; 3.20A {Escherichia coli} SCOP: b.34.18.1 c.37.1.19 c.37.1.19 c.37.1.19 c.37.1.19 d.315.1.1

Probab=93.54  E-value=0.13  Score=47.96  Aligned_cols=77  Identities=14%  Similarity=0.201  Sum_probs=60.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      +++|++|+++-+..+.+.+++.   .|+.++..++|+.+..+....+   .++..+|||+|.     .+.  .++|+.++
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            3689999999888888887776   4578899999998766554433   357899999996     232  58999999


Q ss_pred             cEEEEcchhH
Q 028826           78 VILVLDEADR   87 (203)
Q Consensus        78 ~~lViDEad~   87 (203)
                      .++|+..+|.
T Consensus       884 ~~VIi~~~~~  893 (1151)
T 2eyq_A          884 NTIIIERADH  893 (1151)
T ss_dssp             EEEEETTTTS
T ss_pred             cEEEEeCCCC
Confidence            9999987764

>2v6i_A RNA helicase; membrane, hydrolase, transmembrane, RNA replication, viral replication, nucleotide-binding; 2.10A {Kokobera virus} PDB: 2v6j_A

Probab=92.93  E-value=0.21  Score=41.27  Aligned_cols=66  Identities=17%  Similarity=0.075  Sum_probs=48.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++-+..+++.+++.     ++++..++|+. ..+......++..+|||+|.-     +.  .++|+. +..+
T Consensus       173 ~~lVF~~~~~~~~~l~~~L~~~-----~~~v~~lhg~~-r~~~~~~f~~g~~~vLVaT~v-----~e--~GiDip-~~~V  238 (431)
T 2v6i_A          173 RTVWFVHSIKQGAEIGTCLQKA-----GKKVLYLNRKT-FESEYPKCKSEKWDFVITTDI-----SE--MGANFK-ADRV  238 (431)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHT-----TCCEEEESTTT-HHHHTTHHHHSCCSEEEECGG-----GG--TSCCCC-CSEE
T ss_pred             CEEEEeCCHHHHHHHHHHHHHc-----CCeEEEeCCcc-HHHHHHhhcCCCCeEEEECch-----HH--cCcccC-CcEE
Confidence            4799999999999988888776     67888888873 333444455678999999962     22  578876 6655

>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=92.84  E-value=0.32  Score=39.77  Aligned_cols=72  Identities=21%  Similarity=0.272  Sum_probs=52.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEc--------CcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVG--------GVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMD   70 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~--------g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~   70 (203)
                      +||++++++-+..+.+.+++.     ++++..++|        +.+..++..   ...++..+|||+|. .    +.  .
T Consensus       364 ~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~g~~~~~~~~~~~~~~r~~~~~~F~~~~~~vLv~T~-~----~~--~  431 (494)
T 1wp9_A          364 IIVFTNYRETAKKIVNELVKD-----GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATS-V----GE--E  431 (494)
T ss_dssp             EEEECSCHHHHHHHHHHHHHT-----TCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECG-G----GG--G
T ss_pred             EEEEEccHHHHHHHHHHHHHc-----CCCcEEEeccccccccccCCHHHHHHHHHHHhcCCceEEEECC-c----cc--c
Confidence            799999999999888888775     688888998        555443333   33346789999994 2    22  5


Q ss_pred             CccCCCccEEEEcch
Q 028826           71 VLDFRNLVILVLDEA   85 (203)
Q Consensus        71 ~~~l~~v~~lViDEa   85 (203)
                      ++|+..++++|+-+.
T Consensus       432 Gldl~~~~~Vi~~d~  446 (494)
T 1wp9_A          432 GLDVPEVDLVVFYEP  446 (494)
T ss_dssp             GGGSTTCCEEEESSC
T ss_pred             CCCchhCCEEEEeCC
Confidence            799999999986443

>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=92.37  E-value=0.29  Score=43.71  Aligned_cols=74  Identities=15%  Similarity=0.121  Sum_probs=55.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhh------cCCCceEEEEEcCcchHHHHHHHH--------hCCCeEEEeccHHHHHHHH
Q 028826            2 GMIISPTRELSAQIYHVAQPFIS------TLPDVKSMLLVGGVEVKADVKKIE--------EEGANLLIGTPGRLYDIME   67 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~------~~~~i~~~~~~~g~~~~~~~~~l~--------~~~~~ilV~Tp~~l~~~~~   67 (203)
                      +||++|+++-+.++.+.+.+...      ...++.+..++|+.+..++...+.        ++...|||+|.     .+.
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            69999999999999888876322      224889999999998776655442        23568999996     233


Q ss_pred             hCCCccCCCccEEEE
Q 028826           68 RMDVLDFRNLVILVL   82 (203)
Q Consensus        68 ~~~~~~l~~v~~lVi   82 (203)
                        .++++.++.++|-
T Consensus       381 --~GidIp~v~~VId  393 (773)
T 2xau_A          381 --TSLTIDGIVYVVD  393 (773)
T ss_dssp             --HTCCCTTEEEEEE
T ss_pred             --hCcCcCCeEEEEe
Confidence              4789999997774

>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=92.25  E-value=0.16  Score=42.16  Aligned_cols=67  Identities=6%  Similarity=0.035  Sum_probs=47.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++-+.++++.+++.     ++++..++|.. ..+......++..+|||+|.-     + . ..+|+. ++++
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-----GKSVVVLNRKT-FEREYPTIKQKKPDFILATDI-----A-E-MGANLC-VERV  244 (440)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHT-----TCCEEECCSSS-CC--------CCCSEEEESSS-----T-T-CCTTCC-CSEE
T ss_pred             CEEEEeCCHHHHHHHHHHHHHc-----CCCEEEecchh-HHHHHhhhcCCCceEEEECCh-----h-h-eeeccC-ceEE
Confidence            4799999999999998888775     67888888843 333444445678999999962     2 2 578988 8887


Q ss_pred             E
Q 028826           81 V   81 (203)
Q Consensus        81 V   81 (203)
                      |
T Consensus       245 I  245 (440)
T 1yks_A          245 L  245 (440)
T ss_dssp             E
T ss_pred             E
Confidence            7

>2oca_A DAR protein, ATP-dependent DNA helicase UVSW; ATP-dependant helicase, T4-bacteriophage, recombination, hydrolase; 2.70A {Enterobacteria phage T4}

Probab=92.15  E-value=0.55  Score=39.34  Aligned_cols=73  Identities=14%  Similarity=0.166  Sum_probs=51.3

Q ss_pred             EEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCccE
Q 028826            3 MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVI   79 (203)
Q Consensus         3 lil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~   79 (203)
                      +|+....+-+..+.+.+.+.     +.++..++|+.+..+...   ...++..+|+|+|+..+.      .++|+.++++
T Consensus       351 ~ivf~~~~~~~~l~~~L~~~-----~~~v~~~~g~~~~~~r~~i~~~f~~g~~~vLv~T~~~~~------~GiDip~v~~  419 (510)
T 2oca_A          351 FVMFKHVSHGKAIFDLIKNE-----YDKVYYVSGEVDTETRNIMKTLAENGKGIIIVASYGVFS------TGISVKNLHH  419 (510)
T ss_dssp             EEEESSHHHHHHHHHHHHTT-----CSSEEEESSSTTHHHHHHHHHHHHHCCSCEEEEEHHHHH------HSCCCCSEEE
T ss_pred             EEEEecHHHHHHHHHHHHHc-----CCCeEEEECCCCHHHHHHHHHHHhCCCCCEEEEEcChhh------cccccccCcE
Confidence            45555566565555555543     358888999887655443   233577899999976665      4789999999


Q ss_pred             EEEcchh
Q 028826           80 LVLDEAD   86 (203)
Q Consensus        80 lViDEad   86 (203)
                      +|+...+
T Consensus       420 vi~~~~~  426 (510)
T 2oca_A          420 VVLAHGV  426 (510)
T ss_dssp             EEESSCC
T ss_pred             EEEeCCC
Confidence            9998876

>3rc3_A ATP-dependent RNA helicase SUPV3L1, mitochondrial; SUV3, nucleus, hydrolase; HET: ANP; 2.08A {Homo sapiens} PDB: 3rc8_A

Probab=91.85  E-value=0.64  Score=40.87  Aligned_cols=74  Identities=11%  Similarity=0.182  Sum_probs=55.1

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHH---HHHHHHh--CCCeEEEeccHHHHHHHHhCCCccCCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKA---DVKKIEE--EGANLLIGTPGRLYDIMERMDVLDFRN   76 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~---~~~~l~~--~~~~ilV~Tp~~l~~~~~~~~~~~l~~   76 (203)
                      .+|+++|+.-+.++.+.+++.     ++++..++|+.+..+   ..+...+  +..+|||+|--     + . .++++ +
T Consensus       323 ~iIf~~s~~~ie~la~~L~~~-----g~~v~~lHG~L~~~~R~~~~~~F~~~~g~~~VLVATdi-----~-e-~GlDi-~  389 (677)
T 3rc3_A          323 DCIVCFSKNDIYSVSRQIEIR-----GLESAVIYGSLPPGTKLAQAKKFNDPNDPCKILVATDA-----I-G-MGLNL-S  389 (677)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHCTTSSCCEEEECGG-----G-G-SSCCC-C
T ss_pred             CEEEEcCHHHHHHHHHHHHhc-----CCCeeeeeccCCHHHHHHHHHHHHccCCCeEEEEeCcH-----H-H-CCcCc-C
Confidence            478899998888777777763     688999999988763   3333433  56899999972     2 2 68999 9


Q ss_pred             ccEEEEcchhHh
Q 028826           77 LVILVLDEADRL   88 (203)
Q Consensus        77 v~~lViDEad~l   88 (203)
                      ++++|.-...+.
T Consensus       390 v~~VI~~~~~k~  401 (677)
T 3rc3_A          390 IRRIIFYSLIKP  401 (677)
T ss_dssp             BSEEEESCSBC-
T ss_pred             ccEEEECCcccc
Confidence            999998777553

>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=91.11  E-value=0.21  Score=40.35  Aligned_cols=69  Identities=14%  Similarity=0.174  Sum_probs=46.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||++++++-+..+.+.+.+.     ++++..++|+.+..++...+   .++..+|||+|.-     +.  .++|+.+++
T Consensus       283 ~lvf~~~~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~vlv~T~~-----~~--~Gidip~v~  350 (414)
T 3eiq_A          283 AVIFINTRRKVDWLTEKMHAR-----DFTVSAMHGDMDQKERDVIMREFRSGSSRVLITTDL-----LA--RGIDVQQVS  350 (414)
T ss_dssp             CEEECSCHHHHHHHHHHHHTT-----TCCCEEC---CHHHHHHHHHHHHSCC---CEEECSS-----CC----CCGGGCS
T ss_pred             EEEEeCCHHHHHHHHHHHHhc-----CCeEEEecCCCCHHHHHHHHHHHHcCCCcEEEECCc-----cc--cCCCccCCC
Confidence            689999999999888877664     67888999998766555433   2456889999962     22  578888999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       351 ~Vi~  354 (414)
T 3eiq_A          351 LVIN  354 (414)
T ss_dssp             CEEE
T ss_pred             EEEE
Confidence            8875

>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=90.79  E-value=0.88  Score=39.55  Aligned_cols=66  Identities=14%  Similarity=0.144  Sum_probs=49.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||+++|++-+..+.+.+++.     ++++..++|. ...+..+...++..+|||+|.     .+.  ..+|+. ++++|
T Consensus       358 ~LVF~~s~~~a~~l~~~L~~~-----g~~v~~lhg~-~R~~~l~~F~~g~~~VLVaTd-----v~~--rGiDi~-v~~VI  423 (618)
T 2whx_A          358 TVWFVPSIKAGNDIANCLRKS-----GKRVIQLSRK-TFDTEYPKTKLTDWDFVVTTD-----ISE--MGANFR-AGRVI  423 (618)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTT-THHHHTTHHHHSCCSEEEECG-----GGG--TTCCCC-CSEEE
T ss_pred             EEEEECChhHHHHHHHHHHHc-----CCcEEEEChH-HHHHHHHhhcCCCcEEEEECc-----HHH--cCcccC-ceEEE
Confidence            799999999999988888775     6788888875 333344455567899999997     222  578884 87764

>3oiy_A Reverse gyrase helicase domain; topoisomerase, DNA supercoiling, archaea, isomeras; 2.35A {Thermotoga maritima} PDB: 3p4y_A 3p4x_A*

Probab=90.76  E-value=0.31  Score=39.70  Aligned_cols=69  Identities=19%  Similarity=0.227  Sum_probs=50.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEE-EEEcCcchHHHHHHHHhCCCeEEEe----ccHHHHHHHHhCCCccCC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSM-LLVGGVEVKADVKKIEEEGANLLIG----TPGRLYDIMERMDVLDFR   75 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~-~~~~g~~~~~~~~~l~~~~~~ilV~----Tp~~l~~~~~~~~~~~l~   75 (203)
                      .+||+++|++-|..+.+.+++.     ++++. .++|+ . .+ .....++..+|||+    |. .+     . .++|+.
T Consensus       254 ~~lVF~~~~~~~~~l~~~L~~~-----~~~~~~~~h~~-~-r~-~~~f~~g~~~vLvat~s~T~-~~-----~-~GiDip  318 (414)
T 3oiy_A          254 GILIFAQTEEEGKELYEYLKRF-----KFNVGETWSEF-E-KN-FEDFKVGKINILIGVQAYYG-KL-----T-RGVDLP  318 (414)
T ss_dssp             SEEEEESSHHHHHHHHHHHHHT-----TCCEEESSSCH-H-HH-HHHHHTTSCSEEEEECCTTC-CC-----C-CCCCCT
T ss_pred             CEEEEECCHHHHHHHHHHHHHc-----CCceehhhcCc-c-hH-HHHHhCCCCeEEEEecCcCc-hh-----h-ccCccc
Confidence            3799999999999888888775     67776 55554 2 22 55555678999999    54 22     1 679999


Q ss_pred             C-ccEEEEcc
Q 028826           76 N-LVILVLDE   84 (203)
Q Consensus        76 ~-v~~lViDE   84 (203)
                      + ++++|.-+
T Consensus       319 ~~v~~VI~~~  328 (414)
T 3oiy_A          319 ERIKYVIFWG  328 (414)
T ss_dssp             TTCCEEEEES
T ss_pred             cccCEEEEEC
Confidence            9 99988633

>2wv9_A Flavivirin protease NS2B regulatory subunit, FLAV protease NS3 catalytic subunit; nucleotide-binding, capsid protein; 2.75A {Murray valley encephalitis virus}

Probab=90.70  E-value=0.65  Score=40.81  Aligned_cols=67  Identities=13%  Similarity=0.088  Sum_probs=49.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++-+.++++.+++.     ++++..++|. ...+......++..+|||+|--     +.  ..+|+. ++++
T Consensus       412 ~~lVF~~s~~~~e~la~~L~~~-----g~~v~~lHg~-eR~~v~~~F~~g~~~VLVaTdv-----~e--~GIDip-v~~V  477 (673)
T 2wv9_A          412 KTVWFVASVKMSNEIAQCLQRA-----GKRVIQLNRK-SYDTEYPKCKNGDWDFVITTDI-----SE--MGANFG-ASRV  477 (673)
T ss_dssp             CEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSS-SHHHHGGGGGTCCCSEEEECGG-----GG--TTCCCC-CSEE
T ss_pred             CEEEEECCHHHHHHHHHHHHhC-----CCeEEEeChH-HHHHHHHHHHCCCceEEEECch-----hh--cceeeC-CcEE
Confidence            4799999999999888887765     6888888884 3333333344577899999952     22  578888 8887


Q ss_pred             E
Q 028826           81 V   81 (203)
Q Consensus        81 V   81 (203)
                      |
T Consensus       478 I  478 (673)
T 2wv9_A          478 I  478 (673)
T ss_dssp             E
T ss_pred             E
Confidence            6

>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=89.72  E-value=0.51  Score=41.39  Aligned_cols=63  Identities=8%  Similarity=0.135  Sum_probs=48.6

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++||++-+.++.+.+++.     ++++..++|+.+..+.    .+++.+|||+|.     .+.  ..+|+. ++++|
T Consensus       399 vLVFv~Tr~~ae~la~~L~~~-----g~~v~~lHG~l~q~er----~~~~~~VLVATd-----Vae--rGIDId-V~~VI  461 (666)
T 3o8b_A          399 HLIFCHSKKKCDELAAKLSGL-----GINAVAYYRGLDVSVI----PTIGDVVVVATD-----ALM--TGYTGD-FDSVI  461 (666)
T ss_dssp             EEEECSCHHHHHHHHHHHHTT-----TCCEEEECTTSCGGGS----CSSSCEEEEECT-----THH--HHCCCC-BSEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHhC-----CCcEEEecCCCCHHHH----HhCCCcEEEECC-----hHH--ccCCCC-CcEEE
Confidence            799999999999888888764     7889999999876542    245679999996     233  367774 88777

>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=89.60  E-value=1  Score=35.06  Aligned_cols=67  Identities=18%  Similarity=0.225  Sum_probs=47.6

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||++++++-+..+.+.++         ++..++|+.+..++...+   .++..+|+|+|.     .+.  .++|+.+++
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            6899999988776554332         456778887765554433   346789999995     333  579999999


Q ss_pred             EEEEcc
Q 028826           79 ILVLDE   84 (203)
Q Consensus        79 ~lViDE   84 (203)
                      ++|.-.
T Consensus       287 ~Vi~~~  292 (337)
T 2z0m_A          287 KVINFD  292 (337)
T ss_dssp             EEEESS
T ss_pred             EEEEec
Confidence            998743

>4a15_A XPD helicase, ATP-dependent DNA helicase TA0057; hydrolase, nucleotide excision repair,; 2.20A {Thermoplasma acidophilum} PDB: 2vsf_A*

Probab=88.97  E-value=0.26  Score=42.89  Aligned_cols=36  Identities=17%  Similarity=0.292  Sum_probs=31.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGV   38 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~   38 (203)
                      ++|++||++|+.|+.+++.++.... ++++..+.|+.
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            6899999999999999999998876 78888877754

>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=88.59  E-value=0.084  Score=44.05  Aligned_cols=69  Identities=19%  Similarity=0.241  Sum_probs=0.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||++||++-+..++..+.+.     +.++..++|+.+..++...+   .++..+|||+|.     .+.  .++|+.++.
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            689999999998888877765     67788889987765544332   346789999995     333  578999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       404 ~VI~  407 (479)
T 3fmp_B          404 VVIN  407 (479)
T ss_dssp             ----
T ss_pred             EEEE
Confidence            8873

>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=88.54  E-value=0.6  Score=38.77  Aligned_cols=66  Identities=14%  Similarity=0.129  Sum_probs=48.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++||++-|.++++.+++.     ++++..++|... .+..+...++..+|||+|.     .+.  .++|+.+ .++|
T Consensus       191 ~lVF~~s~~~a~~l~~~L~~~-----g~~~~~lh~~~~-~~~~~~f~~g~~~vLVaT~-----v~~--~GiDip~-~~VI  256 (451)
T 2jlq_A          191 TVWFVPSIKAGNDIANCLRKS-----GKRVIQLSRKTF-DTEYPKTKLTDWDFVVTTD-----ISE--MGANFRA-GRVI  256 (451)
T ss_dssp             EEEECSSHHHHHHHHHHHHTT-----TCCEEEECTTTH-HHHGGGGGSSCCSEEEECG-----GGG--SSCCCCC-SEEE
T ss_pred             EEEEcCCHHHHHHHHHHHHHc-----CCeEEECCHHHH-HHHHHhhccCCceEEEECC-----HHH--hCcCCCC-CEEE
Confidence            799999999999888888764     678888887654 3333344457899999996     222  5788888 6665

>3vkw_A Replicase large subunit; alpha/beta domain, helicase, transferase; 1.90A {Tomato mosaic virus}

Probab=88.11  E-value=1.4  Score=36.76  Aligned_cols=66  Identities=17%  Similarity=0.116  Sum_probs=37.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      .+|++||++++..+.+.+.+.+     ..                   .....-|.|-++++.  +. ........+.+|
T Consensus       187 ~lVlTpT~~aa~~l~~kl~~~~-----~~-------------------~~~~~~V~T~dsfL~--~~-~~~~~~~~d~li  239 (446)
T 3vkw_A          187 DLILVPGRQAAEMIRRRANASG-----II-------------------VATKDNVRTVDSFLM--NY-GKGARCQFKRLF  239 (446)
T ss_dssp             CEEEESCHHHHHHHHHHHTTTS-----CC-------------------CCCTTTEEEHHHHHH--TT-TSSCCCCCSEEE
T ss_pred             eEEEeCCHHHHHHHHHHhhhcC-----cc-------------------ccccceEEEeHHhhc--CC-CCCCCCcCCEEE
Confidence            3799999999988777664321     00                   011122455555431  11 222233588999


Q ss_pred             EcchhHhhhhchHH
Q 028826           82 LDEADRLLDMGFQK   95 (203)
Q Consensus        82 iDEad~l~~~~~~~   95 (203)
                      |||+- |++.++..
T Consensus       240 iDE~s-m~~~~~l~  252 (446)
T 3vkw_A          240 IDEGL-MLHTGCVN  252 (446)
T ss_dssp             EETGG-GSCHHHHH
T ss_pred             EeCcc-cCCHHHHH
Confidence            99996 55655433

>3tbk_A RIG-I helicase domain; DECH helicase, ATP binding, hydrolase; HET: ANP; 2.14A {Mus musculus}

Probab=86.32  E-value=1.4  Score=36.86  Aligned_cols=73  Identities=19%  Similarity=0.247  Sum_probs=45.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEc--------CcchHHHHHHH---Hh-CCCeEEEeccHHHHHHHHhC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVG--------GVEVKADVKKI---EE-EGANLLIGTPGRLYDIMERM   69 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~--------g~~~~~~~~~l---~~-~~~~ilV~Tp~~l~~~~~~~   69 (203)
                      +||.+++++-+..+.+.+++..... ++++..++|        +.+..++...+   .+ +..+|||+|.-     + . 
T Consensus       392 ~lVF~~~~~~~~~l~~~L~~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~R~~~~~~F~~~g~~~vLvaT~~-----~-~-  463 (555)
T 3tbk_A          392 TILFVKTRALVDALKKWIEENPALS-FLKPGILTGRGRTNRATGMTLPAQKCVLEAFRASGDNNILIATSV-----A-D-  463 (555)
T ss_dssp             EEEECSSHHHHHHHHHHHHHCGGGT-TCCEEECCC--------------------------CCSEEEECCC-----T-T-
T ss_pred             EEEEeCcHHHHHHHHHHHhhCcCcC-ceeeeEEEecCCcccccccCHHHHHHHHHHHhcCCCeeEEEEcch-----h-h-
Confidence            7999999999999999998874332 455555555        54444433322   23 56799999962     2 2 


Q ss_pred             CCccCCCccEEEE
Q 028826           70 DVLDFRNLVILVL   82 (203)
Q Consensus        70 ~~~~l~~v~~lVi   82 (203)
                      .++|+.+++++|.
T Consensus       464 ~GlDlp~v~~VI~  476 (555)
T 3tbk_A          464 EGIDIAECNLVIL  476 (555)
T ss_dssp             CCEETTSCSEEEE
T ss_pred             cCCccccCCEEEE
Confidence            6799999999986

>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=86.25  E-value=0.42  Score=41.74  Aligned_cols=74  Identities=24%  Similarity=0.302  Sum_probs=48.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhc-CCCceEEEEEcC--------cchHHHHHHH---HhCCCeEEEeccHHHHHHHHhC
Q 028826            2 GMIISPTRELSAQIYHVAQPFIST-LPDVKSMLLVGG--------VEVKADVKKI---EEEGANLLIGTPGRLYDIMERM   69 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~-~~~i~~~~~~~g--------~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~   69 (203)
                      +||.+++++.+..+.+.+++.... ..++++..++|+        .+..++...+   .++..+|||+|-     .+.  
T Consensus       403 ~IVF~~s~~~~~~l~~~L~~~~~l~~~g~~~~~lhg~~~~~~~~~~~~~eR~~~~~~F~~g~~~VLVaT~-----~~~--  475 (699)
T 4gl2_A          403 GIIFTKTRQSAYALSQWITENEKFAEVGVKAHHLIGAGHSSEFKPMTQNEQKEVISKFRTGKINLLIATT-----VAE--  475 (699)
T ss_dssp             EEEECSCHHHHHHHHHHHHSSCSCC-----CEECCCSCCCTTCCCCCHHHHHHHHHHHCC---CCSEEEC-----SCC--
T ss_pred             EEEEECcHHHHHHHHHHHHhCccccccCcceEEEECCCCccCCCCCCHHHHHHHHHHHhcCCCcEEEEcc-----ccc--
Confidence            799999999999999988874111 116888899998        6666555543   236789999995     222  


Q ss_pred             CCccCCCccEEEE
Q 028826           70 DVLDFRNLVILVL   82 (203)
Q Consensus        70 ~~~~l~~v~~lVi   82 (203)
                      .++|+.+++++|.
T Consensus       476 ~GIDip~v~~VI~  488 (699)
T 4gl2_A          476 EGLDIKECNIVIR  488 (699)
T ss_dssp             TTSCCCSCCCCEE
T ss_pred             cCCccccCCEEEE
Confidence            4677778877774

>4ddu_A Reverse gyrase; topoisomerase, DNA supercoiling, archaea, helicase, hydrolas; 3.00A {Thermotoga maritima} PDB: 4ddt_A 4ddv_A 4ddw_A 4ddx_A

Probab=85.96  E-value=1.1  Score=41.64  Aligned_cols=76  Identities=16%  Similarity=0.198  Sum_probs=53.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEE-EEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCC-cc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSM-LLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRN-LV   78 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~-~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~-v~   78 (203)
                      .+||++||++-+..+...+++.     ++++. .++|.  ..+ .....++..+|||+|+.. .+.+.  .++|+.+ ++
T Consensus       311 ~~LVF~~s~~~a~~l~~~L~~~-----g~~~~~~lhg~--rr~-l~~F~~G~~~VLVatas~-Tdvla--rGIDip~~V~  379 (1104)
T 4ddu_A          311 GILIFAQTEEEGKELYEYLKRF-----KFNVGETWSEF--EKN-FEDFKVGKINILIGVQAY-YGKLT--RGVDLPERIK  379 (1104)
T ss_dssp             SEEEEESSSHHHHHHHHHHHHT-----TCCEEESSSSH--HHH-HHHHHHTSCSEEEEETTT-HHHHC--CSCCCTTTCC
T ss_pred             CEEEEECcHHHHHHHHHHHHhC-----CCCeeeEecCc--HHH-HHHHHCCCCCEEEEecCC-CCeeE--ecCcCCCCCC
Confidence            4799999999999998888775     67777 66663  223 555557889999994210 01222  6899999 99


Q ss_pred             EEEEcchhH
Q 028826           79 ILVLDEADR   87 (203)
Q Consensus        79 ~lViDEad~   87 (203)
                      ++|.=++-.
T Consensus       380 ~VI~~d~P~  388 (1104)
T 4ddu_A          380 YVIFWGTPS  388 (1104)
T ss_dssp             EEEEESCCE
T ss_pred             EEEEECCCC
Confidence            998765443

>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=85.89  E-value=1.1  Score=41.08  Aligned_cols=74  Identities=14%  Similarity=0.173  Sum_probs=54.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCC--CeEEEeccHHHHHHHHhCCCccCCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEG--ANLLIGTPGRLYDIMERMDVLDFRN   76 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~--~~ilV~Tp~~l~~~~~~~~~~~l~~   76 (203)
                      +||++++++-+..+...+.+.   . ++++..++|+.+..+....+   .++.  ++|||+|. .+     . .++|+.+
T Consensus       506 ~iVF~~~~~~~~~l~~~L~~~---~-g~~~~~lhG~~~~~~R~~~l~~F~~g~~~~~vLvaT~-v~-----~-~GlDl~~  574 (968)
T 3dmq_A          506 VLVICAKAATALQLEQVLRER---E-GIRAAVFHEGMSIIERDRAAAWFAEEDTGAQVLLCSE-IG-----S-EGRNFQF  574 (968)
T ss_dssp             CCEECSSTHHHHHHHHHHHTT---T-CCCEEEECTTSCTTHHHHHHHHHHSTTSSCEEEECSC-CT-----T-CSSCCTT
T ss_pred             EEEEeCcHHHHHHHHHHHHHH---c-CCcEEEEeCCCCHHHHHHHHHHHhCCCCcccEEEecc-hh-----h-cCCCccc
Confidence            689999999888887777642   2 78899999998765544433   2344  99999993 32     2 6899999


Q ss_pred             ccEEEEcchh
Q 028826           77 LVILVLDEAD   86 (203)
Q Consensus        77 v~~lViDEad   86 (203)
                      +..+|+-+.+
T Consensus       575 ~~~VI~~d~p  584 (968)
T 3dmq_A          575 ASHMVMFDLP  584 (968)
T ss_dssp             CCEEECSSCC
T ss_pred             CcEEEEecCC
Confidence            9999986654

>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=84.52  E-value=1.2  Score=41.23  Aligned_cols=72  Identities=25%  Similarity=0.272  Sum_probs=50.3

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEec---cHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGT---PGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~T---p~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||+++|++-|..+.+.+++.      +++..++|+..  +..+...++..+|||+|   .+-+    .  .++|+.++
T Consensus       277 ~~LVF~~t~~~a~~l~~~L~~~------~~v~~lhg~~~--~~l~~F~~G~~~VLVaTas~Tdv~----~--rGIDip~V  342 (1054)
T 1gku_B          277 GGIIYARTGEEAEEIYESLKNK------FRIGIVTATKK--GDYEKFVEGEIDHLIGTAHYYGTL----V--RGLDLPER  342 (1054)
T ss_dssp             CEEEEESSHHHHHHHHHTTTTS------SCEEECTTSSS--HHHHHHHHTSCSEEEEECC------------CCSCCTTT
T ss_pred             CEEEEEcCHHHHHHHHHHHhhc------cCeeEEeccHH--HHHHHHHcCCCcEEEEecCCCCee----E--eccccCCc
Confidence            3799999999888776655543      67888888874  33444556789999995   2222    2  68999995


Q ss_pred             -cEEEEcchh
Q 028826           78 -VILVLDEAD   86 (203)
Q Consensus        78 -~~lViDEad   86 (203)
                       +++|.-.+.
T Consensus       343 I~~VI~~~~P  352 (1054)
T 1gku_B          343 IRFAVFVGCP  352 (1054)
T ss_dssp             CCEEEEESCC
T ss_pred             ccEEEEeCCC
Confidence             998876555

>2gno_A DNA polymerase III, gamma subunit-related protein; structural genomics, joint center for structural genomics, J protein structure initiative; HET: DNA; 2.00A {Thermotoga maritima} SCOP: a.80.1.1 c.37.1.20

Probab=82.90  E-value=15  Score=28.64  Aligned_cols=89  Identities=11%  Similarity=0.129  Sum_probs=48.5

Q ss_pred             ceEEEEEcCcch--HHHHHHHHh-------CCCeEEEeccHH-------HHHHHHhC-CCccCCCccEEEEcchhHhhhh
Q 028826           29 VKSMLLVGGVEV--KADVKKIEE-------EGANLLIGTPGR-------LYDIMERM-DVLDFRNLVILVLDEADRLLDM   91 (203)
Q Consensus        29 i~~~~~~~g~~~--~~~~~~l~~-------~~~~ilV~Tp~~-------l~~~~~~~-~~~~l~~v~~lViDEad~l~~~   91 (203)
                      .....++|-...  ..-...+.+       ..++++.-.|+.       +.+++... ......+-+++|+||||.|-..
T Consensus        18 ~~~~Lf~Gp~G~GKtt~a~~la~~~~~~~~~~~d~~~l~~~~~~~~id~ir~li~~~~~~p~~~~~kvviIdead~lt~~   97 (305)
T 2gno_A           18 GISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQQ   97 (305)
T ss_dssp             SEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCHH
T ss_pred             CcEEEEECCCCCCHHHHHHHHHHhCchhhccCCCEEEEcCCcCCCCHHHHHHHHHHHhhccccCCceEEEeccHHHhCHH
Confidence            567777775432  222333322       257888877641       33444331 1223456899999999998544


Q ss_pred             chHHHHHHHHHhCCCCCcEEEEeeecCh
Q 028826           92 GFQKQISYIISRLPKLRRTGLFSATQTE  119 (203)
Q Consensus        92 ~~~~~~~~il~~~~~~~q~i~~SAT~~~  119 (203)
                      . ...+...++.-|...-+++. ++-+.
T Consensus        98 a-~naLLk~LEep~~~t~fIl~-t~~~~  123 (305)
T 2gno_A           98 A-ANAFLKALEEPPEYAVIVLN-TRRWH  123 (305)
T ss_dssp             H-HHHTHHHHHSCCTTEEEEEE-ESCGG
T ss_pred             H-HHHHHHHHhCCCCCeEEEEE-ECChH
Confidence            3 33455555555544444444 34443

>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=82.87  E-value=0.24  Score=39.68  Aligned_cols=69  Identities=10%  Similarity=0.176  Sum_probs=0.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||++++++-+..+.+.+++.     ++.+..++|+.+..++...+   .++..+|+|+|.     .+.  .++|+.+++
T Consensus       262 ~lVf~~~~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~~~~f~~~~~~vlv~T~-----~~~--~Gldi~~~~  329 (394)
T 1fuu_A          262 AVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTD-----LLA--RGIDVQQVS  329 (394)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             EEEEECCHHHHHHHHHHHHHc-----CCeEEEeeCCCCHHHHHHHHHHHHCCCCcEEEECC-----hhh--cCCCcccCC
Confidence            689999999888887777664     67788888887655444322   345678999985     232  478888888


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       330 ~Vi~  333 (394)
T 1fuu_A          330 LVIN  333 (394)
T ss_dssp             ----
T ss_pred             EEEE
Confidence            8875

>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=82.65  E-value=6.5  Score=36.35  Aligned_cols=36  Identities=8%  Similarity=0.119  Sum_probs=28.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhh-------cCCCceEEEEEcC
Q 028826            2 GMIISPTRELSAQIYHVAQPFIS-------TLPDVKSMLLVGG   37 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~-------~~~~i~~~~~~~g   37 (203)
                      |+|+|+|++-|...++.+.++.+       ...++++..+++|
T Consensus       540 amVf~~S~~~A~~~~~~l~~~~~~~~~~~~~~~~~k~avv~s~  582 (1038)
T 2w00_A          540 AMLAVSSVDAAKAYYATFKRLQEEAANKSATYKPLRIATIFSF  582 (1038)
T ss_dssp             EEEEESSHHHHHHHHHHHHHHHHHHTTTSSSCCCCCEEEECCC
T ss_pred             EEEEECCHHHHHHHHHHHHhhhhhhcccccccccCcEEEEEeC
Confidence            79999999999999999999863       2235777666554

>2ykg_A Probable ATP-dependent RNA helicase DDX58; hydrolase, innate immunity; 2.50A {Homo sapiens} PDB: 3tmi_A*

Probab=82.19  E-value=0.66  Score=40.49  Aligned_cols=76  Identities=20%  Similarity=0.234  Sum_probs=42.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEc--------CcchHHHHHHH---Hh-CCCeEEEeccHHHHHHHHhC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVG--------GVEVKADVKKI---EE-EGANLLIGTPGRLYDIMERM   69 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~--------g~~~~~~~~~l---~~-~~~~ilV~Tp~~l~~~~~~~   69 (203)
                      +||.+++++-+..+.+.+++.... +++++..++|        |.+..++...+   .+ +..+|||+|--     + . 
T Consensus       401 ~IIF~~~~~~~~~l~~~L~~~~~~-~~~~~~~l~G~~~~~~h~~~~~~eR~~v~~~F~~~g~~~vLVaT~v-----~-~-  472 (696)
T 2ykg_A          401 TILFVKTRALVDALKNWIEGNPKL-SFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSV-----A-D-  472 (696)
T ss_dssp             EEEECSCHHHHHHHHHHHHHCTTC-CSCCEEC-----------------------------CCSCSEEEES-----S-C-
T ss_pred             EEEEeCcHHHHHHHHHHHHhCCCc-cccceeEEEccCCCccccCCCHHHHHHHHHHHHhcCCccEEEEech-----h-h-
Confidence            799999999999999998886422 2478888865        65554444433   23 56799999942     2 2 


Q ss_pred             CCccCCCccEEEEcch
Q 028826           70 DVLDFRNLVILVLDEA   85 (203)
Q Consensus        70 ~~~~l~~v~~lViDEa   85 (203)
                      .++|+.+++++|.-+.
T Consensus       473 ~GiDip~v~~VI~~d~  488 (696)
T 2ykg_A          473 EGIDIAQCNLVILYEY  488 (696)
T ss_dssp             CC---CCCSEEEEESC
T ss_pred             cCCcCccCCEEEEeCC
Confidence            5789999999886443

>3bos_A Putative DNA replication factor; P-loop containing nucleoside triphosphate hydrolases, struct genomics; HET: MSE CDP; 1.75A {Shewanella amazonensis} PDB: 3sc3_A

Probab=82.08  E-value=7.8  Score=28.16  Aligned_cols=99  Identities=14%  Similarity=0.124  Sum_probs=47.9

Q ss_pred             HHHHHhhhcCCCceEEEEEcC--cchHHHHHHH----HhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEEcchhHhhh
Q 028826           17 HVAQPFISTLPDVKSMLLVGG--VEVKADVKKI----EEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLD   90 (203)
Q Consensus        17 ~~~~~l~~~~~~i~~~~~~~g--~~~~~~~~~l----~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lViDEad~l~~   90 (203)
                      ..++.+.... ..+...++|.  .....-.+.+    ...+..++..+...+...+.. ..-.+.+-.++++||+|.+..
T Consensus        41 ~~l~~~~~~~-~~~~~ll~G~~G~GKT~la~~l~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~vliiDe~~~~~~  118 (242)
T 3bos_A           41 GALKSAASGD-GVQAIYLWGPVKSGRTHLIHAACARANELERRSFYIPLGIHASISTA-LLEGLEQFDLICIDDVDAVAG  118 (242)
T ss_dssp             HHHHHHHHTC-SCSEEEEECSTTSSHHHHHHHHHHHHHHTTCCEEEEEGGGGGGSCGG-GGTTGGGSSEEEEETGGGGTT
T ss_pred             HHHHHHHhCC-CCCeEEEECCCCCCHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHH-HHHhccCCCEEEEeccccccC
Confidence            3444443332 3456677763  3333333322    223456666666554432221 111235568999999998854


Q ss_pred             hc-hHHHHHHHHHhCCC-CCcEEEEeeec
Q 028826           91 MG-FQKQISYIISRLPK-LRRTGLFSATQ  117 (203)
Q Consensus        91 ~~-~~~~~~~il~~~~~-~~q~i~~SAT~  117 (203)
                      .. ....+..++..... ....++++++.
T Consensus       119 ~~~~~~~l~~~l~~~~~~~~~~ii~~~~~  147 (242)
T 3bos_A          119 HPLWEEAIFDLYNRVAEQKRGSLIVSASA  147 (242)
T ss_dssp             CHHHHHHHHHHHHHHHHHCSCEEEEEESS
T ss_pred             CHHHHHHHHHHHHHHHHcCCCeEEEEcCC
Confidence            32 24444455444322 23324444443

>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=81.76  E-value=0.77  Score=38.23  Aligned_cols=67  Identities=13%  Similarity=0.060  Sum_probs=45.8

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||++-+..+.+.+++.     ++++..++|... ........++..+|||+|--     +.  .++|+.+ +++
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-DTEYPKCKNGDWDFVITTDI-----SE--MGANFGA-SRV  257 (459)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHT-----TCCEEEESTTCC-CCCGGGSSSCCCSEEEESSC-----C-----CCCSC-SEE
T ss_pred             CEEEEeCChHHHHHHHHHHHhc-----CCcEEecCHHHH-HHHHhhccCCCceEEEECCh-----HH--hCeecCC-CEE
Confidence            3799999999999998888775     678888887532 22222333467899999962     22  4788887 665


Q ss_pred             E
Q 028826           81 V   81 (203)
Q Consensus        81 V   81 (203)
                      |
T Consensus       258 I  258 (459)
T 2z83_A          258 I  258 (459)
T ss_dssp             E
T ss_pred             E
Confidence            5

>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=81.59  E-value=5.2  Score=35.15  Aligned_cols=74  Identities=9%  Similarity=0.098  Sum_probs=51.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcC-------------C---------------CceEEEEEcCcchHHHHHH---HHh
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTL-------------P---------------DVKSMLLVGGVEVKADVKK---IEE   49 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~-------------~---------------~i~~~~~~~g~~~~~~~~~---l~~   49 (203)
                      .+||++|||+-+..+...+.+.....             .               ...+..++||.+..++...   ..+
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            47999999999998888887643210             0               1248888999887665542   334


Q ss_pred             CCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826           50 EGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus        50 ~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +..+|||+|.--     .  .++|+..+.++|
T Consensus       319 g~~~vlvaT~~l-----~--~Gvdip~~~~VI  343 (720)
T 2zj8_A          319 GIIKAVVATPTL-----S--AGINTPAFRVII  343 (720)
T ss_dssp             TSSCEEEECSTT-----G--GGCCCCBSEEEE
T ss_pred             CCCeEEEECcHh-----h--ccCCCCceEEEE
Confidence            678999999622     2  478888887644

>2va8_A SSO2462, SKI2-type helicase; hydrolase, DNA repair, ATP-bindin nucleotide-binding; 2.30A {Sulfolobus solfataricus}

Probab=80.64  E-value=6.7  Score=34.33  Aligned_cols=75  Identities=7%  Similarity=0.100  Sum_probs=52.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhc--CC-----------------------------CceEEEEEcCcchHHHHHHH--
Q 028826            1 MGMIISPTRELSAQIYHVAQPFIST--LP-----------------------------DVKSMLLVGGVEVKADVKKI--   47 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~--~~-----------------------------~i~~~~~~~g~~~~~~~~~l--   47 (203)
                      .+||++|+++-+.++...+.+....  ++                             +..+..++||.+..++....  
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            3799999999999888888764321  00                             13478899998876555432  


Q ss_pred             -HhCCCeEEEeccHHHHHHHHhCCCccCCCccEEEE
Q 028826           48 -EEEGANLLIGTPGRLYDIMERMDVLDFRNLVILVL   82 (203)
Q Consensus        48 -~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lVi   82 (203)
                       .++..+|||+|.--     .  .++++..+.++|-
T Consensus       334 f~~g~~~vlvaT~~l-----~--~Gidip~~~~VI~  362 (715)
T 2va8_A          334 FRQRKIKVIVATPTL-----A--AGVNLPARTVIIG  362 (715)
T ss_dssp             HHTTCSCEEEECGGG-----G--GSSCCCBSEEEEC
T ss_pred             HHcCCCeEEEEChHH-----h--cccCCCceEEEEe
Confidence             34678999999622     2  5788888887653

---

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	203
d1hv8a1	208	c.37.1.19 (A:3-210) Putative DEAD box RNA helicase	3e-33
d1t6na_	207	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	3e-25
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 (	1e-21
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	5e-18
d1wrba1	238	c.37.1.19 (A:164-401) putative ATP-dependent RNA h	1e-16
d1s2ma1	206	c.37.1.19 (A:46-251) Putative ATP-dependent RNA he	7e-16
d1q0ua_	209	c.37.1.19 (A:) Probable DEAD box RNA helicase YqfR	2e-14
d1gkub1	237	c.37.1.16 (B:1-250) Helicase-like "domain" of reve	2e-10
d1oywa2	206	c.37.1.19 (A:1-206) RecQ helicase domain {Escheric	4e-08
d2bmfa2	305	c.37.1.14 (A:178-482) Dengue virus helicase {Dengu	6e-08
d1wp9a1	200	c.37.1.19 (A:1-200) putative ATP-dependent RNA hel	9e-07
d2p6ra3	202	c.37.1.19 (A:1-202) Hel308 helicase {Archaeoglobus	5e-06
d1t5ia_	168	c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP5	0.002

>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 (291), Expect = 3e-33
 Identities = 39/138 (28%), Positives = 69/138 (50%), Gaps = 3/138 (2%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
           +  II       A         +    ++K   + GG  +   +K ++   AN+++GTPG
Sbjct: 73  IEAIILTPTRELAIQVADEIESLKGNKNLKIAKIYGGKAIYPQIKALK--NANIVVGTPG 130

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           R+ D + R   L+ +N+   +LDEAD +L+MGF K +  I++   K +R  LFSAT    
Sbjct: 131 RILDHINR-GTLNLKNVKYFILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPRE 189

Query: 121 VEELSKAGLRNPVRIEVR 138
           +  L+K  + +   I+ +
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 = 95.7 bits (237), Expect = 3e-25
 Identities = 34/136 (25%), Positives = 78/136 (57%), Gaps = 2/136 (1%)

Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +++  TREL+ QI    + F   +P+VK  +  GG+ +K D + +++   ++++GTPGR+
Sbjct: 73  LVMCHTRELAFQISKEYERFSKYMPNVKVAVFFGGLSIKKDEEVLKKNCPHIVVGTPGRI 132

Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
             +      L+ +++   +LDE D++L+ +  ++ +  I    P  ++  +FSAT ++ +
Sbjct: 133 LALARNK-SLNLKHIKHFILDECDKMLEQLDMRRDVQEIFRMTPHEKQVMMFSATLSKEI 191

Query: 122 EELSKAGLRNPVRIEV 137
             + +  +++P+ I 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 = 90.3 bits (223), Expect = 3e-23
 Identities = 34/88 (38%), Positives = 52/88 (59%), Gaps = 1/88 (1%)

Query: 50  EGANLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRR 109
             A +++GTPGR++D ++R        + + +LDEAD +L  GF++QI  I + LP   +
Sbjct: 126 RDAQIVVGTPGRVFDNIQRR-RFRTDKIKMFILDEADEMLSSGFKEQIYQIFTLLPPTTQ 184

Query: 110 TGLFSATQTEAVEELSKAGLRNPVRIEV 137
             L SAT    V E++   +RNPVRI 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 = 86.1 bits (212), Expect = 1e-21
 Identities = 48/137 (35%), Positives = 80/137 (58%), Gaps = 2/137 (1%)

Query: 2   GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGR 61
            ++++PTREL+ QI  V                +GG  V+A+V+K++ E  ++++GTPGR
Sbjct: 83  ALVLAPTRELAQQIQKVVMALGDY-MGASCHACIGGTNVRAEVQKLQMEAPHIIVGTPGR 141

Query: 62  LYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAV 121
           ++D++ R   L  + + + VLDEAD +L  GF+ QI  I  +L    +  L SAT    V
Sbjct: 142 VFDMLNRRY-LSPKYIKMFVLDEADEMLSRGFKDQIYDIFQKLNSNTQVVLLSATMPSDV 200

Query: 122 EELSKAGLRNPVRIEVR 138
            E++K  +R+P+RI 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 = 83.7 bits (206), Expect = 1e-20
 Identities = 48/138 (34%), Positives = 79/138 (57%), Gaps = 3/138 (2%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             +I++PTREL+ QI            +V+    +GG  V  D++K++  G +++ GTPG
Sbjct: 87  QALILAPTRELAVQIQKGLLAL-GDYMNVQCHACIGGTNVGEDIRKLDY-GQHVVAGTPG 144

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           R++D M R   L  R + +LVLDEAD +L+ GF++QI  +   LP   +  L SAT    
Sbjct: 145 RVFD-MIRRRSLRTRAIKMLVLDEADEMLNKGFKEQIYDVYRYLPPATQVVLISATLPHE 203

Query: 121 VEELSKAGLRNPVRIEVR 138
           + E++   + +P+RI 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 = 76.2 bits (186), Expect = 5e-18
 Identities = 42/135 (31%), Positives = 71/135 (52%), Gaps = 2/135 (1%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             M+I PTREL+ Q+  +       +   K M   GG  ++ D+ ++++    + I TPG
Sbjct: 73  QAMVIVPTRELALQVSQICIQVSKHMGGAKVMATTGGTNLRDDIMRLDDTVHVV-IATPG 131

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA 120
           R+ D++++          ++VLDEAD+LL   F + +  II  LPK R+  L+SAT   +
Sbjct: 132 RILDLIKKGVAKVDHVQ-MIVLDEADKLLSQDFVQIMEDIILTLPKNRQILLYSATFPLS 190

Query: 121 VEELSKAGLRNPVRI 135
           V++   + L  P  I
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 = 73.4 bits (179), Expect = 1e-16
 Identities = 50/139 (35%), Positives = 83/139 (59%), Gaps = 7/139 (5%)

Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTREL+ QI   +Q F    P ++S ++ GG +  + +++++  G +LL+ TPGRL
Sbjct: 102 LILAPTRELAIQILSESQKFSLNTP-LRSCVVYGGADTHSQIREVQM-GCHLLVATPGRL 159

Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRL----PKLRRTGLFSATQT 118
            D +E+   +       +VLDEADR+LDMGF+ QI  II          R+T +FSAT  
Sbjct: 160 VDFIEKN-KISLEFCKYIVLDEADRMLDMGFEPQIRKIIEESNMPSGINRQTLMFSATFP 218

Query: 119 EAVEELSKAGLRNPVRIEV 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 = 70.8 bits (172), Expect = 7e-16
 Identities = 29/85 (34%), Positives = 45/85 (52%), Gaps = 1/85 (1%)

Query: 53  NLLIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGL 112
           ++L+GTPGR    +    V D  +  + ++DEAD++L   F+  I  I+S LP   ++ L
Sbjct: 121 HILVGTPGR-VLDLASRKVADLSDCSLFIMDEADKMLSRDFKTIIEQILSFLPPTHQSLL 179

Query: 113 FSATQTEAVEELSKAGLRNPVRIEV 137
           FSAT    V+E     L  P  I +
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 = 66.6 bits (161), Expect = 2e-14
 Identities = 28/83 (33%), Positives = 42/83 (50%)

Query: 55  LIGTPGRLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFS 114
           ++       +   R   LD     ILV+DEAD +LDMGF   +  I +R+PK  +  +FS
Sbjct: 126 IVIGTPGRINDFIREQALDVHTAHILVVDEADLMLDMGFITDVDQIAARMPKDLQMLVFS 185

Query: 115 ATQTEAVEELSKAGLRNPVRIEV 137
           AT  E ++   K  + NP  + 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 = 56.1 bits (134), Expect = 2e-10
 Identities = 17/137 (12%), Positives = 38/137 (27%), Gaps = 20/137 (14%)

Query: 3   MIISPTRELSAQIYHVAQPFISTLP----DVKSMLLVGGVEVKADVKKIEEEGANLLIGT 58
            +I PT  L  Q     + +         ++         + + +          ++I T
Sbjct: 90  YVIFPTSLLVIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITT 149

Query: 59  PGRLYDIMERMDVLDFRNLVILVLDEADRLLD-----------MGFQKQISYIISRLPKL 107
              L      +   DF     + +D+ D +L            +GF   +          
Sbjct: 150 TQFLSKHYRELGHFDF-----IFVDDVDAILKASKNVDKLLHLLGFHYDLKTKSWVGEAR 204

Query: 108 RRTGLFSATQTEAVEEL 124
               + +AT  +  +  
Sbjct: 205 GCLMVSTATAKKGKKAE 221

>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 = 49.2 bits (116), Expect = 4e-08
 Identities = 27/142 (19%), Positives = 48/142 (33%), Gaps = 12/142 (8%)

Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +++SP   L        Q        + S       +    +         LL   P RL
Sbjct: 69  VVVSPLISLMKDQVDQLQANGVAAACLNSTQTRE--QQLEVMTGCRTGQIRLLYIAPERL 126

Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISY-----IISRLPKLRRTGLFSATQ 117
                 ++ L   N V+L +DEA  +   G   +  Y     +  R P        +AT 
Sbjct: 127 ML-DNFLEHLAHWNPVLLAVDEAHCISQWGHDFRPEYAALGQLRQRFPT-LPFMALTATA 184

Query: 118 TEAVEE--LSKAGLRNPVRIEV 137
            +   +  +   GL +P+ I++
Sbjct: 185 DDTTRQDIVRLLGLNDPL-IQI 205

>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 = 6e-08
 Identities = 11/123 (8%), Positives = 36/123 (29%), Gaps = 15/123 (12%)

Query: 3   MIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRL 62
           +I++PTR ++A++              +++  +        ++        + +      
Sbjct: 42  LILAPTRVVAAEME-------------EALRGLPIRYQTPAIRAEHTGREIVDLMCHATF 88

Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
              +     +   N  ++++DEA          +                 +AT   + +
Sbjct: 89  TMRLLSP--IRVPNYNLIIMDEAHFTDPASIAARGYISTRVEMGEAAGIFMTATPPGSRD 146

Query: 123 ELS 125
              
Sbjct: 147 PFP 149

>d1wp9a1 c.37.1.19 (A:1-200) putative ATP-dependent RNA helicase PF2015 {Pyrococcus furiosus [TaxId: 2261]} Length = 200

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: putative ATP-dependent RNA helicase PF2015
species: Pyrococcus furiosus [TaxId: 2261]

 Score = 45.5 bits (106), Expect = 9e-07
 Identities = 14/81 (17%), Positives = 29/81 (35%), Gaps = 1/81 (1%)

Query: 63  YDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVE 122
            +       +   ++ ++V DEA R +       I+    R  K       +A+     E
Sbjct: 112 IENDLLAGRISLEDVSLIVFDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPE 171

Query: 123 ELSK-AGLRNPVRIEVRAESK 142
           ++ +         IE 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 = 43.0 bits (100), Expect = 5e-06
 Identities = 18/129 (13%), Positives = 48/129 (37%), Gaps = 11/129 (8%)

Query: 1   MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPG 60
             + + P R L+ + Y   + +       K  L +G      + +       ++++ T  
Sbjct: 70  KSLYVVPLRALAGEKYESFKKWE------KIGLRIGISTGDYESRDEHLGDCDIIVTTSE 123

Query: 61  RLYDIMERMDVLDFRNLVILVLDEADRLLDMGFQKQISYIISRLPKL---RRTGLFSATQ 117
           +   ++        + +  LV+DE   L        +  +++++ ++    R    SAT 
Sbjct: 124 KADSLIRNRA-SWIKAVSCLVVDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATA 182

Query: 118 TEAVEELSK 126
                E+++
Sbjct: 183 PNV-TEIAE 190

>d1t5ia_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]} Length = 168

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.0 bits (79), Expect = 0.002
 Identities = 9/35 (25%), Positives = 22/35 (62%)

Query: 161 GLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQ 195
           GL   Y++ + ++K  +L DLL   +  +++++V+
Sbjct: 1   GLQQYYVKLKDNEKNRKLFDLLDVLEFNQVVIFVK 35

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	203
d2j0sa1	222	Probable ATP-dependent RNA helicase DDX48 {Human (	100.0
d1t6na_	207	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	99.97
d1veca_	206	DEAD box RNA helicase rck/p54 {Human (Homo sapiens	99.97
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	99.96
d1wrba1	238	putative ATP-dependent RNA helicase VlgB {Flatworm	99.96
d1s2ma1	206	Putative ATP-dependent RNA helicase DHH1 {Baker's	99.96
d1q0ua_	209	Probable DEAD box RNA helicase YqfR {Bacillus stea	99.91
d1gkub1	237	Helicase-like "domain" of reverse gyrase {Archaeon	99.7
d2p6ra3	202	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	99.67
d1wp9a1	200	putative ATP-dependent RNA helicase PF2015 {Pyroco	99.67
d1oywa2	206	RecQ helicase domain {Escherichia coli [TaxId: 562	99.59
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	99.57
d2eyqa3	233	Transcription-repair coupling factor, TRCF {Escher	99.31
d1gm5a3	264	RecG helicase domain {Thermotoga maritima [TaxId:	99.26
d1rifa_	282	DNA helicase UvsW {Bacteriophage T4 [TaxId: 10665]	99.2
d1yksa1	140	YFV helicase domain {Yellow fever virus [TaxId: 11	99.09
d1a1va1	136	HCV helicase domain {Human hepatitis C virus (HCV)	98.96
d2fz4a1	206	DNA repair protein RAD25 {Archaeoglobus fulgidus [	98.9
d1z3ix2	298	Rad54-like, Rad54L {Zebra fish (Danio rerio) [TaxI	98.17
d1c4oa2	174	Nucleotide excision repair enzyme UvrB {Thermus th	97.4
d1nkta3	288	Translocation ATPase SecA, nucleotide-binding doma	97.29
d1tf5a3	273	Translocation ATPase SecA, nucleotide-binding doma	97.28
d2eyqa5	211	Transcription-repair coupling factor, TRCF {Escher	97.12
d1t5la2	181	Nucleotide excision repair enzyme UvrB {Bacillus c	96.82
d1fuka_	162	Initiation factor 4a {Baker's yeast (Saccharomyces	96.6
d1z63a1	230	Helicase of the SNF2/Rad54 hamily {Sulfolobus solf	96.59
d1hv8a2	155	Putative DEAD box RNA helicase {Archaeon Methanoco	96.42
d1s2ma2	171	Putative ATP-dependent RNA helicase DHH1 {Baker's	96.36
d1t5ia_	168	Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo	96.31
d1oywa3	200	RecQ helicase domain {Escherichia coli [TaxId: 562	96.17
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	95.71
d2j0sa2	168	Probable ATP-dependent RNA helicase DDX48 {Human (	95.7
d2rb4a1	168	ATP-dependent RNA helicase DDX25 {Human (Homo sapi	95.6
d1jr6a_	138	HCV helicase domain {Human hepatitis C virus (HCV)	95.24
d1l8qa2	213	Chromosomal replication initiation factor DnaA {Aq	94.16
d2p6ra4	201	Hel308 helicase {Archaeoglobus fulgidus [TaxId: 22	92.51
d1yksa2	299	YFV helicase domain {Yellow fever virus [TaxId: 11	91.85
d1gm5a4	206	RecG helicase domain {Thermotoga maritima [TaxId:	90.71
d2gnoa2	198	gamma subunit of DNA polymerase III, N-domain {The	89.19
d1wp9a2	286	putative ATP-dependent RNA helicase PF2015 {Pyroco	89.0
d1gkub2	248	Helicase-like "domain" of reverse gyrase {Archaeon	87.35
d1g5ta_	157	ATP:corrinoid adenosyltransferase CobA {Salmonella	86.53
d1a1va2	299	HCV helicase domain {Human hepatitis C virus (HCV)	85.91
d2bmfa2	305	Dengue virus helicase {Dengue virus type 2 [TaxId:	84.29
d1njfa_	239	delta prime subunit of DNA polymerase III, N-domai	83.71
d2fwra1	200	DNA repair protein RAD25 {Archaeoglobus fulgidus [	82.22

>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=3.4e-33  Score=213.22  Aligned_cols=135  Identities=35%  Similarity=0.601  Sum_probs=127.8

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +|+|++||||||.|+++++++++++. ++++..+.||....++...+ +.++||+||||+|+.+++.. +.+++++++++
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            58999999999999999999999877 89999999999988888887 46799999999999999988 88999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEec
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVR  138 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~  138 (203)
                      |+||||.|++.||.+++..+++.+|+.+|+++||||+|+++.++++.++++|+.|.+.
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            9999999999999999999999999999999999999999999999999999988764

>d1t6na_ c.37.1.19 (A:) Spliceosome RNA helicase BAT1 (UAP56) {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: Spliceosome RNA helicase BAT1 (UAP56)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=2.1e-31  Score=201.47  Aligned_cols=136  Identities=25%  Similarity=0.531  Sum_probs=127.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +++|++||||||.|+++.++.++.+.+.+++..+.||.+...+...+...++||+||||+++.++++. +.+++++++++
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            48999999999999999999999988778899999999988888888778999999999999999998 88999999999


Q ss_pred             EEcchhHhhh-hchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEe
Q 028826           81 VLDEADRLLD-MGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEV  137 (203)
Q Consensus        81 ViDEad~l~~-~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~  137 (203)
                      |+||||.|++ .+|.+++..+++.+++.+|+++||||+|++++++++.++++|+.|.+
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            9999999997 48999999999999999999999999999999999999999988754

>d1veca_ c.37.1.19 (A:) DEAD box RNA helicase rck/p54 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DEAD box RNA helicase rck/p54
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=3.4e-31  Score=200.18  Aligned_cols=133  Identities=32%  Similarity=0.567  Sum_probs=124.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ++||++||+|||.|+++++.++.+...++.+....||.....+...+ ..+++|+||||+|+.+++.. +.+++++++++
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            48999999999999999999998877778888888888887777766 67899999999999999998 88999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEE
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRI  135 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i  135 (203)
                      |+||||.|++.+|.+++..|++.+++++|+++||||+|+++.++++.++++|+.|
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            9999999999999999999999999999999999999999999999999999876

>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=2.9e-31  Score=202.13  Aligned_cols=136  Identities=35%  Similarity=0.609  Sum_probs=123.5

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +|||++||+|||.|++++++++.+.. ++++..+.+|....++......+++||+||||+++.+++.. +...+++++++
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            58999999999999999999999888 78888888887766555554456899999999999999998 88999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEec
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVR  138 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~  138 (203)
                      |+||||.|++.+|.+.+..+++.+++++|+++||||+|+++.++++.++++|..|.+.
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            9999999999999999999999999999999999999999999999999999998774

>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=1.4e-30  Score=197.08  Aligned_cols=134  Identities=32%  Similarity=0.550  Sum_probs=125.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      ++||++||++||.|+++.++++.... +.++....|+.+..++.+.+  .++||+||||+++.++++. +.+++++++++
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            58999999999999999999999877 89999999999888887766  3699999999999999998 88999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEec
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVR  138 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~  138 (203)
                      |+||||.|++.++.+++..+++.+++++|++++|||+|+++.+++++++++|..|++.
T Consensus       150 ViDEad~l~~~~~~~~i~~I~~~~~~~~Q~i~~SAT~~~~v~~~~~~~l~~~~~I~~~  207 (208)
T d1hv8a1         150 ILDEADEMLNMGFIKDVEKILNACNKDKRILLFSATMPREILNLAKKYMGDYSFIKAK  207 (208)
T ss_dssp             EEETHHHHHTTTTHHHHHHHHHTSCSSCEEEEECSSCCHHHHHHHHHHCCSEEEEECC
T ss_pred             EEEChHHhhcCCChHHHHHHHHhCCCCCeEEEEEccCCHHHHHHHHHHCCCCeEEEEE
Confidence            9999999999999999999999999999999999999999999999999999988763

>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=99.96  E-value=9.8e-30  Score=192.83  Aligned_cols=133  Identities=35%  Similarity=0.591  Sum_probs=115.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +++|++||+||+.|++..+..+.... ++++..+.++....++...+  +++||+||||+++..++.. +.+++++++++
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            58999999999999999999998877 78999999888877776655  4789999999999999998 88999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEe
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEV  137 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~  137 (203)
                      |+||||.|++.+|.+++..+++.+++.+|+++||||+|+++.++++.++++|+.|.+
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            999999999999999999999999999999999999999999999999999988753

>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=99.96  E-value=2.4e-29  Score=193.88  Aligned_cols=135  Identities=36%  Similarity=0.574  Sum_probs=124.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      +|||++||+|||.|+++++..++.+. ++++..+.|+.....+.+.. ..++||+||||++|.++++. +.+++++++++
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            58999999999999999999999887 79999999999888777766 57899999999999999998 88999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCC----CCCcEEEEeeecChhHHHHHHhcCCCCeEEEec
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLP----KLRRTGLFSATQTEAVEELSKAGLRNPVRIEVR  138 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~----~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~  138 (203)
                      |+||||.|++.+|.+++..+++.+.    .++|+++||||+|++++.+++.++++|+.|.++
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            9999999999999999999999774    367999999999999999999999999988763

>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=2.9e-28  Score=183.94  Aligned_cols=135  Identities=33%  Similarity=0.567  Sum_probs=126.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+++++|+++++.|.+..+..+.... ++++...+|+.....+...+ ..++||||+||++|.++++. +.+++++++++
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            47899999999999999999998877 89999999999988887777 67899999999999999998 88999999999


Q ss_pred             EEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEec
Q 028826           81 VLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEVR  138 (203)
Q Consensus        81 ViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~~  138 (203)
                      |+||||.|++.+|.+++..|++.+++.+|+++||||+|+++.++++.++++|+.|.+.
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            9999999999999999999999999999999999999999999999999999888653

>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=99.91  E-value=2.7e-24  Score=162.10  Aligned_cols=134  Identities=36%  Similarity=0.577  Sum_probs=117.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcC---CCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTL---PDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~---~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      .++++|+++++.|.+..+.......   ....+..+.++.+...+.... ..+++|+|+||+++..++.+ +...+++++
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            5889999999999999888876543   245666777776665554444 57899999999999999988 788899999


Q ss_pred             EEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcCCCCeEEEe
Q 028826           79 ILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGLRNPVRIEV  137 (203)
Q Consensus        79 ~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~~~~i~~  137 (203)
                      ++|+||||.+++++|.+++..+++.+++++|+++||||+|+++.++++.++++|+.|.+
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            99999999999999999999999999999999999999999999999999999998875

>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=99.70  E-value=4.1e-18  Score=130.23  Aligned_cols=115  Identities=13%  Similarity=0.122  Sum_probs=82.3

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCce----EEEEEcCcchHHHHHHHH-hCCCeEEEeccHHHHHHHHhCCCccCC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVK----SMLLVGGVEVKADVKKIE-EEGANLLIGTPGRLYDIMERMDVLDFR   75 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~----~~~~~~g~~~~~~~~~l~-~~~~~ilV~Tp~~l~~~~~~~~~~~l~   75 (203)
                      .+||++||++|+.|+++.++++++.. +++    .....++.....+...+. ...++|+|+||++|.+     ....++
T Consensus        88 rvliv~Pt~~La~Q~~~~l~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~Ilv~Tp~~l~~-----~~~~~~  161 (237)
T d1gkub1          88 RCYVIFPTSLLVIQAAETIRKYAEKA-GVGTENLIGYYHGRIPKREKENFMQNLRNFKIVITTTQFLSK-----HYRELG  161 (237)
T ss_dssp             CEEEEESCHHHHHHHHHHHHHHHTTT-CCSGGGSEEECCSSCCSHHHHHHHHSGGGCSEEEEEHHHHHH-----CSTTSC
T ss_pred             eEEEEeccHHHHHHHHHHHHHHHHHc-CCceEEEEeeeecccchhhhhhhhccccccceeccChHHHHH-----hhhhcC
Confidence            37999999999999999999998765 443    344445555444444432 2468999999998765     344577


Q ss_pred             CccEEEEcchhHhhhhchHHHHHHHHHh-------------CCCCCcEEEEeeecChhHHH
Q 028826           76 NLVILVLDEADRLLDMGFQKQISYIISR-------------LPKLRRTGLFSATQTEAVEE  123 (203)
Q Consensus        76 ~v~~lViDEad~l~~~~~~~~~~~il~~-------------~~~~~q~i~~SAT~~~~v~~  123 (203)
                      +++++|+||+|.+++.+..  +..++..             .+...|++++|||+++.+..
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            8999999999999876532  2222222             24577999999999876544

>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=99.67  E-value=1.3e-16  Score=118.79  Aligned_cols=121  Identities=17%  Similarity=0.242  Sum_probs=92.5

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +|+++|+++|+.|+++.++++.+.  ..++....|+.......    ...++++++||..+..++.. ....+.+++++|
T Consensus        71 vl~l~P~~~L~~q~~~~~~~~~~~--~~~v~~~~~~~~~~~~~----~~~~~ii~~~~~~~~~~~~~-~~~~~~~~~~ii  143 (202)
T d2p6ra3          71 SLYVVPLRALAGEKYESFKKWEKI--GLRIGISTGDYESRDEH----LGDCDIIVTTSEKADSLIRN-RASWIKAVSCLV  143 (202)
T ss_dssp             EEEEESSHHHHHHHHHHHTTTTTT--TCCEEEECSSCBCCSSC----STTCSEEEEEHHHHHHHHHT-TCSGGGGCCEEE
T ss_pred             ceeecccHHHHHHHHHHHHHHhhc--cccceeeccCccccccc----ccccceeeeccHHHHHHHhc-cchhhhhhhhcc
Confidence            799999999999999999998765  45666666654432211    25689999999999999987 777889999999


Q ss_pred             EcchhHhhhhchHHHHHHHH---HhCCCCCcEEEEeeecChhHHHHHHhcCCC
Q 028826           82 LDEADRLLDMGFQKQISYII---SRLPKLRRTGLFSATQTEAVEELSKAGLRN  131 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il---~~~~~~~q~i~~SAT~~~~v~~~~~~~l~~  131 (203)
                      +||+|.+.+.++...+..++   ...+++.|++++|||+|+ .+++.+ |+..
T Consensus       144 ~DE~h~~~~~~r~~~~~~~l~~i~~~~~~~~~l~lSATl~n-~~~~~~-~l~~  194 (202)
T d2p6ra3         144 VDEIHLLDSEKRGATLEILVTKMRRMNKALRVIGLSATAPN-VTEIAE-WLDA  194 (202)
T ss_dssp             ETTGGGGGCTTTHHHHHHHHHHHHHHCTTCEEEEEECCCTT-HHHHHH-HTTC
T ss_pred             ccHHHHhcccccchHHHHHHHHHHhcCCCCcEEEEcCCCCc-HHHHHH-HcCC
Confidence            99999998766544444443   344678999999999976 567765 4443

>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=99.67  E-value=3.9e-16  Score=115.74  Aligned_cols=135  Identities=19%  Similarity=0.167  Sum_probs=100.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++|+++|+.|.++.++++.... +.++....++..........  ..++++++||+.+..++.. ..+.+++++++|
T Consensus        55 il~i~P~~~L~~q~~~~~~~~~~~~-~~~v~~~~~~~~~~~~~~~~--~~~~i~i~t~~~~~~~~~~-~~~~~~~~~~vI  130 (200)
T d1wp9a1          55 VLMLAPTKPLVLQHAESFRRLFNLP-PEKIVALTGEKSPEERSKAW--ARAKVIVATPQTIENDLLA-GRISLEDVSLIV  130 (200)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHBCSC-GGGEEEECSCSCHHHHHHHH--HHCSEEEECHHHHHHHHHT-TSCCTTSCSEEE
T ss_pred             EEEEcCchHHHHHHHHHHHHhhccc-ccceeeeecccchhHHHHhh--hcccccccccchhHHHHhh-hhhhccccceEE
Confidence            7999999999999999999997665 78888877777765554443  2468999999999998887 778899999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcC-CCCeEEEeccC
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKAGL-RNPVRIEVRAE  140 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l-~~~~~i~~~~~  140 (203)
                      +||||.+........+...+......++++++|||.+.....+.+..- .+...+.+..+
T Consensus       131 iDE~H~~~~~~~~~~~~~~~~~~~~~~~~l~~SATp~~~~~~~~~~~~~l~~~~i~~~~~  190 (200)
T d1wp9a1         131 FDEAHRAVGNYAYVFIAREYKRQAKNPLVIGLTASPGSTPEKIMEVINNLGIEHIEYRSE  190 (200)
T ss_dssp             EETGGGCSTTCHHHHHHHHHHHHCSSCCEEEEESCSCSSHHHHHHHHHHTTCCEEEECCT
T ss_pred             EEehhhhhcchhHHHHHHHHHhcCCCCcEEEEEecCCCcHHHHHHHHhcCCceEEEeCCC
Confidence            999999876554444444444445678999999998665555443211 13345555443

>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=99.59  E-value=3.9e-16  Score=116.49  Aligned_cols=125  Identities=19%  Similarity=0.186  Sum_probs=88.6

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchH---HHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVK---ADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~---~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +++++|+++|+.|..+.++.++.     ......+.....   ...........+++++||.++...... ......+++
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            68999999999999999988742     333333332222   222233356799999999998655444 455678899


Q ss_pred             EEEEcchhHhhhhch--HH---HHHHHHHhCCCCCcEEEEeeecChhHHH-HHHh-cCCCCe
Q 028826           79 ILVLDEADRLLDMGF--QK---QISYIISRLPKLRRTGLFSATQTEAVEE-LSKA-GLRNPV  133 (203)
Q Consensus        79 ~lViDEad~l~~~~~--~~---~~~~il~~~~~~~q~i~~SAT~~~~v~~-~~~~-~l~~~~  133 (203)
                      ++|+||+|.+.++++  ..   .+..+...+ ++.|++++|||+++++.+ +.+. .+.+|+
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            999999999987752  22   234455555 478999999999999865 4444 478885

>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=99.57  E-value=8.4e-16  Score=120.70  Aligned_cols=103  Identities=13%  Similarity=0.062  Sum_probs=70.0

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEE
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVIL   80 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~l   80 (203)
                      .+||++||||||.|+++.++++.........     +        ........++++||+.+..++..  ...+.+++++
T Consensus        40 ~~lvi~Ptr~La~q~~~~l~~~~~~~~~~~~-----~--------~~~~~~~~i~~~t~~~l~~~~~~--~~~~~~~~~v  104 (305)
T d2bmfa2          40 RTLILAPTRVVAAEMEEALRGLPIRYQTPAI-----R--------AEHTGREIVDLMCHATFTMRLLS--PIRVPNYNLI  104 (305)
T ss_dssp             CEEEEESSHHHHHHHHHHTTTSCCBCCC---------------------CCCSEEEEEHHHHHHHHTS--SSCCCCCSEE
T ss_pred             EEEEEccHHHHHHHHHHHHhcCCcceeeeEE-----e--------ecccCccccccCCcHHHHHHHhc--CccccceeEE
Confidence            3799999999999999887776433211111     0        11135678999999988776653  5567899999


Q ss_pred             EEcchhHhhhhch--HHHHHHHHHhCCCCCcEEEEeeecChh
Q 028826           81 VLDEADRLLDMGF--QKQISYIISRLPKLRRTGLFSATQTEA  120 (203)
Q Consensus        81 ViDEad~l~~~~~--~~~~~~il~~~~~~~q~i~~SAT~~~~  120 (203)
                      |+||+|.+..+++  ...+..+..  ....|++++|||.+..
T Consensus       105 ViDE~H~~~~~~~~~~~~l~~~~~--~~~~~~v~~SAT~~~~  144 (305)
T d2bmfa2         105 IMDEAHFTDPASIAARGYISTRVE--MGEAAGIFMTATPPGS  144 (305)
T ss_dssp             EEESTTCCSHHHHHHHHHHHHHHH--HTSCEEEEECSSCTTC
T ss_pred             EeeeeeecchhhHHHHHHHHHhhc--cccceEEEeecCCCcc
Confidence            9999999876653  222222222  3568999999999753

>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=99.31  E-value=1.4e-11  Score=92.81  Aligned_cols=115  Identities=20%  Similarity=0.266  Sum_probs=91.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      ++++++||-.|+.|.++.++++...+ ++++..++|+.+..+...   .+.++.++|||||-..+.      ..+.++++
T Consensus       106 qv~~l~Pt~~La~Q~~~~~~~~~~~~-~~~v~~l~~~~~~~~~~~~~~~~~~g~~~iviGths~l~------~~~~f~~L  178 (233)
T d2eyqa3         106 QVAVLVPTTLLAQQHYDNFRDRFANW-PVRIEMISRFRSAKEQTQILAEVAEGKIDILIGTHKLLQ------SDVKFKDL  178 (233)
T ss_dssp             EEEEECSSHHHHHHHHHHHHHHSTTT-TCCEEEESTTSCHHHHHHHHHHHHTTCCSEEEECTHHHH------SCCCCSSE
T ss_pred             ceEEEccHHHhHHHHHHHHHHHHhhC-CCEEEeccCcccchhHHHHHHHHhCCCCCEEEeehhhhc------cCCccccc
Confidence            58999999999999999999998887 799999999888665444   455678999999987664      56788999


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHHh
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSKA  127 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~  127 (203)
                      .++|+||=|..   |+...  ..++....+..+++.|||..+....++..
T Consensus       179 gLiIiDEeH~f---g~kQ~--~~l~~~~~~~~~l~~SATPiprtl~~~~~  223 (233)
T d2eyqa3         179 GLLIVDEEHRF---GVRHK--ERIKAMRANVDILTLTATPIPRTLNMAMS  223 (233)
T ss_dssp             EEEEEESGGGS---CHHHH--HHHHHHHTTSEEEEEESSCCCHHHHHHHT
T ss_pred             cceeeechhhh---hhHHH--HHHHhhCCCCCEEEEecchhHHHHHHHHH
Confidence            99999999964   43332  22333346789999999999877666654

>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=99.26  E-value=1.9e-11  Score=93.76  Aligned_cols=114  Identities=23%  Similarity=0.341  Sum_probs=87.2

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      ++++++||-.||.|.++.++++.+.+ ++++..++|+.+..+...   .+.++.++|||||-.-+.      ..+.++++
T Consensus       134 q~~~m~Pt~~La~Qh~~~~~~~f~~~-~~~v~~l~~~~~~~~r~~~~~~~~~g~~~iiIGThsl~~------~~~~f~~L  206 (264)
T d1gm5a3         134 QTAFMVPTSILAIQHYRRTVESFSKF-NIHVALLIGATTPSEKEKIKSGLRNGQIDVVIGTHALIQ------EDVHFKNL  206 (264)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHHHTCS-SCCEEECCSSSCHHHHHHHHHHHHSSCCCEEEECTTHHH------HCCCCSCC
T ss_pred             ceeEEeehHhhhHHHHHHHHHhhhhc-cccceeeccccchHHHHHHHHHHHCCCCCEEEeehHHhc------CCCCcccc
Confidence            68999999999999999999999888 899999999987655443   455678999999986654      35677899


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHH
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEAVEELSK  126 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~  126 (203)
                      .++||||-|.+   |+...  ..+..-.+++.+++.|||..+....+..
T Consensus       207 glviiDEqH~f---gv~Qr--~~l~~~~~~~~~l~~SATPiprtl~~~~  250 (264)
T d1gm5a3         207 GLVIIDEQHRF---GVKQR--EALMNKGKMVDTLVMSATPIPRSMALAF  250 (264)
T ss_dssp             CEEEEESCCCC----------CCCCSSSSCCCEEEEESSCCCHHHHHHH
T ss_pred             ceeeecccccc---chhhH--HHHHHhCcCCCEEEEECCCCHHHHHHHH
Confidence            99999999976   32221  1223334578999999998887666554

>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=99.20  E-value=5.7e-12  Score=98.04  Aligned_cols=106  Identities=21%  Similarity=0.143  Sum_probs=78.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +|||||+++|+.|..+.+.+++... ...+..+.+|.......    ....+++|+|+..+..+.    ...+++++++|
T Consensus       160 ~Liivp~~~Lv~Q~~~~f~~~~~~~-~~~~~~~~~g~~~~~~~----~~~~~i~i~t~qs~~~~~----~~~~~~f~~VI  230 (282)
T d1rifa_         160 ILIIVPTTALTTQMADDFVDYRLFS-HAMIKKIGGGASKDDKY----KNDAPVVVGTWQTVVKQP----KEWFSQFGMMM  230 (282)
T ss_dssp             EEEECSSHHHHHHHHHHHHHHTSCC-GGGEEECSTTCSSTTCC----CTTCSEEEECHHHHTTSC----GGGGGGEEEEE
T ss_pred             EEEEEcCchhHHHHHHHHHHhhccc-cccceeecceecccccc----cccceEEEEeeehhhhhc----ccccCCCCEEE
Confidence            6999999999999999999986543 45666677775533221    245789999998865433    23467899999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecChh
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTEA  120 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~~  120 (203)
                      +||||++-    ...+..++..+.+....+++|||++..
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            99999874    345667777776555679999998654

>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=99.09  E-value=1.2e-10  Score=80.06  Aligned_cols=100  Identities=18%  Similarity=0.115  Sum_probs=65.2

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ++|++|+++++.|.++.+...     +..+....+....        .....+.+.|...+.....  ....+.+++++|
T Consensus        39 vli~~p~~~l~~q~~~~~~~~-----~~~~~~~~~~~~~--------~~~~~~~~~~~~~l~~~~~--~~~~~~~~~lvI  103 (140)
T d1yksa1          39 TLVLAPTRVVLSEMKEAFHGL-----DVKFHTQAFSAHG--------SGREVIDAMCHATLTYRML--EPTRVVNWEVII  103 (140)
T ss_dssp             EEEEESSHHHHHHHHHHTTTS-----CEEEESSCCCCCC--------CSSCCEEEEEHHHHHHHHT--SSSCCCCCSEEE
T ss_pred             eeeeecchhHHHHHHHHhhhh-----hhhhccccccccc--------ccccchhhhhHHHHHHHHh--ccccccceeEEE
Confidence            689999999999998766443     2222211111111        2345677888877766543  466788999999


Q ss_pred             EcchhHhhhhch--HHHHHHHHHhCCCCCcEEEEeeecC
Q 028826           82 LDEADRLLDMGF--QKQISYIISRLPKLRRTGLFSATQT  118 (203)
Q Consensus        82 iDEad~l~~~~~--~~~~~~il~~~~~~~q~i~~SAT~~  118 (203)
                      +||||.+...++  +..+..+ .. .++.+++++|||.|
T Consensus       104 iDEaH~~~~~~~~~~~~~~~~-~~-~~~~~~l~lTATPp  140 (140)
T d1yksa1         104 MDEAHFLDPASIAARGWAAHR-AR-ANESATILMTATPP  140 (140)
T ss_dssp             ETTTTCCSHHHHHHHHHHHHH-HH-TTSCEEEEECSSCT
T ss_pred             EccccccChhhHHHHHHHHHH-hh-CCCCCEEEEEcCCC
Confidence            999998744432  2222222 23 35799999999987

>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=98.96  E-value=1.9e-09  Score=74.24  Aligned_cols=98  Identities=13%  Similarity=0.078  Sum_probs=67.3

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      ++|++|+++|+.|+.+.+.+....    ......+|...        .....++++|.+.....    ....+++++++|
T Consensus        36 vli~~P~~~l~~q~~~~~~~~~~~----~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~----~~~~~~~~~~vI   99 (136)
T d1a1va1          36 VLVLNPSVAATLGFGAYMSKAHGV----DPNIRTGVRTI--------TTGSPITYSTYGKFLAD----GGCSGGAYDIII   99 (136)
T ss_dssp             EEEEESCHHHHHHHHHHHHHHHSC----CCEEECSSCEE--------CCCCSEEEEEHHHHHHT----TGGGGCCCSEEE
T ss_pred             EEEEcChHHHHHHHHHHHHHHhhc----ccccccccccc--------ccccceEEEeeeeeccc----cchhhhcCCEEE
Confidence            799999999999999998887543    23344444332        23456888998876533    334678999999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCC--CCCcEEEEeee
Q 028826           82 LDEADRLLDMGFQKQISYIISRLP--KLRRTGLFSAT  116 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~--~~~q~i~~SAT  116 (203)
                      +||+|.+-. .....+..+++.+.  ...+++++|||
T Consensus       100 iDE~H~~~~-~~~~~~~~~l~~~~~~~~~~~l~~TAT  135 (136)
T d1a1va1         100 CDECHSTDA-TSILGIGTVLDQAETAGARLVVLATAT  135 (136)
T ss_dssp             EETTTCCSH-HHHHHHHHHHHHTTTTTCSEEEEEESS
T ss_pred             EecccccCH-HHHHHHHHHHHHHHHCCCCcEEEEeCC
Confidence            999997632 22334555666554  35578888888

>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=98.90  E-value=2.9e-09  Score=78.59  Aligned_cols=94  Identities=20%  Similarity=0.104  Sum_probs=67.1

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||+||+++|+.|+.+.+++++..    .+....|+.          ....+++|+|...+......    ..++.+++|
T Consensus       113 ~Liv~p~~~L~~q~~~~~~~~~~~----~~~~~~~~~----------~~~~~i~i~t~~~~~~~~~~----~~~~~~lvI  174 (206)
T d2fz4a1         113 TLIVVPTLALAEQWKERLGIFGEE----YVGEFSGRI----------KELKPLTVSTYDSAYVNAEK----LGNRFMLLI  174 (206)
T ss_dssp             EEEEESSHHHHHHHHHHHGGGCGG----GEEEESSSC----------BCCCSEEEEEHHHHHHTHHH----HTTTCSEEE
T ss_pred             eeEEEcccchHHHHHHHHHhhccc----chhhccccc----------ccccccccceehhhhhhhHh----hCCcCCEEE
Confidence            699999999999999999887533    333333332          23567999999988765543    235678999


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecC
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT  118 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~  118 (203)
                      +||||++-...    +..++..+ +....+++|||+.
T Consensus       175 iDEaH~~~a~~----~~~i~~~~-~~~~~lgLTATl~  206 (206)
T d2fz4a1         175 FDEVHHLPAES----YVQIAQMS-IAPFRLGLTATFE  206 (206)
T ss_dssp             EECSSCCCTTT----HHHHHHTC-CCSEEEEEEESCC
T ss_pred             EECCeeCCcHH----HHHHHhcc-CCCcEEEEecCCC
Confidence            99999975433    34555555 3556789999974

>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=98.17  E-value=9.8e-06  Score=62.40  Aligned_cols=109  Identities=22%  Similarity=0.296  Sum_probs=69.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHH---HHHh----CCCeEEEeccHHHHHHHHhCCCccC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVK---KIEE----EGANLLIGTPGRLYDIMERMDVLDF   74 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~---~l~~----~~~~ilV~Tp~~l~~~~~~~~~~~l   74 (203)
                      +|||+|.. |..|..+++.++...  ...++.++|+........   ....    ...+++|+|.+.+.....   .+.-
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 889999999998765  456666666654332222   1111    235789999887765432   2333


Q ss_pred             CCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecCh
Q 028826           75 RNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQTE  119 (203)
Q Consensus        75 ~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~~  119 (203)
                      .+..++|+||+|.+-..+  ......+..+ +....+++|||.-.
T Consensus       191 ~~~~~vI~DEaH~ikn~~--s~~~~a~~~l-~~~~rllLTGTPi~  232 (298)
T d1z3ix2         191 GKVGLVICDEGHRLKNSD--NQTYLALNSM-NAQRRVLISGTPIQ  232 (298)
T ss_dssp             SCCCEEEETTGGGCCTTC--HHHHHHHHHH-CCSEEEEECSSCSG
T ss_pred             cceeeeeccccccccccc--chhhhhhhcc-ccceeeeecchHHh
Confidence            456799999999985433  1222233334 45667899999743

>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=97.40  E-value=0.0019  Score=45.33  Aligned_cols=112  Identities=13%  Similarity=0.177  Sum_probs=76.1

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.|+|+.-|..+.+.+.+.     |+++..++|+.+..+..+.+   .++..+|||+|.     ++.  ..+|+.+++
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            699999999999888887775     89999999999877666644   458899999997     232  589999999


Q ss_pred             EEEEcchhHhhhhchHHHHHHHHHhCCCC--CcEEEEeeecChhHHHHH
Q 028826           79 ILVLDEADRLLDMGFQKQISYIISRLPKL--RRTGLFSATQTEAVEELS  125 (203)
Q Consensus        79 ~lViDEad~l~~~~~~~~~~~il~~~~~~--~q~i~~SAT~~~~v~~~~  125 (203)
                      ++|+=.++...-..-...+.....+..+.  ...+++....+..+..++
T Consensus       102 ~Vi~~~~~~~~~~~~~~~~iq~~GR~gR~~~g~~~~~~~~~~~~~~~~i  150 (174)
T d1c4oa2         102 LVAILDADKEGFLRSERSLIQTIGRAARNARGEVWLYADRVSEAMQRAI  150 (174)
T ss_dssp             EEEETTTTSCSGGGSHHHHHHHHGGGTTSTTCEEEEECSSCCHHHHHHH
T ss_pred             EEEEeccccccccchhHHHHHHhhhhhhcCCCeeEEeecCCCHHHHHHH
Confidence            99997666532111123333333333222  345555555555555444

>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=97.28  E-value=0.00073  Score=50.54  Aligned_cols=121  Identities=15%  Similarity=0.116  Sum_probs=82.9

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHH-HHHHhCC-----CccCC
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLY-DIMERMD-----VLDFR   75 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~-~~~~~~~-----~~~l~   75 (203)
                      +=|++.+--||..=.+++..+-..+ |+.+.++..+.+.++....-   .+||+.||...+. ++++..-     ..-..
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            3478888899998899999999998 99999998887776555443   5899999999885 7777611     11246


Q ss_pred             CccEEEEcchhHhh-hhchHH-------------HHHHHHHhCCCCCcEEEEeeecChhHHHHHHhcC
Q 028826           76 NLVILVLDEADRLL-DMGFQK-------------QISYIISRLPKLRRTGLFSATQTEAVEELSKAGL  129 (203)
Q Consensus        76 ~v~~lViDEad~l~-~~~~~~-------------~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~~~l  129 (203)
                      .+.+.|+||+|.++ |....+             .+..+.+.   -.+....+.|.-....++.+.|-
T Consensus       200 ~~~~aIvDEvDsiliDeartpliisg~~~~~a~it~q~~f~~---y~~l~gmtgta~~~~~e~~~iy~  264 (273)
T d1tf5a3         200 PLHFAVIDEVDSILIDEARTPLIISGQSMTLATITFQNYFRM---YEKLAGMTGTAKTEEEEFRNIYN  264 (273)
T ss_dssp             CCCEEEEETHHHHHTTTTTCEEEEEEEEEEEEEEEHHHHHTT---SSEEEEEESCCGGGHHHHHHHHC
T ss_pred             CCCEEEEEcchhhhhhccCCceEeccCccchhhhhHHHHHHH---HHHHhCCccccHHHHHHHHhccC
Confidence            78999999999986 431100             01222222   24566666666655566665553

>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=97.12  E-value=0.00049  Score=49.83  Aligned_cols=92  Identities=15%  Similarity=0.236  Sum_probs=68.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      |+.+|+|.-+-...++..++++   +|++++..++|..+.++..+.+   .++..+|||+|.     .+.  ..+|+.+.
T Consensus        33 Qvy~V~p~I~~~e~~~~~l~~~---~p~~~i~~lHGkm~~~eke~im~~F~~g~~~ILv~Tt-----vIE--vGiDvpnA  102 (211)
T d2eyqa5          33 QVYYLYNDVENIQKAAERLAEL---VPEARIAIGHGQMRERELERVMNDFHHQRFNVLVCTT-----IIE--TGIDIPTA  102 (211)
T ss_dssp             EEEEECCCSSCHHHHHHHHHHH---CTTSCEEECCSSCCHHHHHHHHHHHHTTSCCEEEESS-----TTG--GGSCCTTE
T ss_pred             eEEEEEcCccchhhHHHHHHHh---CCceEEEEEEeccCHHHHHHHHHHHHcCCcceEEEeh-----hhh--hccCCCCC
Confidence            5789999777666666555554   6689999999988877666544   357899999998     333  57999999


Q ss_pred             cEEEEcchhHhhhhchHHHHHHHHHhCCC
Q 028826           78 VILVLDEADRLLDMGFQKQISYIISRLPK  106 (203)
Q Consensus        78 ~~lViDEad~l~~~~~~~~~~~il~~~~~  106 (203)
                      .++||..||++   | ...+..+..+..+
T Consensus       103 ~~iiI~~a~rf---G-LaQLhQLRGRVGR  127 (211)
T d2eyqa5         103 NTIIIERADHF---G-LAQLHQLRGRVGR  127 (211)
T ss_dssp             EEEEETTTTSS---C-HHHHHHHHTTCCB
T ss_pred             cEEEEecchhc---c-ccccccccceeee
Confidence            99999999976   4 3446666666654

>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=96.82  E-value=0.0026  Score=44.86  Aligned_cols=75  Identities=13%  Similarity=0.266  Sum_probs=61.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||.++|++-+..+...+++.     ++++..++|+.+..+....+   .++..+|||+|.-     +.  .++|+.++
T Consensus        33 ~~iif~~~~~~~~~~~~~l~~~-----g~~~~~~hg~~~~~eR~~~l~~Fr~g~~~vLVaTdv-----~~--rGiDip~v  100 (181)
T d1t5la2          33 RTLVTTLTKKMAEDLTDYLKEA-----GIKVAYLHSEIKTLERIEIIRDLRLGKYDVLVGINL-----LR--EGLDIPEV  100 (181)
T ss_dssp             EEEEECSSHHHHHHHHHHHHTT-----TCCEEEECSSCCHHHHHHHHHHHHHTSCSEEEESCC-----CS--SSCCCTTE
T ss_pred             eEEEEeehhhhhHHHHHHHHhC-----CcceeEecCCccHHHHHHHHHHHHCCCCCEEEehhH-----HH--ccCCCCCC
Confidence            3799999999998888877765     89999999999987766644   4578999999962     22  68999999


Q ss_pred             cEEEEcchhH
Q 028826           78 VILVLDEADR   87 (203)
Q Consensus        78 ~~lViDEad~   87 (203)
                      +++|.-+++.
T Consensus       101 ~~VI~~d~p~  110 (181)
T d1t5la2         101 SLVAILDADK  110 (181)
T ss_dssp             EEEEETTTTS
T ss_pred             CEEEEecCCc
Confidence            9999988775

>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=96.60  E-value=0.0078  Score=41.43  Aligned_cols=72  Identities=10%  Similarity=0.105  Sum_probs=57.6

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||.|.|+.-+.++.+.+.+.     ++++..++|+.+..+....+   ..+...|||+|--.      . .++|+.++
T Consensus        29 k~iIF~~s~~~~~~l~~~L~~~-----~~~~~~~~~~~~~~~r~~~l~~f~~~~~~iLv~Tdv~------~-rGiDi~~v   96 (162)
T d1fuka_          29 QAVIFCNTRRKVEELTTKLRND-----KFTVSAIYSDLPQQERDTIMKEFRSGSSRILISTDLL------A-RGIDVQQV   96 (162)
T ss_dssp             CEEEEESSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEEEGGG------T-TTCCCCSC
T ss_pred             cEEEEEEEEchHHHHHHHHhhc-----CceEEEeccCCchhhHHHHHHHHhhcccceeeccccc------c-ccccCCCc
Confidence            4799999999999888776664     78899999998877666644   34778999999732      2 68999999


Q ss_pred             cEEEEcc
Q 028826           78 VILVLDE   84 (203)
Q Consensus        78 ~~lViDE   84 (203)
                      +++|.=+
T Consensus        97 ~~VI~~d  103 (162)
T d1fuka_          97 SLVINYD  103 (162)
T ss_dssp             SEEEESS
T ss_pred             eEEEEec
Confidence            9999744

>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=96.59  E-value=0.00069  Score=49.56  Aligned_cols=105  Identities=13%  Similarity=0.131  Sum_probs=62.5

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||++| ..+..|..+++.+++..   .++....+..... .     ....+|+++|.+.+......    .--...++|
T Consensus        64 ~LIv~p-~~l~~~W~~e~~~~~~~---~~~~~~~~~~~~~-~-----~~~~~vvi~~~~~~~~~~~l----~~~~~~~vI  129 (230)
T d1z63a1          64 SLVICP-LSVLKNWEEELSKFAPH---LRFAVFHEDRSKI-K-----LEDYDIILTTYAVLLRDTRL----KEVEWKYIV  129 (230)
T ss_dssp             EEEEEC-STTHHHHHHHHHHHCTT---SCEEECSSSTTSC-C-----GGGSSEEEEEHHHHTTCHHH----HTCCEEEEE
T ss_pred             cceecc-hhhhhHHHHHHHhhccc---ccceeeccccchh-h-----ccCcCEEEeeHHHHHhHHHH----hcccceEEE
Confidence            588888 55778899999888643   3443332222111 1     23578999999887543221    112456899


Q ss_pred             EcchhHhhhhchHHHHHHHHHhCCCCCcEEEEeeecC-hhHHH
Q 028826           82 LDEADRLLDMGFQKQISYIISRLPKLRRTGLFSATQT-EAVEE  123 (203)
Q Consensus        82 iDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SAT~~-~~v~~  123 (203)
                      +||+|.+-....  .....+..+. ....+++|+|.- +...+
T Consensus       130 ~DEah~~k~~~s--~~~~~~~~l~-a~~r~~LTgTPi~n~~~d  169 (230)
T d1z63a1         130 IDEAQNIKNPQT--KIFKAVKELK-SKYRIALTGTPIENKVDD  169 (230)
T ss_dssp             EETGGGGSCTTS--HHHHHHHTSC-EEEEEEECSSCSTTCHHH
T ss_pred             EEhhhcccccch--hhhhhhhhhc-cceEEEEecchHHhHHHH
Confidence            999999854432  2223344443 445688899964 33444

>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=96.42  E-value=0.012  Score=40.01  Aligned_cols=70  Identities=17%  Similarity=0.272  Sum_probs=55.1

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||.++|++-|.++...+++.     ++.+..++|+.+..+....+   ..+...|+|+|..     +.  .++|+..+
T Consensus        30 k~IIF~~s~~~~~~l~~~L~~~-----g~~~~~~~~~~~~~~r~~~~~~f~~~~~~ilv~T~~-----~~--~Gid~~~v   97 (155)
T d1hv8a2          30 YGLVFCKTKRDTKELASMLRDI-----GFKAGAIHGDLSQSQREKVIRLFKQKKIRILIATDV-----MS--RGIDVNDL   97 (155)
T ss_dssp             CEEEECSSHHHHHHHHHHHHHT-----TCCEEEECSSSCHHHHHHHHHHHHTTSSSEEEECTT-----HH--HHCCCSCC
T ss_pred             CEEEEECchHHHHHHHhhhccc-----ccccccccccchhhhhhhhhhhhhcccceeeeehhH-----Hh--hhhhhccC
Confidence            3799999999999888888765     78899999998776665544   3467899999962     22  47899999


Q ss_pred             cEEEE
Q 028826           78 VILVL   82 (203)
Q Consensus        78 ~~lVi   82 (203)
                      +++|.
T Consensus        98 ~~Vi~  102 (155)
T d1hv8a2          98 NCVIN  102 (155)
T ss_dssp             SEEEE
T ss_pred             cEEEE
Confidence            99885

>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=96.36  E-value=0.01  Score=41.05  Aligned_cols=72  Identities=6%  Similarity=0.034  Sum_probs=57.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.|+|++-+..+...+...     ++++..++|+.+..+....+   ..+..+++|+|..-      . .++|+.+++
T Consensus        35 ~iVF~~~~~~~~~l~~~L~~~-----g~~~~~~h~~~~~~~r~~~~~~f~~~~~~ilv~Td~~------~-~Gid~~~v~  102 (171)
T d1s2ma2          35 AIIFCNSTNRVELLAKKITDL-----GYSCYYSHARMKQQERNKVFHEFRQGKVRTLVCSDLL------T-RGIDIQAVN  102 (171)
T ss_dssp             EEEECSSHHHHHHHHHHHHHH-----TCCEEEECTTSCHHHHHHHHHHHHTTSSSEEEESSCS------S-SSCCCTTEE
T ss_pred             eEEEEeeeehhhHhHHhhhcc-----cccccccccccchhhhhhhhhhcccCccccccchhHh------h-hccccceeE
Confidence            799999999998888877765     78899999998877666544   34789999999842      2 689999999


Q ss_pred             EEEEcch
Q 028826           79 ILVLDEA   85 (203)
Q Consensus        79 ~lViDEa   85 (203)
                      ++|.=+.
T Consensus       103 ~VI~~d~  109 (171)
T d1s2ma2         103 VVINFDF  109 (171)
T ss_dssp             EEEESSC
T ss_pred             EEEecCC
Confidence            9986443

>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=96.31  E-value=0.01  Score=41.03  Aligned_cols=72  Identities=8%  Similarity=0.088  Sum_probs=56.3

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCc
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNL   77 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v   77 (203)
                      .+||.|++++-+..+.+.+.+.     ++++..++|+.+..++...+   .++..+|||+|-..      . .++++..+
T Consensus        29 k~iIF~~~~~~~~~l~~~L~~~-----~~~~~~ihg~~~~~~r~~~l~~F~~g~~~iLv~T~~~------~-~Gid~~~~   96 (168)
T d1t5ia_          29 QVVIFVKSVQRCIALAQLLVEQ-----NFPAIAIHRGMPQEERLSRYQQFKDFQRRILVATNLF------G-RGMDIERV   96 (168)
T ss_dssp             SEEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEESSCC------S-TTCCGGGC
T ss_pred             eEEEEEeeeecchhhhhhhccc-----cccccccccccchhhhhhhhhhhccccceeeeccccc------c-chhhcccc
Confidence            3799999999998888777664     78899999998877666544   34779999999531      2 57899999


Q ss_pred             cEEEEcc
Q 028826           78 VILVLDE   84 (203)
Q Consensus        78 ~~lViDE   84 (203)
                      .++|.=+
T Consensus        97 ~~vi~~~  103 (168)
T d1t5ia_          97 NIAFNYD  103 (168)
T ss_dssp             SEEEESS
T ss_pred             hhhhhhh
Confidence            9988744

>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=96.17  E-value=0.013  Score=41.70  Aligned_cols=69  Identities=13%  Similarity=0.142  Sum_probs=55.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.++|+.-+..+...++..     ++.+..++|+.+..+....+   ..+..+|||+|-..      . .++|+.+++
T Consensus        33 ~IIF~~t~~~~~~l~~~l~~~-----~~~~~~~h~~~~~~~r~~~~~~f~~g~~~ilvaTd~~------~-~GiD~p~v~  100 (200)
T d1oywa3          33 GIIYCNSRAKVEDTAARLQSK-----GISAAAYHAGLENNVRADVQEKFQRDDLQIVVATVAF------G-MGINKPNVR  100 (200)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCHHHHHHHHHHHHTTSCSEEEECTTS------C-TTTCCTTCC
T ss_pred             EEEEEeeehhhHHhhhhhccC-----CceeEEecCCCcHHHHHHHHHHHhcccceEEEecchh------h-hccCCCCCC
Confidence            799999999998887777664     78899999998876655543   34788999999732      2 579999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       101 ~VI~  104 (200)
T d1oywa3         101 FVVH  104 (200)
T ss_dssp             EEEE
T ss_pred             EEEE
Confidence            9985

>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=95.71  E-value=0.00015  Score=49.32  Aligned_cols=46  Identities=7%  Similarity=-0.041  Sum_probs=29.7

Q ss_pred             CCCCceeEEEEEcCCCCcHHHHHHHHhcCCCCeEEEEeccCCcccC
Q 028826          157 KTPLGLHLEYLECESDKKPSQLVDLLIKNKSKKIIMYVQHGNFSED  202 (203)
Q Consensus       157 ~~~~~i~~~~~~~~~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e~  202 (203)
                      ...++|++.++..+++.+.....-.++..+.+++||||||++.||+
T Consensus         5 ~~~p~I~~~~~~~~~~~~~~~~~i~l~~~~~~k~IVFc~t~~~ae~   50 (138)
T d1jr6a_           5 VPHPNIEEVALSTTGEIPFYGKAIPLEVIKGGRHLIFCHSKKKCDE   50 (138)
T ss_dssp             CCCTTEEEEECCBCSSEECSSCEECHHHHTTSCEEEECSCHHHHHH
T ss_pred             CcCCCeEEEEeccCChhHHHHhhChHhhcCCCCEEEEeCcHHHHHH
Confidence            3456788887665543322221222455677899999999998874

>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=95.70  E-value=0.03  Score=38.55  Aligned_cols=69  Identities=13%  Similarity=0.145  Sum_probs=55.8

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCCccCCCcc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDVLDFRNLV   78 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~   78 (203)
                      +||.|++++-+..+...++..     ++.+..++|+.+..+....+   .++..+|+|+|-..      . .++|+.+++
T Consensus        37 ~iiF~~~~~~~~~~~~~l~~~-----~~~~~~~~~~~~~~~r~~~~~~fk~g~~~iLv~Td~~------~-rGiDi~~v~  104 (168)
T d2j0sa2          37 AVIFCNTKRKVDWLTEKMREA-----NFTVSSMHGDMPQKERESIMKEFRSGASRVLISTDVW------A-RGLDVPQVS  104 (168)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCCEEECTTSCHHHHHHHHHHHHHTSSCEEEECGGG------S-SSCCCTTEE
T ss_pred             eEEEeeeHHHHHHHHHHhhhc-----ccchhhhhhhhhHHHHHHHHHHHhcCCccEEeccchh------c-ccccccCcc
Confidence            789999999999888877775     67888999998877665543   34778999999732      2 689999999


Q ss_pred             EEEE
Q 028826           79 ILVL   82 (203)
Q Consensus        79 ~lVi   82 (203)
                      ++|.
T Consensus       105 ~VIn  108 (168)
T d2j0sa2         105 LIIN  108 (168)
T ss_dssp             EEEE
T ss_pred             eEEE
Confidence            9986

>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=95.24  E-value=0.012  Score=39.48  Aligned_cols=63  Identities=8%  Similarity=0.201  Sum_probs=49.6

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      +||.|+|+.-|.++.+.+++.     ++++..++|+.+..+.    .++..+++|+|-     .+.  ..+| .+++++|
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            799999999999988888776     7899999999875443    257899999996     222  4577 6788875

>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=94.16  E-value=0.089  Score=37.49  Aligned_cols=113  Identities=14%  Similarity=0.187  Sum_probs=62.6

Q ss_pred             EEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCc--chHHHHHHH----HhCCCeEEEeccHHHHHHHHh---CCCc--
Q 028826            4 IISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGV--EVKADVKKI----EEEGANLLIGTPGRLYDIMER---MDVL--   72 (203)
Q Consensus         4 il~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~--~~~~~~~~l----~~~~~~ilV~Tp~~l~~~~~~---~~~~--   72 (203)
                      |+.|.-++|.+..+.+-+-.+.  ..+...++|..  ...+-...+    .+.+..++..+...+...+..   .+..  
T Consensus        13 ~vg~~N~~a~~~~~~~~~~~~~--~~n~l~l~G~~G~GKTHLl~A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   90 (213)
T d1l8qa2          13 IVGEGNRLAYEVVKEALENLGS--LYNPIFIYGSVGTGKTHLLQAAGNEAKKRGYRVIYSSADDFAQAMVEHLKKGTINE   90 (213)
T ss_dssp             CCCTTTHHHHHHHHHHHHTTTT--SCSSEEEECSSSSSHHHHHHHHHHHHHHTTCCEEEEEHHHHHHHHHHHHHHTCHHH
T ss_pred             cCCCcHHHHHHHHHHHHhCcCC--CCCcEEEECCCCCcHHHHHHHHHHHhccCccceEEechHHHHHHHHHHHHccchhh
Confidence            3467677776655554332111  23446777753  344433322    235677888777776554322   0111  


Q ss_pred             ---cCCCccEEEEcchhHhhhh-chHHHHHHHHHhCC-CCCcEEEEeeecC
Q 028826           73 ---DFRNLVILVLDEADRLLDM-GFQKQISYIISRLP-KLRRTGLFSATQT  118 (203)
Q Consensus        73 ---~l~~v~~lViDEad~l~~~-~~~~~~~~il~~~~-~~~q~i~~SAT~~  118 (203)
                         .+.+.+++++|++|.+... .....+..++..+. ...++++.|...|
T Consensus        91 ~~~~~~~~dll~iDDi~~i~~~~~~~~~lf~lin~~~~~~~~iiits~~~p  141 (213)
T d1l8qa2          91 FRNMYKSVDLLLLDDVQFLSGKERTQIEFFHIFNTLYLLEKQIILASDRHP  141 (213)
T ss_dssp             HHHHHHTCSEEEEECGGGGTTCHHHHHHHHHHHHHHHHTTCEEEEEESSCG
T ss_pred             HHHHHhhccchhhhhhhhhcCchHHHHHHHHHHHHHhhccceEEEecCCcc
Confidence               1457899999999998643 24555666666654 4455555544433

>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=92.51  E-value=0.32  Score=34.11  Aligned_cols=75  Identities=8%  Similarity=0.065  Sum_probs=48.9

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCC-------------------------ceEEEEEcCcchHHHHH---HHHhCCC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPD-------------------------VKSMLLVGGVEVKADVK---KIEEEGA   52 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~-------------------------i~~~~~~~g~~~~~~~~---~l~~~~~   52 (203)
                      ++||.+|||.-|..+...+.+.......                         -.++..+||.+..+...   ...++..
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            4899999997777666666554332110                         12667788877554333   2345789


Q ss_pred             eEEEeccHHHHHHHHhCCCccCCCccEEEE
Q 028826           53 NLLIGTPGRLYDIMERMDVLDFRNLVILVL   82 (203)
Q Consensus        53 ~ilV~Tp~~l~~~~~~~~~~~l~~v~~lVi   82 (203)
                      +|||+|..--       ..+++.....+|.
T Consensus       122 ~vlvaT~~l~-------~Gin~p~~~vvi~  144 (201)
T d2p6ra4         122 KVVVATPTLA-------AGVNLPARRVIVR  144 (201)
T ss_dssp             CEEEECSTTT-------SSSCCCBSEEEEC
T ss_pred             eEEEechHHH-------hhcCCCCceEEEe
Confidence            9999998543       4688876666664

>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=91.85  E-value=0.13  Score=38.71  Aligned_cols=66  Identities=6%  Similarity=0.003  Sum_probs=44.4

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCCCccEEE
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFRNLVILV   81 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~~v~~lV   81 (203)
                      .+|+||+..-+.++...+++.     +.+|..++|.....++. ...++..+|||+|.-.      . .++++ ++.++|
T Consensus        39 ~~~F~~s~~~~~~~a~~L~~~-----g~~V~~l~~~~~~~e~~-~~~~~~~~~~~~t~~~------~-~~~~~-~~~~vi  104 (299)
T d1yksa2          39 TAWFLPSIRAANVMAASLRKA-----GKSVVVLNRKTFEREYP-TIKQKKPDFILATDIA------E-MGANL-CVERVL  104 (299)
T ss_dssp             EEEECSCHHHHHHHHHHHHHT-----TCCEEECCSSSCC---------CCCSEEEESSST------T-CCTTC-CCSEEE
T ss_pred             EEEEeCCHHHHHHHHHHHHhc-----CCeEEEEcCcCcHhHHh-hhhcCCcCEEEEechh------h-hceec-CceEEE
Confidence            689999999999888888764     66788888877655544 4457789999999732      2 45666 466554

>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=90.71  E-value=0.0065  Score=43.66  Aligned_cols=94  Identities=17%  Similarity=0.261  Sum_probs=56.9

Q ss_pred             CEEEEcCcHHHHH-----HHHHHHHHhhh-cCCCceEEEEEcCcchHHHHHHH---HhCCCeEEEeccHHHHHHHHhCCC
Q 028826            1 MGMIISPTRELSA-----QIYHVAQPFIS-TLPDVKSMLLVGGVEVKADVKKI---EEEGANLLIGTPGRLYDIMERMDV   71 (203)
Q Consensus         1 ~alil~PtreLa~-----Qi~~~~~~l~~-~~~~i~~~~~~~g~~~~~~~~~l---~~~~~~ilV~Tp~~l~~~~~~~~~   71 (203)
                      |+.+|+|.-|-..     ...+....+.+ .+|++++..++|..+.++..+.+   .++..+|||+|.-     + . ..
T Consensus        31 QvyvVcP~Ieese~~~~~~~~e~~~~l~~~~~p~~~v~~lHG~m~~~eke~~m~~F~~g~~~iLVaTtV-----i-E-~G  103 (206)
T d1gm5a4          31 QAFIVYPLIEESDKLNVKSAVEMYEYLSKEVFPEFKLGLMHGRLSQEEKDRVMLEFAEGRYDILVSTTV-----I-E-VG  103 (206)
T ss_dssp             CBCCBCCCC--------CHHHHHHHSGGGSCC---CBCCCCSSSCCSCSHHHHHHHTTTSSSBCCCSSC-----C-C-SC
T ss_pred             CEEEEEeeecccccccchhhHHHHHHHHHhcCCCCeEEEEeecccHHHHHHHHHHHHCCCEEEEEEehh-----h-h-cc
Confidence            3456777533221     22234444443 34688999999998766555543   3578999999972     2 2 57


Q ss_pred             ccCCCccEEEEcchhHhhhhchHHHHHHHHHhCC
Q 028826           72 LDFRNLVILVLDEADRLLDMGFQKQISYIISRLP  105 (203)
Q Consensus        72 ~~l~~v~~lViDEad~l~~~~~~~~~~~il~~~~  105 (203)
                      +|+.++.++|+..|+.+-    ...+-++..+..
T Consensus       104 IDip~a~~iii~~a~~fg----lsqlhQlrGRvG  133 (206)
T d1gm5a4         104 IDVPRANVMVIENPERFG----LAQLHQLRGRVG  133 (206)
T ss_dssp             SCCTTCCEEEBCSCSSSC----TTHHHHHHHTSC
T ss_pred             ccccCCcEEEEEccCCcc----HHHHHhhhhhee
Confidence            999999999999998752    223344455553

>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=89.19  E-value=2.4  Score=29.24  Aligned_cols=89  Identities=11%  Similarity=0.118  Sum_probs=52.8

Q ss_pred             CceEEEEEcCcchHHHHH--H----HH---hCCCeEEEeccHH-------HHHHHHhC-CCccCCCccEEEEcchhHhhh
Q 028826           28 DVKSMLLVGGVEVKADVK--K----IE---EEGANLLIGTPGR-------LYDIMERM-DVLDFRNLVILVLDEADRLLD   90 (203)
Q Consensus        28 ~i~~~~~~~g~~~~~~~~--~----l~---~~~~~ilV~Tp~~-------l~~~~~~~-~~~~l~~v~~lViDEad~l~~   90 (203)
                      ......++|.........  .    +.   ...||++.-.|+.       +.++.... .....+.-+++|+||||.|-.
T Consensus        14 ~~~~~l~~G~~g~gk~~~a~~l~~~i~~~~~~h~D~~~i~~~~~~I~Id~IR~i~~~~~~~~~~~~~KviIId~ad~l~~   93 (198)
T d2gnoa2          14 EGISILINGEDLSYPREVSLELPEYVEKFPPKASDVLEIDPEGENIGIDDIRTIKDFLNYSPELYTRKYVIVHDCERMTQ   93 (198)
T ss_dssp             SSEEEEEECSSSSHHHHHHHHHHHHHHTSCCCTTTEEEECCSSSCBCHHHHHHHHHHHTSCCSSSSSEEEEETTGGGBCH
T ss_pred             CCceEEEECCCCCCHHHHHHHHHHHHhccccCCCCEEEEeCCcCCCCHHHHHHHHHHHhhCcccCCCEEEEEeCccccch
Confidence            456667777544322211  1    11   2457999988852       23333221 122346778999999999954


Q ss_pred             hchHHHHHHHHHhCCCCCcEEEEeeec
Q 028826           91 MGFQKQISYIISRLPKLRRTGLFSATQ  117 (203)
Q Consensus        91 ~~~~~~~~~il~~~~~~~q~i~~SAT~  117 (203)
                      . ....+..+++.-|++..+++.|...
T Consensus        94 ~-aqNaLLK~LEEPp~~t~fiLit~~~  119 (198)
T d2gnoa2          94 Q-AANAFLKALEEPPEYAVIVLNTRRW  119 (198)
T ss_dssp             H-HHHHTHHHHHSCCTTEEEEEEESCG
T ss_pred             h-hhhHHHHHHhCCCCCceeeeccCCh
Confidence            4 3556666777777777777775553

>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=89.00  E-value=1.1  Score=32.81  Aligned_cols=70  Identities=19%  Similarity=0.238  Sum_probs=49.4

Q ss_pred             CEEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchH--------HH---HHHHHhCCCeEEEeccHHHHHHHHhC
Q 028826            1 MGMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVK--------AD---VKKIEEEGANLLIGTPGRLYDIMERM   69 (203)
Q Consensus         1 ~alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~--------~~---~~~l~~~~~~ilV~Tp~~l~~~~~~~   69 (203)
                      .+||++++++-+.-+.+.+.+-     ++++..+.|.....        ++   .....++.++|||+|--     ..  
T Consensus       163 k~iiF~~~~~~~~~~~~~L~~~-----~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~F~~g~~~vLv~T~~-----~~--  230 (286)
T d1wp9a2         163 KIIVFTNYRETAKKIVNELVKD-----GIKAKRFVGQASKENDRGLSQREQKLILDEFARGEFNVLVATSV-----GE--  230 (286)
T ss_dssp             CEEEECSCHHHHHHHHHHHHHT-----TCCEEEECCSSCC-------CCHHHHHHHHHHHTSCSEEEECGG-----GG--
T ss_pred             cEEEEeCcHHhHHHHHHHHHHc-----CCceEEeeccccccccchhchHHHHHHHHHHHcCCCcEEEEccc-----ee--
Confidence            3799999999998888776653     67777777643321        22   22334568899999942     22  


Q ss_pred             CCccCCCccEEEE
Q 028826           70 DVLDFRNLVILVL   82 (203)
Q Consensus        70 ~~~~l~~v~~lVi   82 (203)
                      .++|+.+++++|.
T Consensus       231 ~Gld~~~~~~Vi~  243 (286)
T d1wp9a2         231 EGLDVPEVDLVVF  243 (286)
T ss_dssp             GGGGSTTCCEEEE
T ss_pred             ccccCCCCCEEEE
Confidence            5799999999997

>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=87.35  E-value=0.38  Score=34.65  Aligned_cols=71  Identities=25%  Similarity=0.321  Sum_probs=45.0

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchH---HHHHHHHhCCCeEEEeccHHHHHHHHhCCCccCC-Cc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVK---ADVKKIEEEGANLLIGTPGRLYDIMERMDVLDFR-NL   77 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~---~~~~~l~~~~~~ilV~Tp~~l~~~~~~~~~~~l~-~v   77 (203)
                      +||.++|++-|..++..+++.           ++||.+..   +-.....++..+|+|||... ...+.  .++|+. .+
T Consensus        28 ~iif~~~~~~~~~l~~~l~~~-----------~hg~~~~~~R~~~~~~f~~g~~~vLVaT~a~-~~v~~--rGlDip~~v   93 (248)
T d1gkub2          28 GIIYARTGEEAEEIYESLKNK-----------FRIGIVTATKKGDYEKFVEGEIDHLIGTAHY-YGTLV--RGLDLPERI   93 (248)
T ss_dssp             EEEEESSHHHHHHHHHTTTTS-----------SCEEECTTSSSHHHHHHHHTSCSEEEEECC---------CCSCCTTTC
T ss_pred             EEEEECCHHHHHHHHHHHHHh-----------ccCCCCHHHHHHHHHHHHhCCCeEEEEeccc-cchhh--hccCccccc
Confidence            799999999888777665431           23443322   23344556889999999742 11222  578986 49


Q ss_pred             cEEEEcchh
Q 028826           78 VILVLDEAD   86 (203)
Q Consensus        78 ~~lViDEad   86 (203)
                      +++|.=++.
T Consensus        94 ~~VI~~d~P  102 (248)
T d1gkub2          94 RFAVFVGCP  102 (248)
T ss_dssp             CEEEEESCC
T ss_pred             cEEEEeCCC
Confidence            999965544

>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=86.53  E-value=0.55  Score=31.63  Aligned_cols=53  Identities=13%  Similarity=0.113  Sum_probs=44.9

Q ss_pred             CCCccEEEEcchhHhhhhc--hHHHHHHHHHhCCCCCcEEEEeeecChhHHHHHH
Q 028826           74 FRNLVILVLDEADRLLDMG--FQKQISYIISRLPKLRRTGLFSATQTEAVEELSK  126 (203)
Q Consensus        74 l~~v~~lViDEad~l~~~~--~~~~~~~il~~~~~~~q~i~~SAT~~~~v~~~~~  126 (203)
                      -...+++|+||+-..++.|  -.+++..++..-|...-+|+..-..|+++.++++
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            4568899999999888887  4777888888888889999999999988877765

>d1a1va2 c.37.1.14 (A:326-624) HCV helicase domain {Human hepatitis C virus (HCV), different isolates [TaxId: 11103]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: RNA helicase
domain: HCV helicase domain
species: Human hepatitis C virus (HCV), different isolates [TaxId: 11103]

Probab=85.91  E-value=0.35  Score=36.13  Aligned_cols=35  Identities=9%  Similarity=0.248  Sum_probs=29.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchH
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVK   41 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~   41 (203)
                      +||.++||+-+.++...+++.     ++++..++||.+.+
T Consensus        39 ~LVFcnSR~~aE~La~~L~~~-----Gi~a~~~Hgglsq~   73 (299)
T d1a1va2          39 HLIFCHSKKKCDELAAKLVAL-----GINAVAYYRGLDVS   73 (299)
T ss_dssp             EEEECSSHHHHHHHHHHHHHT-----TCCEEEECTTSCGG
T ss_pred             EEEECCcHHHHHHHHHHHHHC-----CCCEEEEeCCchHH
Confidence            699999999999888887765     78899999987754

>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=84.29  E-value=0.53  Score=34.44  Aligned_cols=52  Identities=12%  Similarity=0.045  Sum_probs=39.7

Q ss_pred             EEEEcCcHHHHHHHHHHHHHhhhcCCCceEEEEEcCcchHHHHHHHHhCCCeEEEecc
Q 028826            2 GMIISPTRELSAQIYHVAQPFISTLPDVKSMLLVGGVEVKADVKKIEEEGANLLIGTP   59 (203)
Q Consensus         2 alil~PtreLa~Qi~~~~~~l~~~~~~i~~~~~~~g~~~~~~~~~l~~~~~~ilV~Tp   59 (203)
                      ++|++|+++-+..+.+.+++.     +.++..++|+..... .....++..+++|+|.
T Consensus       181 ~lvf~~~~~~~~~l~~~L~~~-----~~~~~~l~~~~~~~~-~~~~~~~~~~~lvaT~  232 (305)
T d2bmfa2         181 TVWFVPSIKAGNDIAACLRKN-----GKKVIQLSRKTFDSE-YIKTRTNDWDFVVTTD  232 (305)
T ss_dssp             EEEECSCHHHHHHHHHHHHHH-----TCCCEECCTTCHHHH-GGGGGTSCCSEEEECG
T ss_pred             EEEEeccHHHHHHHHHHHHhC-----CCCEEEeCCcChHHH-HhhhhccchhhhhhhH
Confidence            689999999998888888765     566777888765443 3334467889999998

>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=83.71  E-value=0.55  Score=33.52  Aligned_cols=40  Identities=13%  Similarity=0.117  Sum_probs=26.6

Q ss_pred             CCccEEEEcchhHhhhhchHHHHHHHHHhCCCCCcEEEEee
Q 028826           75 RNLVILVLDEADRLLDMGFQKQISYIISRLPKLRRTGLFSA  115 (203)
Q Consensus        75 ~~v~~lViDEad~l~~~~~~~~~~~il~~~~~~~q~i~~SA  115 (203)
                      .+-+++|+||+|.|-.. ....+..+++..+....+++.+-
T Consensus       114 ~~~kviiIde~d~l~~~-~q~~Llk~lE~~~~~~~~il~tn  153 (239)
T d1njfa_         114 GRFKVYLIDEVHMLSRH-SFNALLKTLEEPPEHVKFLLATT  153 (239)
T ss_dssp             SSSEEEEEETGGGSCHH-HHHHHHHHHHSCCTTEEEEEEES
T ss_pred             CCCEEEEEECcccCCHH-HHHHHHHHHhcCCCCeEEEEEcC
Confidence            45679999999998433 34556666766555565555543

>d2fwra1 c.37.1.19 (A:257-456) DNA repair protein RAD25 {Archaeoglobus fulgidus [TaxId: 2234]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: Tandem AAA-ATPase domain
domain: DNA repair protein RAD25
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=82.22  E-value=0.077  Score=37.21  Aligned_cols=31  Identities=26%  Similarity=0.509  Sum_probs=26.1

Q ss_pred             CCCcHHHHHHHHhcCCCCeEEEEeccCCccc
Q 028826          171 SDKKPSQLVDLLIKNKSKKIIMYVQHGNFSE  201 (203)
Q Consensus       171 ~~~k~~~l~~ll~~~~~~~~lIF~ns~~~~e  201 (203)
                      ...|++.|.++++.+.+.++||||++...++
T Consensus        77 ~~~K~~~l~~ll~~~~~~k~lvf~~~~~~~~  107 (200)
T d2fwra1          77 SKNKIRKLREILERHRKDKIIIFTRHNELVY  107 (200)
T ss_dssp             CSHHHHHHHHHHHHTSSSCBCCBCSCHHHHH
T ss_pred             cHHHHHHHHHHHHhCCCCcEEEEeCcHHHHH
Confidence            4568999999999998899999999875543